NCBI Bos indicus Annotation Release 100
The RefSeq genome records for Bos indicus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.
The annotation products are available in the sequence databases and on the FTP site.
This report provides:
- Annotation Release information: The name of the release, important dates, the software version
- Assemblies: A brief description of the annotated assembly(ies)
- Gene and feature statistics: The counts and characteristics of the annotated features
- Alignment of the annotated proteins to a set of high-quality proteins: The number of annotated proteins with hits to a set of high-quality proteins
- Masking of genomic sequence: How much of the genome was masked
- Transcript and protein alignments: The number and type of evidence retrieved from public databases and used for gene prediction
For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.
Annotation Release information
This annotation should be referred to as NCBI Bos indicus Annotation Release 100Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Jan 4 2017
Date of submission of annotation to the public databases: Jan 12 2017
Software version: 7.2
Assemblies
The following assemblies were included in this annotation run:Assembly name | Assembly accession | Submitter | Assembly date | Reference/Alternate | Assembly content |
---|---|---|---|---|---|
Bos_indicus_1.0 | GCF_000247795.1 | Genoa Biotecnologia SA | 11-25-2014 | Reference | 32 assembled chromosomes |
Gene and feature statistics
Counts and length of annotated features are provided below for each assembly.Feature counts
Feature | Bos_indicus_1.0 |
---|---|
Genes and pseudogenes | 26,192 |
protein-coding | 19,900 |
non-coding | 2,780 |
pseudogenes | 3,512 |
genes with variants | 7,084 |
mRNAs | 35,979 |
fully-supported | 32,654 |
with > 5% ab initio | 1,267 |
partial | 569 |
with filled gap(s) | 164 |
known RefSeq (NM_) | 0 |
model RefSeq (XM_) | 35,979 |
Other RNAs | 4,278 |
fully-supported | 3,444 |
with > 5% ab initio | 0 |
partial | 0 |
with filled gap(s) | 0 |
known RefSeq (NR_) | 0 |
model RefSeq (XR_) | 3,444 |
CDSs | 36,106 |
fully-supported | 32,654 |
with > 5% ab initio | 1,591 |
partial | 529 |
with major correction(s) | 1,434 |
known RefSeq (NP_) | 0 |
model RefSeq (XP_) | 35,979 |
Detailed reports
Feature lengths
Feature | Count | Mean length (bp) | Median length (bp) | Min length (bp) | Max length (bp) |
---|---|---|---|---|---|
Genes | 22,680 | 43,556 | 14,066 | 66 | 2,365,586 |
All transcripts | 40,257 | 3,004 | 2,439 | 66 | 101,949 |
mRNA | 35,979 | 3,173 | 2,589 | 153 | 101,949 |
misc_RNA | 907 | 2,935 | 2,539 | 161 | 14,924 |
tRNA | 834 | 73 | 73 | 66 | 84 |
lncRNA | 2,537 | 1,591 | 1,064 | 100 | 20,986 |
Single-exon transcripts | 2,085 | 1,375 | 957 | 153 | 7,798 |
coding transcripts (NM_/XM_ ) | 2,083 | 1,375 | 957 | 153 | 7,798 |
non-coding transcripts (NR_/XR_ ) | 2 | 879 | 1,149 | 609 | 1,149 |
CDSs | 35,979 | 1,821 | 1,359 | 96 | 100,701 |
Exons | 218,320 | 309 | 137 | 1 | 20,612 |
in coding transcripts (NM_/XM_ ) | 210,217 | 301 | 136 | 1 | 17,106 |
in non-coding transcripts (NR_/XR_ ) | 13,677 | 386 | 150 | 2 | 20,612 |
Introns | 193,564 | 5,543 | 1,365 | 30 | 1,059,742 |
in coding transcripts (NM_/XM_ ) | 188,094 | 5,491 | 1,356 | 30 | 1,059,742 |
in non-coding transcripts (NR_/XR_ ) | 10,855 | 5,647 | 1,429 | 36 | 299,138 |
Transcripts per gene, exons per transcript
Mean | Median | Min | Max | |
---|---|---|---|---|
Number of transcripts per gene | 1.82 | 1 | 1 | 50 |
Number of exons per transcript | 10.99 | 8 | 1 | 314 |
Alignment of the annotated proteins to a set of high-quality proteins
The final set of annotated proteins was searched with BLASTP against the UniProtKB/Swiss-Prot curated proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 19773 coding genes, 19433 genes had a protein with an alignment covering 50% or more of the query and 15936 had an alignment covering 95% or more of the query.Definition of query and target coverage. The query coverage is the percentage of the annotated protein length that is included in the alignment. The target coverage is the percentage of the target length that is included in the alignment.
Below is a cumulative graph displaying the number of genes with alignments above a given query or target coverage threshold. For comparison, corresponding statistics for other organisms annotated by the NCBI eukaryotic annotation pipeline were added to the graph.
Query: annotated proteinsTarget: UniProtKB/Swiss-Prot curated proteins
Masking of genomic sequence
Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker for each assembly. RepeatMasker results are only used for organisms for which a comprehensive repeat library is available.
For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.Assembly name | Assembly accession | % Masked with RepeatMasker | % Masked with WindowMasker |
---|---|---|---|
Bos_indicus_1.0 | GCF_000247795.1 | 43.40% | 36.07% |
Transcript and protein alignments
The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign or ProSplign and passed to Gnomon, NCBI's gene prediction software.
Depending on the other evidence available, long 454 reads (with average length above 250 nt) may be aligned as traditional evidence and reported in the Transcript alignments section or aligned with RNA-Seq reads and reported in the RNA-Seq alignments section.
Transcript alignments
Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by Splign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|
Same-species Genbank | 217 | 209 (96.31%) | 182 (83.87%) | 99.24% | 99.24% |
Same-species EST | 19,458 | 14,125 (72.59%) | 12,807 (65.82%) | 98.94% | 99.13% |
Homo sapiens known RefSeq (NM_/NR_) | 58,494 | 45,082 (77.07%) | 10,078 (17.23%) | 89.11% | 78.96% |
Homo sapiens Genbank | 286,453 | 138,288 (48.28%) | 43,747 (15.27%) | 89.77% | 87.83% |
Bos taurus known RefSeq (NM_/NR_) | 14,251 | 13,755 (96.52%) | 11,394 (79.95%) | 99.50% | 98.78% |
Bos taurus Genbank | 18,989 | 17,565 (92.50%) | 12,967 (68.29%) | 99.30% | 98.27% |
Bos taurus EST | 1,583,270 | 1,360,849 (85.95%) | 1,198,817 (75.72%) | 98.87% | 98.58% |
RNA-Seq alignments
The following RNA-Seq reads from the Sequence Read Archive were also used for gene prediction:
Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)Sample Id | Track name | Number of reads | Percent aligned reads | Percent spliced reads | Number of introns |
---|---|---|---|---|---|
All | Aggregate of all aligned samples | 8,324,786,874 | 82% | 25% | 204,785 |
ERS684626 | liver (Bos indicus, male, SAMEA3308496) | 49,908,408 | 75% | 23% | 128,497 |
SAMEA2646392 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646392) | 29,596,611 | 91% | 27% | 127,891 |
SAMEA2646393 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646393) | 19,173,297 | 90% | 26% | 120,359 |
SAMEA2646394 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646394) | 21,378,647 | 91% | 25% | 119,629 |
SAMEA2646395 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646395) | 24,002,661 | 91% | 25% | 122,683 |
SAMEA2646396 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646396) | 20,660,356 | 91% | 27% | 118,229 |
SAMEA2646397 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646397) | 21,712,898 | 91% | 27% | 123,238 |
SAMEA2646398 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646398) | 19,794,353 | 90% | 24% | 121,651 |
SAMEA2646399 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646399) | 35,556,270 | 90% | 24% | 132,315 |
SAMEA2646400 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646400) | 20,125,026 | 90% | 24% | 119,085 |
SAMEA2646401 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646401) | 37,506,309 | 90% | 23% | 132,371 |
SAMEA2646402 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646402) | 15,908,450 | 90% | 25% | 111,549 |
SAMEA2646403 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646403) | 23,042,497 | 90% | 24% | 122,996 |
SAMEA2646404 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646404) | 19,878,306 | 90% | 25% | 119,304 |
SAMEA2646405 | Bos indicus; Steer_Nellore (Bos indicus, male, SAMEA2646405) | 24,827,167 | 90% | 25% | 124,520 |
SAMEA3112153 | liver, low RFI (Bos indicus, SAMEA3112153) | 18,594,797 | 82% | 22% | 117,409 |
SAMEA3112173 | liver, low RFI (Bos indicus, SAMEA3112173) | 18,594,797 | 82% | 22% | 117,409 |
SAMEA3112174 | liver, low RFI (Bos indicus, SAMEA3112174) | 24,141,674 | 83% | 23% | 121,749 |
SAMEA3112175 | liver, low RFI (Bos indicus, SAMEA3112175) | 15,784,462 | 82% | 23% | 108,249 |
SAMEA3112176 | liver, low RFI (Bos indicus, SAMEA3112176) | 18,004,352 | 85% | 23% | 115,483 |
SAMEA3112177 | liver, low RFI (Bos indicus, SAMEA3112177) | 15,472,815 | 83% | 24% | 113,156 |
SAMEA3112178 | liver, low RFI (Bos indicus, SAMEA3112178) | 21,185,451 | 83% | 23% | 116,546 |
SAMEA3112179 | liver, low RFI (Bos indicus, SAMEA3112179) | 19,695,418 | 84% | 23% | 114,782 |
SAMEA3112181 | liver, low RFI (Bos indicus, SAMEA3112181) | 18,674,570 | 83% | 23% | 117,974 |
SAMEA3112182 | liver, low RFI (Bos indicus, SAMEA3112182) | 18,163,741 | 84% | 23% | 114,512 |
SAMEA3112183 | liver, high RFI (Bos indicus, SAMEA3112183) | 20,377,249 | 83% | 23% | 120,084 |
SAMEA3112184 | liver, high RFI (Bos indicus, SAMEA3112184) | 15,855,156 | 82% | 22% | 111,716 |
SAMEA3112186 | liver, high RFI (Bos indicus, SAMEA3112186) | 23,212,082 | 84% | 24% | 117,228 |
SAMEA3112187 | liver, high RFI (Bos indicus, SAMEA3112187) | 16,759,753 | 82% | 23% | 114,541 |
SAMEA3112188 | liver, high RFI (Bos indicus, SAMEA3112188) | 19,940,616 | 84% | 23% | 117,488 |
SAMEA3112189 | liver, high RFI (Bos indicus, SAMEA3112189) | 17,865,590 | 85% | 23% | 114,594 |
SAMEA3112190 | liver, high RFI (Bos indicus, SAMEA3112190) | 20,135,604 | 83% | 23% | 118,867 |
SAMEA3112191 | liver, high RFI (Bos indicus, SAMEA3112191) | 17,579,778 | 81% | 21% | 114,510 |
SAMEA3112192 | liver, high RFI (Bos indicus, SAMEA3112192) | 19,134,717 | 84% | 24% | 112,721 |
SAMEA3306037 | liver (Bos indicus, male, SAMEA3306037) | 45,161,226 | 79% | 25% | 125,692 |
SAMEA3306038 | liver (Bos indicus, male, SAMEA3306038) | 53,644,598 | 80% | 26% | 127,401 |
SAMEA3306039 | liver (Bos indicus, male, SAMEA3306039) | 77,733,556 | 78% | 23% | 145,603 |
SAMEA3306040 | liver (Bos indicus, male, SAMEA3306040) | 97,504,628 | 72% | 18% | 140,663 |
SAMEA3306041 | liver (Bos indicus, male, SAMEA3306041) | 43,497,974 | 77% | 24% | 128,618 |
SAMEA3306042 | liver (Bos indicus, male, SAMEA3306042) | 59,620,930 | 77% | 24% | 134,659 |
SAMEA3306043 | liver (Bos indicus, male, SAMEA3306043) | 44,222,768 | 78% | 23% | 126,856 |
SAMEA3306044 | liver (Bos indicus, male, SAMEA3306044) | 35,920,234 | 76% | 25% | 120,369 |
SAMEA3306045 | liver (Bos indicus, male, SAMEA3306045) | 50,777,674 | 78% | 26% | 128,021 |
SAMEA3306046 | liver (Bos indicus, male, SAMEA3306046) | 62,511,294 | 76% | 23% | 129,693 |
SAMEA3306047 | liver (Bos indicus, male, SAMEA3306047) | 50,067,630 | 76% | 23% | 129,639 |
SAMEA3306048 | liver (Bos indicus, male, SAMEA3306048) | 48,503,506 | 76% | 22% | 124,493 |
SAMEA3306049 | liver (Bos indicus, male, SAMEA3306049) | 74,893,188 | 74% | 18% | 137,339 |
SAMEA3306050 | liver (Bos indicus, male, SAMEA3306050) | 45,968,518 | 79% | 25% | 134,113 |
SAMEA3306051 | liver (Bos indicus, male, SAMEA3306051) | 46,707,470 | 77% | 25% | 123,282 |
SAMEA4395184 | A1 (Bos indicus, SAMEA4395184) | 61,556,698 | 83% | 27% | 140,312 |
SAMEA4395185 | A2 (Bos indicus, SAMEA4395185) | 68,563,680 | 82% | 27% | 139,716 |
SAMEA4395186 | A3 (Bos indicus, SAMEA4395186) | 16,442,701 | 84% | 27% | 117,573 |
SAMEA4395187 | A4 (Bos indicus, SAMEA4395187) | 64,392,218 | 82% | 30% | 118,036 |
SAMEA4395188 | A5 (Bos indicus, SAMEA4395188) | 21,899,328 | 82% | 24% | 119,430 |
SAMEA4395189 | A6 (Bos indicus, SAMEA4395189) | 20,061,751 | 83% | 24% | 113,955 |
SAMEA4395190 | A7 (Bos indicus, SAMEA4395190) | 33,437,469 | 82% | 24% | 127,745 |
SAMEA4395191 | A8 (Bos indicus, SAMEA4395191) | 61,437,181 | 83% | 28% | 138,861 |
SAMEA4395192 | A9 (Bos indicus, SAMEA4395192) | 45,653,787 | 86% | 30% | 134,369 |
SAMEA4395193 | A10 (Bos indicus, SAMEA4395193) | 32,010,032 | 83% | 25% | 124,602 |
SAMEA4395194 | A11 (Bos indicus, SAMEA4395194) | 27,862,255 | 83% | 25% | 121,534 |
SAMEA4395195 | A12 (Bos indicus, SAMEA4395195) | 19,419,078 | 84% | 26% | 115,121 |
SAMEA4395196 | A13 (Bos indicus, SAMEA4395196) | 23,495,287 | 84% | 26% | 120,565 |
SAMEA4395197 | A14 (Bos indicus, SAMEA4395197) | 38,872,885 | 85% | 26% | 132,116 |
SAMEA4395198 | A15 (Bos indicus, SAMEA4395198) | 33,162,394 | 83% | 25% | 125,325 |
SAMEA4395199 | A16 (Bos indicus, SAMEA4395199) | 25,811,117 | 84% | 25% | 122,922 |
SAMEA4395200 | A17 (Bos indicus, SAMEA4395200) | 23,051,034 | 81% | 25% | 116,451 |
SAMEA4395201 | A18 (Bos indicus, SAMEA4395201) | 8,784,301 | 83% | 26% | 101,773 |
SAMEA4395202 | A19 (Bos indicus, SAMEA4395202) | 28,966,656 | 84% | 26% | 122,441 |
SAMEA4395203 | A20 (Bos indicus, SAMEA4395203) | 27,015,587 | 85% | 26% | 119,903 |
SAMEA4395204 | A21 (Bos indicus, SAMEA4395204) | 18,567,317 | 85% | 19% | 107,809 |
SAMEA4395205 | A22 (Bos indicus, SAMEA4395205) | 19,280,653 | 82% | 18% | 104,818 |
SAMEA4395206 | A23 (Bos indicus, SAMEA4395206) | 25,738,074 | 90% | 28% | 93,687 |
SAMEA4395207 | A24 (Bos indicus, SAMEA4395207) | 25,109,422 | 77% | 27% | 119,367 |
SAMEA4395208 | A25 (Bos indicus, SAMEA4395208) | 27,738,220 | 83% | 25% | 120,873 |
SAMEA4395209 | A26 (Bos indicus, SAMEA4395209) | 17,421,638 | 85% | 29% | 112,622 |
SAMEA4395210 | A27 (Bos indicus, SAMEA4395210) | 23,828,720 | 85% | 27% | 116,668 |
SAMEA4395211 | A28 (Bos indicus, SAMEA4395211) | 24,527,238 | 83% | 25% | 116,435 |
SAMEA4395212 | A29 (Bos indicus, SAMEA4395212) | 22,690,679 | 84% | 26% | 120,400 |
SAMEA4395213 | A30 (Bos indicus, SAMEA4395213) | 27,253,114 | 81% | 25% | 120,134 |
SAMEA4395214 | A31 (Bos indicus, SAMEA4395214) | 26,405,090 | 85% | 26% | 121,091 |
SAMEA4395215 | A32 (Bos indicus, SAMEA4395215) | 51,312,519 | 82% | 28% | 138,612 |
SAMEA4395216 | A33 (Bos indicus, SAMEA4395216) | 20,149,233 | 81% | 28% | 117,776 |
SAMEA4395217 | A34 (Bos indicus, SAMEA4395217) | 22,665,604 | 86% | 26% | 119,831 |
SAMEA4395218 | A35 (Bos indicus, SAMEA4395218) | 30,834,955 | 86% | 27% | 127,771 |
SAMEA4395219 | A36 (Bos indicus, SAMEA4395219) | 26,312,898 | 83% | 25% | 123,360 |
SAMEA4395220 | A37 (Bos indicus, SAMEA4395220) | 51,265,274 | 83% | 28% | 138,378 |
SAMEA4395221 | A38 (Bos indicus, SAMEA4395221) | 34,209,200 | 84% | 29% | 128,526 |
SAMEA4395222 | A39 (Bos indicus, SAMEA4395222) | 49,919,180 | 84% | 28% | 136,311 |
SAMEA4395223 | A40 (Bos indicus, SAMEA4395223) | 51,181,205 | 82% | 27% | 140,731 |
SAMEA4395224 | A41 (Bos indicus, SAMEA4395224) | 20,607,715 | 81% | 23% | 118,025 |
SAMEA4395225 | A42 (Bos indicus, SAMEA4395225) | 24,873,315 | 82% | 26% | 112,377 |
SAMEA4395226 | A43 (Bos indicus, SAMEA4395226) | 17,678,846 | 84% | 25% | 114,176 |
SAMEA4395227 | A44 (Bos indicus, SAMEA4395227) | 17,542,180 | 85% | 28% | 116,820 |
SAMEA4395228 | A45 (Bos indicus, SAMEA4395228) | 19,489,335 | 84% | 28% | 114,905 |
SAMEA4395229 | A46 (Bos indicus, SAMEA4395229) | 50,743,480 | 85% | 29% | 137,582 |
SAMEA4395230 | A47 (Bos indicus, SAMEA4395230) | 24,314,488 | 81% | 25% | 117,741 |
SAMEA4395231 | A48 (Bos indicus, SAMEA4395231) | 25,900,934 | 82% | 25% | 115,507 |
SAMEA4395232 | A49 (Bos indicus, SAMEA4395232) | 20,667,316 | 85% | 25% | 118,610 |
SAMEA4395233 | A50 (Bos indicus, SAMEA4395233) | 22,841,569 | 82% | 25% | 123,666 |
SAMEA4395234 | A51 (Bos indicus, SAMEA4395234) | 33,810,413 | 81% | 22% | 131,556 |
SAMEA4395235 | A52 (Bos indicus, SAMEA4395235) | 29,236,432 | 84% | 25% | 125,141 |
SAMEA4395236 | A53 (Bos indicus, SAMEA4395236) | 30,827,676 | 84% | 25% | 120,280 |
SAMEA4395237 | A54 (Bos indicus, SAMEA4395237) | 25,874,902 | 81% | 25% | 118,353 |
SAMEA4395238 | A55 (Bos indicus, SAMEA4395238) | 22,472,477 | 82% | 25% | 116,786 |
SAMEA4395239 | A56 (Bos indicus, SAMEA4395239) | 14,359,259 | 82% | 24% | 108,649 |
SAMEA4395240 | A57 (Bos indicus, SAMEA4395240) | 10,707,004 | 85% | 27% | 107,222 |
SAMEA4395241 | A58 (Bos indicus, SAMEA4395241) | 37,591,798 | 83% | 25% | 129,855 |
SAMEA4395242 | A59 (Bos indicus, SAMEA4395242) | 16,588,325 | 79% | 26% | 93,151 |
SAMEA4395243 | A60 (Bos indicus, SAMEA4395243) | 25,323,016 | 82% | 24% | 125,094 |
SAMEA4395244 | A61 (Bos indicus, SAMEA4395244) | 27,395,946 | 80% | 24% | 118,693 |
SAMEA4395245 | A62 (Bos indicus, SAMEA4395245) | 24,763,860 | 81% | 23% | 126,523 |
SAMEA4395246 | A63 (Bos indicus, SAMEA4395246) | 33,031,998 | 84% | 28% | 129,934 |
SAMEA4395247 | A64 (Bos indicus, SAMEA4395247) | 40,532,079 | 84% | 26% | 127,433 |
SAMEA4395248 | A65 (Bos indicus, SAMEA4395248) | 20,564,868 | 81% | 18% | 105,188 |
SAMEA4395249 | A66 (Bos indicus, SAMEA4395249) | 26,049,330 | 82% | 23% | 123,179 |
SAMEA4395250 | A67 (Bos indicus, SAMEA4395250) | 17,834,158 | 83% | 26% | 115,495 |
SAMEA4395251 | A68 (Bos indicus, SAMEA4395251) | 20,276,888 | 73% | 22% | 108,869 |
SAMEA4395252 | A69 (Bos indicus, SAMEA4395252) | 16,109,623 | 86% | 28% | 115,159 |
SAMEA4395253 | A70 (Bos indicus, SAMEA4395253) | 25,719,559 | 85% | 30% | 122,390 |
SAMEA4395254 | A71 (Bos indicus, SAMEA4395254) | 24,307,035 | 83% | 26% | 116,100 |
SAMEA4395255 | A72 (Bos indicus, SAMEA4395255) | 16,674,213 | 81% | 23% | 112,402 |
SAMEA4395256 | A73 (Bos indicus, SAMEA4395256) | 31,801,491 | 80% | 29% | 114,372 |
SAMEA4395257 | A74 (Bos indicus, SAMEA4395257) | 18,800,054 | 80% | 24% | 113,368 |
SAMEA4395258 | A75 (Bos indicus, SAMEA4395258) | 37,146,548 | 82% | 26% | 126,753 |
SAMEA4395259 | A76 (Bos indicus, SAMEA4395259) | 21,954,495 | 82% | 25% | 119,792 |
SAMEA4395260 | A77 (Bos indicus, SAMEA4395260) | 25,760,515 | 84% | 25% | 123,179 |
SAMEA4395261 | A78 (Bos indicus, SAMEA4395261) | 23,732,319 | 81% | 28% | 120,969 |
SAMEA4395262 | A79 (Bos indicus, SAMEA4395262) | 30,913,112 | 81% | 23% | 122,633 |
SAMEA4395263 | A80 (Bos indicus, SAMEA4395263) | 21,153,577 | 85% | 26% | 116,437 |
SAMEA4395264 | A81 (Bos indicus, SAMEA4395264) | 63,194,876 | 82% | 28% | 141,977 |
SAMEA4395265 | A82 (Bos indicus, SAMEA4395265) | 18,277,857 | 81% | 20% | 99,443 |
SAMEA4395266 | A83 (Bos indicus, SAMEA4395266) | 22,588,117 | 84% | 25% | 122,437 |
SAMEA4395267 | A84 (Bos indicus, SAMEA4395267) | 23,496,049 | 82% | 23% | 119,684 |
SAMEA4395268 | A85 (Bos indicus, SAMEA4395268) | 26,156,168 | 84% | 20% | 119,158 |
SAMEA4395269 | A86 (Bos indicus, SAMEA4395269) | 38,782,745 | 83% | 29% | 132,229 |
SAMEA4395270 | A87 (Bos indicus, SAMEA4395270) | 23,390,667 | 84% | 24% | 126,530 |
SAMEA4395271 | A88 (Bos indicus, SAMEA4395271) | 21,183,490 | 76% | 22% | 108,949 |
SAMEA4395272 | A89 (Bos indicus, SAMEA4395272) | 36,855,732 | 81% | 24% | 124,341 |
SAMEA4395273 | A90 (Bos indicus, SAMEA4395273) | 36,729,545 | 82% | 31% | 116,971 |
SAMEA4395274 | A91 (Bos indicus, SAMEA4395274) | 30,191,509 | 81% | 25% | 123,686 |
SAMEA4395275 | A92 (Bos indicus, SAMEA4395275) | 31,937,028 | 82% | 26% | 126,580 |
SAMEA4395276 | A93 (Bos indicus, SAMEA4395276) | 26,722,298 | 84% | 26% | 124,974 |
SAMEA4395277 | A94 (Bos indicus, SAMEA4395277) | 43,273,170 | 84% | 26% | 127,324 |
SAMEA4395278 | A95 (Bos indicus, SAMEA4395278) | 35,618,809 | 85% | 26% | 126,340 |
SAMEA4395279 | A96 (Bos indicus, SAMEA4395279) | 24,371,205 | 82% | 26% | 120,165 |
SAMEA4395280 | A97 (Bos indicus, SAMEA4395280) | 32,805,468 | 85% | 30% | 126,635 |
SAMEA4395281 | A98 (Bos indicus, SAMEA4395281) | 31,693,280 | 82% | 26% | 130,050 |
SAMEA4395282 | A99 (Bos indicus, SAMEA4395282) | 24,383,815 | 83% | 24% | 121,369 |
SAMEA4395283 | A100 (Bos indicus, SAMEA4395283) | 33,798,501 | 84% | 24% | 131,761 |
SAMEA4395284 | A101 (Bos indicus, SAMEA4395284) | 34,588,500 | 82% | 24% | 128,376 |
SAMEA4395285 | A102 (Bos indicus, SAMEA4395285) | 41,750,705 | 83% | 28% | 134,265 |
SAMEA4395286 | A103 (Bos indicus, SAMEA4395286) | 50,107,991 | 80% | 27% | 137,814 |
SAMEA4395287 | A104 (Bos indicus, SAMEA4395287) | 26,725,063 | 81% | 24% | 121,263 |
SAMEA4395288 | A105 (Bos indicus, SAMEA4395288) | 24,869,300 | 82% | 24% | 121,181 |
SAMEA4395289 | A106 (Bos indicus, SAMEA4395289) | 12,195,258 | 83% | 24% | 102,158 |
SAMEA4395290 | A107 (Bos indicus, SAMEA4395290) | 27,511,938 | 81% | 25% | 120,763 |
SAMEA4395291 | A108 (Bos indicus, SAMEA4395291) | 21,074,391 | 82% | 25% | 118,887 |
SAMEA4395292 | A109 (Bos indicus, SAMEA4395292) | 46,493,997 | 81% | 27% | 136,374 |
SAMEA4395293 | A110 (Bos indicus, SAMEA4395293) | 38,696,169 | 81% | 25% | 112,913 |
SAMEA4395294 | A111 (Bos indicus, SAMEA4395294) | 21,251,854 | 84% | 25% | 122,513 |
SAMEA4395295 | A112 (Bos indicus, SAMEA4395295) | 48,964,741 | 86% | 29% | 140,588 |
SAMEA4395296 | A113 (Bos indicus, SAMEA4395296) | 26,799,439 | 83% | 25% | 123,404 |
SAMEA4395297 | A114 (Bos indicus, SAMEA4395297) | 28,113,041 | 79% | 23% | 124,749 |
SAMEA4395298 | A115 (Bos indicus, SAMEA4395298) | 23,610,709 | 82% | 24% | 121,737 |
SAMEA4395299 | A116 (Bos indicus, SAMEA4395299) | 33,935,133 | 82% | 26% | 127,499 |
SAMEA4395300 | A117 (Bos indicus, SAMEA4395300) | 25,514,916 | 84% | 25% | 121,518 |
SAMEA4395301 | A118 (Bos indicus, SAMEA4395301) | 40,936,683 | 83% | 25% | 129,323 |
SAMEA4395302 | A119 (Bos indicus, SAMEA4395302) | 23,321,602 | 83% | 25% | 123,469 |
SAMEA4395303 | A120 (Bos indicus, SAMEA4395303) | 18,818,979 | 83% | 25% | 106,348 |
SAMEA4395304 | A121 (Bos indicus, SAMEA4395304) | 19,487,733 | 77% | 22% | 112,007 |
SAMEA4395305 | A122 (Bos indicus, SAMEA4395305) | 33,433,195 | 80% | 24% | 125,982 |
SAMEA4395306 | A123 (Bos indicus, SAMEA4395306) | 35,436,399 | 85% | 30% | 125,585 |
SAMEA4395307 | A124 (Bos indicus, SAMEA4395307) | 17,145,156 | 82% | 26% | 108,828 |
SAMEA4395308 | A125 (Bos indicus, SAMEA4395308) | 32,352,920 | 85% | 23% | 127,741 |
SAMEA4395309 | A126 (Bos indicus, SAMEA4395309) | 22,656,765 | 82% | 25% | 120,565 |
SAMEA4395310 | A127 (Bos indicus, SAMEA4395310) | 33,061,108 | 83% | 26% | 121,164 |
SAMEA4395311 | A128 (Bos indicus, SAMEA4395311) | 29,227,327 | 82% | 26% | 120,861 |
SAMEA4395312 | A129 (Bos indicus, SAMEA4395312) | 35,259,698 | 85% | 26% | 129,102 |
SAMEA4395313 | A130 (Bos indicus, SAMEA4395313) | 60,322,162 | 84% | 28% | 140,653 |
SAMEA4395314 | A131 (Bos indicus, SAMEA4395314) | 11,262,077 | 83% | 27% | 107,873 |
SAMEA4395315 | A132 (Bos indicus, SAMEA4395315) | 28,281,821 | 85% | 26% | 123,495 |
SAMEA4395316 | A133 (Bos indicus, SAMEA4395316) | 14,999,496 | 80% | 25% | 108,810 |
SAMEA4395317 | A134 (Bos indicus, SAMEA4395317) | 40,311,469 | 83% | 28% | 134,636 |
SAMEA4395318 | A135 (Bos indicus, SAMEA4395318) | 26,731,354 | 83% | 20% | 114,087 |
SAMEA4395319 | A136 (Bos indicus, SAMEA4395319) | 32,216,029 | 84% | 25% | 131,972 |
SAMEA4395320 | A137 (Bos indicus, SAMEA4395320) | 48,847,474 | 83% | 30% | 132,640 |
SAMEA4395321 | A138 (Bos indicus, SAMEA4395321) | 43,122,357 | 83% | 28% | 133,319 |
SAMEA4395322 | A139 (Bos indicus, SAMEA4395322) | 35,648,325 | 84% | 25% | 128,425 |
SAMEA4395323 | A140 (Bos indicus, SAMEA4395323) | 18,594,473 | 77% | 24% | 106,998 |
SAMEA4395324 | A141 (Bos indicus, SAMEA4395324) | 26,430,368 | 83% | 25% | 124,425 |
SAMEA4395325 | A142 (Bos indicus, SAMEA4395325) | 46,029,114 | 84% | 28% | 136,716 |
SAMEA4395326 | A143 (Bos indicus, SAMEA4395326) | 24,467,143 | 82% | 25% | 121,166 |
SAMEA4395327 | A144 (Bos indicus, SAMEA4395327) | 16,660,446 | 83% | 27% | 114,870 |
SAMEA4395328 | A145 (Bos indicus, SAMEA4395328) | 60,747,375 | 84% | 28% | 141,024 |
SAMEA4395329 | A146 (Bos indicus, SAMEA4395329) | 33,155,009 | 84% | 26% | 117,249 |
SAMEA4395330 | A147 (Bos indicus, SAMEA4395330) | 29,171,261 | 80% | 24% | 121,749 |
SAMEA4395331 | A148 (Bos indicus, SAMEA4395331) | 32,910,711 | 84% | 24% | 129,570 |
SAMEA4395332 | A149 (Bos indicus, SAMEA4395332) | 25,874,550 | 83% | 25% | 121,927 |
SAMEA4395333 | A150 (Bos indicus, SAMEA4395333) | 57,242,608 | 82% | 29% | 136,042 |
SAMEA4395334 | A151 (Bos indicus, SAMEA4395334) | 25,984,773 | 83% | 25% | 119,344 |
SAMEA4395335 | A152 (Bos indicus, SAMEA4395335) | 56,321,543 | 85% | 29% | 139,038 |
SAMEA4395336 | A153 (Bos indicus, SAMEA4395336) | 32,224,113 | 82% | 25% | 124,721 |
SAMEA4395337 | A154 (Bos indicus, SAMEA4395337) | 22,794,044 | 82% | 25% | 115,498 |
SAMEA4395338 | A155 (Bos indicus, SAMEA4395338) | 38,542,877 | 84% | 28% | 134,683 |
SAMEA4395339 | A156 (Bos indicus, SAMEA4395339) | 28,563,050 | 83% | 24% | 123,144 |
SAMEA4395340 | A157 (Bos indicus, SAMEA4395340) | 22,851,195 | 82% | 25% | 117,761 |
SAMEA4395341 | A158 (Bos indicus, SAMEA4395341) | 35,187,170 | 83% | 26% | 126,327 |
SAMEA4395342 | A159 (Bos indicus, SAMEA4395342) | 16,643,712 | 83% | 19% | 102,774 |
SAMEA4395343 | A160 (Bos indicus, SAMEA4395343) | 23,627,778 | 80% | 24% | 119,468 |
SAMEA4395344 | A161 (Bos indicus, SAMEA4395344) | 36,958,062 | 80% | 20% | 95,932 |
SAMEA4395346 | A163 (Bos indicus, SAMEA4395346) | 25,621,232 | 78% | 21% | 102,758 |
SAMEA4395347 | A164 (Bos indicus, SAMEA4395347) | 27,335,579 | 84% | 26% | 120,396 |
SAMEA4430986 | muscle_HRFI0; extremes_RFI (Bos indicus, SAMEA4430986) | 38,592,343 | 83% | 27% | 136,592 |
SAMEA4430987 | muscle_HRFI1; extremes_RFI (Bos indicus, SAMEA4430987) | 39,544,202 | 80% | 24% | 140,729 |
SAMEA4430988 | muscle_HRFI2; extremes_RFI (Bos indicus, SAMEA4430988) | 32,433,543 | 82% | 27% | 131,341 |
SAMEA4430989 | muscle_HRFI3; extremes_RFI (Bos indicus, SAMEA4430989) | 36,763,519 | 82% | 26% | 136,509 |
SAMEA4430990 | muscle_HRFI4; extremes_RFI (Bos indicus, SAMEA4430990) | 35,142,380 | 84% | 26% | 137,204 |
SAMEA4430991 | muscle_HRFI5; extremes_RFI (Bos indicus, SAMEA4430991) | 41,776,616 | 84% | 27% | 140,913 |
SAMEA4430992 | muscle_HRFI6; extremes_RFI (Bos indicus, SAMEA4430992) | 36,290,367 | 85% | 29% | 137,622 |
SAMEA4430993 | muscle_HRFI7; extremes_RFI (Bos indicus, SAMEA4430993) | 31,247,423 | 84% | 28% | 133,632 |
SAMEA4430994 | muscle_HRFI8; extremes_RFI (Bos indicus, SAMEA4430994) | 28,655,373 | 82% | 26% | 131,661 |
SAMEA4430995 | muscle_HRFI9; extremes_RFI (Bos indicus, SAMEA4430995) | 37,716,558 | 83% | 26% | 138,846 |
SAMEA4430996 | muscle_LRFI0; extremes_RFI (Bos indicus, SAMEA4430996) | 35,932,319 | 80% | 24% | 132,122 |
SAMEA4430997 | muscle_LRFI1; extremes_RFI (Bos indicus, SAMEA4430997) | 44,061,153 | 81% | 27% | 123,046 |
SAMEA4430998 | muscle_LRFI2; extremes_RFI (Bos indicus, SAMEA4430998) | 31,595,933 | 82% | 28% | 130,787 |
SAMEA4430999 | muscle_LRFI3; extremes_RFI (Bos indicus, SAMEA4430999) | 30,543,172 | 83% | 26% | 132,054 |
SAMEA4431000 | muscle_LRFI4; extremes_RFI (Bos indicus, SAMEA4431000) | 43,632,783 | 82% | 27% | 138,184 |
SAMEA4431001 | muscle_LRFI5; extremes_RFI (Bos indicus, SAMEA4431001) | 31,013,213 | 82% | 27% | 134,331 |
SAMEA4431002 | muscle_LRFI6; extremes_RFI (Bos indicus, SAMEA4431002) | 31,005,223 | 82% | 27% | 133,628 |
SAMEA4431003 | muscle_LRFI7; extremes_RFI (Bos indicus, SAMEA4431003) | 33,568,358 | 77% | 18% | 126,591 |
SAMEA4431004 | muscle_LRFI8; extremes_RFI (Bos indicus, SAMEA4431004) | 30,585,865 | 82% | 27% | 131,946 |
SAMEA4431005 | muscle_LRFI9; extremes_RFI (Bos indicus, SAMEA4431005) | 29,019,655 | 81% | 27% | 131,457 |
SAMN02223057 | blood (Bos indicus, SAMN02223057) | 41,880,126 | 68% | 14% | 114,676 |
SAMN02903326 | Ampulla (Bos indicus, 36 months, female, SAMN02903326) | 28,294,892 | 82% | 21% | 155,251 |
SAMN02903327 | Ampulla (Bos indicus, 36 months, female, SAMN02903327) | 29,829,960 | 83% | 22% | 154,862 |
SAMN02903328 | ampulla (Bos indicus, 36 montjs, female, SAMN02903328) | 27,307,140 | 82% | 22% | 154,385 |
SAMN02903329 | ampulla (Bos indicus, 36 months, female, SAMN02903329) | 36,669,350 | 82% | 22% | 157,001 |
SAMN02903330 | ampulla (Bos indicus, 36 months, female, SAMN02903330) | 31,291,198 | 81% | 20% | 154,376 |
SAMN03246806 | endometrial biopsy, pregnant (Bos indicus, female, SAMN03246806) | 30,390,520 | 81% | 19% | 150,152 |
SAMN03246807 | endometrial biopsy, pregnant (Bos indicus, female, SAMN03246807) | 36,781,714 | 82% | 20% | 142,754 |
SAMN03246808 | endometrial biopsy, pregnant (Bos indicus, female, SAMN03246808) | 22,723,096 | 81% | 18% | 144,870 |
SAMN03246809 | endometrial biopsy, pregnant (Bos indicus, female, SAMN03246809) | 21,942,142 | 84% | 22% | 144,669 |
SAMN03246810 | endometrial biopsy, pregnant (Bos indicus, female, SAMN03246810) | 26,030,542 | 84% | 21% | 151,444 |
SAMN03246811 | endometrial biopsy, non-pregnant (Bos indicus, female, SAMN03246811) | 28,986,268 | 84% | 20% | 152,339 |
SAMN03246812 | endometrial biopsy, non-pregnant (Bos indicus, female, SAMN03246812) | 22,287,222 | 85% | 21% | 146,112 |
SAMN03246813 | endometrial biopsy, non-pregnant (Bos indicus, female, SAMN03246813) | 27,936,518 | 85% | 20% | 129,152 |
SAMN03246814 | endometrial biopsy, non-pregnant (Bos indicus, female, SAMN03246814) | 23,988,804 | 85% | 20% | 145,905 |
SAMN03246815 | endometrial biopsy, non-pregnant (Bos indicus, female, SAMN03246815) | 20,528,376 | 84% | 21% | 145,601 |
SAMN03246816 | endometrial biopsy, non-pregnant (Bos indicus, female, SAMN03246816) | 24,377,208 | 84% | 19% | 139,520 |
SAMN03249358 | Isthmus (Bos indicus, 36 months, female, SAMN03249358) | 76,198,884 | 82% | 21% | 169,922 |
SAMN03249359 | Isthmus (Bos indicus, 36 months, female, SAMN03249359) | 67,260,770 | 81% | 22% | 166,797 |
SAMN03249381 | Isthmus (Bos indicus, 36 months, female, SAMN03249381) | 68,197,674 | 82% | 21% | 169,995 |
SAMN03249382 | Isthmus (Bos indicus, 36 monts, female, SAMN03249382) | 63,610,666 | 82% | 21% | 168,815 |
SAMN03249383 | Isthmus (Bos indicus, 36 months, female, SAMN03249383) | 85,955,492 | 83% | 23% | 173,644 |
SAMN03249384 | Isthmus (Bos indicus, 36 months, female, SAMN03249384) | 78,573,462 | 80% | 17% | 146,669 |
SAMN03266149 | Inter-caruncular Endometrium (Bos indicus, multiparous cow, female, SAMN03266149) | 17,195,868 | 80% | 21% | 144,928 |
SAMN03266175 | Endometrial fragment (Bos indicus, multiparous cow, female, SAMN03266175) | 16,252,480 | 80% | 21% | 144,082 |
SAMN03266176 | Inter-caruncular Endometrium (Bos indicus, multiparous cow, female, SAMN03266176) | 39,899,514 | 80% | 20% | 160,607 |
SAMN03266177 | Inter-caruncular Endometrium (Bos indicus, multiparous cow, female, SAMN03266177) | 16,836,518 | 81% | 21% | 147,603 |
SAMN03266178 | Inter-caruncular Endometrium (Bos indicus, multiparous cow, female, SAMN03266178) | 29,746,752 | 81% | 21% | 157,543 |
SAMN03266179 | Inter-caruncular Endometrium (Bos indicus, multiparous cow, female, SAMN03266179) | 14,192,264 | 81% | 22% | 142,847 |
SAMN03801558 | Blood (Bos indicus, male, SAMN03801558) | 111,279,920 | 57% | 9% | 133,285 |
SAMN06035899 | horn tissue, squamous cell (Bos indicus, neuter, SAMN06035899) | 583,491 | 65% | 26% | 81,384 |
SAMN06035900 | horn tissue, squamous cell, horn cancer (Bos indicus, neuter, SAMN06035900) | 909,364 | 61% | 23% | 80,702 |
Protein alignments
Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by ProSplign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|
Homo sapiens known RefSeq (NP_) | 45,075 | 43,505 (96.52%) | 43,505 (96.52%) | 75.76% | 82.37% |
Bovidae GenBank | 21,836 | 21,088 (96.57%) | 21,088 (96.57%) | 81.18% | 87.40% |
Bovidae known RefSeq (NP_) | 14,860 | 14,572 (98.06%) | 14,572 (98.06%) | 82.30% | 87.10% |
Same-species GenBank | 196 | 195 (99.49%) | 195 (99.49%) | 83.60% | 90.87% |
References
- RefSeq: Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, Dicuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Nucleic Acids Research 2014, 42(Database issue):D756-63
- RepeatMasker: Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2004. http://www.repeatmasker.org
- WindowMasker: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. Bioinformatics 2006, 2:134-41
- Splign: Kapustin Y, Souvorov A, Tatusova T, Lipman D. Biology Direct 2008, 3:20