NCBI CCDS banner
PubMed Entrez Gene BLAST OMIM
  

CCDS
Home
FTP
Process
Releases & Statistics

Collaborators
EBI
HGNC
MGI
NCBI

Contact Us
email CCDS

Genome Displays

Ensembl
NCBI
UCSC
VEGA

Related Resources
Gene
HomoloGene
MANE
RefSeq


Report for CCDS47925.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
47925.2 Public Homo sapiens 8 PSCA 24 110 108 CCDS HistoryNCBI Gene:8000Re-query CCDS DB by CCDS ID:47925.2See the combined annotation on chromosome 8 in Sequence Viewer

Public Note for CCDS 47925.1
The coding region has been updated to shorten the N-terminus to one that is supported by the reference genome allele (GRCh37 assembly). The previous representation used a polymorphic start codon that exists as ACG in the reference genome allele versus ATG in the alternate allele (also known as the T allele). This corresponds to the reference SNP rs2294008. Some individuals contain the reference genome allele, while others contain the T allele. Data in PMIDs 18488030, 19554573, 19582881 and 19648920 indicate that the T allele may be a risk allele for gastric and bladder cancers. It is also associated with decreased promoter activity (PMIDs 18488030 and 19648920). The current update results in a protein that is 9 aa shorter at the N-terminus.

Public since: CCDS release 6, NCBI annotation release 37.1, Ensembl annotation release 55

Review status: Reviewed (by RefSeq, Havana and CCDS collaboration)

Sequence IDs included in CCDS 47925.2

Original Current Source Nucleotide ID Protein ID MANE Status in CCDS Seq. Status Links
Original member Current member EBI ENST00000301258.5 ENSP00000301258.4 MANE Select Accepted alive Link to Ensembl Transcript Viewer:ENST00000301258.5Link to Ensembl Protein Viewer:ENSP00000301258.4Re-query CCDS DB by Nucleotide ID:ENST00000301258Re-query CCDS DB by Protein ID:ENSP00000301258
Original member Current member NCBI NM_005672.5 NP_005663.2 MANE Select Accepted alive Link to Nucleotide Sequence:NM_005672.5Link to Protein Sequence:NP_005663.2Re-query CCDS DB by Nucleotide ID:NM_005672Re-query CCDS DB by Protein ID:NP_005663Link to BLAST:NP_005663.2

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_005663.2 114 O43653 114 100% 0 0

Chromosomal Locations for CCDS 47925.2

Assembly GRCh38.p14 (GCF_000001405.40)

On '+' strand of Chromosome 8 (NC_000008.11)
Genome Browser links: Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8See the combined annotation on chromosome 8 in Sequence Viewer

Chromosome Start Stop Links
8 142680539 142680563 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 142681327 142681434 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 142681921 142682132 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8

CCDS Sequence Data
Blue highlighting indicates alternating exons.
Red highlighting indicates amino acids encoded across a splice junction.
 
Mouse over the nucleotide or protein sequence below and click on the highlighted codon or residue to select the pair.

Nucleotide Sequence (345 nt):
ATGGCAGGCTTGGCCCTGCAGCCAGGCACTGCCCTGCTGTGCTACTCCTGCAAAGCCCAGGTGAGCAACG
AGGACTGCCTGCAGGTGGAGAACTGCACCCAGCTGGGGGAGCAGTGCTGGACCGCGCGCATCCGCGCAGT
TGGCCTCCTGACCGTCATCAGCAAAGGCTGCAGCTTGAACTGCGTGGATGACTCACAGGACTACTACGTG
GGCAAGAAGAACATCACGTGCTGTGACACCGACTTGTGCAACGCCAGCGGGGCCCATGCCCTGCAGCCGG
CTGCTGCCATCCTTGCGCTGCTCCCTGCACTCGGCCTGCTGCTCTGGGGACCCGGCCAGCTCTAG

Translation (114 aa):
MAGLALQPGTALLCYSCKAQVSNEDCLQVENCTQLGEQCWTARIRAVGLLTVISKGCSLNCVDDSQDYYV
GKKNITCCDTDLCNASGAHALQPAAAILALLPALGLLLWGPGQL


Links Key
 Links to:   History report
  BLAST report
  Entrez Gene
  Nucleotide report
  Protein report
 Re-query CCDS DB by:   CCDS ID
  Gene ID
  Nucleotide ID
  Protein ID
 Genome Browser Links:   Ensembl Genome Browser
  NCBI Sequence Viewer
  UCSC Genome Browser
  VEGA Genome Browser

Disclaimer | Write to the Help Desk
NCBI | NLM | NIH