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Report for CCDS716.1 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
716.1 Public Homo sapiens 1 RBMXL1 24 110 108 CCDS HistoryNCBI Gene:494115Re-query CCDS DB by CCDS ID:716.1See the combined annotation on chromosome 1 in Sequence Viewer

Public Note for CCDS 716.1
This CCDS represents a retrogene of RBMX (RNA binding motif protein, X-linked), which is located on chromosome X. While all introns in the coding sequence have been processed out compared to the RBMX locus, the ORF is intact and there is specific evidence for transcription at this location. Studies in PMID:16201836 indicate that this locus is likely to be functional because the ORF has been preserved by purifying selection in all six Old World primates carrying this retrogene. Given that X chromosomal genes in mammals can generate a statistically significant excess of autosomal retrogenes relative to genes on other chromosomes (PMID:14739461), it is possible that this retrogene may be functional during male meiosis when X chromosomal genes are silenced or during haploid stages of spermatogenesis (PMID:16201836). In addition, it should be noted that this retrogene shares its first non-coding exon with the cysteine conjugate-beta lyase 2 (CCBL2) locus on chromosome 1, but the coding sequences are non-overlapping.

Public since: CCDS release 1, NCBI annotation release 35.1, Ensembl annotation release 23

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

Sequence IDs included in CCDS 716.1

Original Current Source Nucleotide ID Protein ID MANE Status in CCDS Seq. Status Links
Original member Current member EBI ENST00000321792.5 ENSP00000318415.5 Accepted alive Link to Ensembl Transcript Viewer:ENST00000321792.5Link to Ensembl Protein Viewer:ENSP00000318415.5Re-query CCDS DB by Nucleotide ID:ENST00000321792Re-query CCDS DB by Protein ID:ENSP00000318415
Original member Current member EBI ENST00000399794.6 ENSP00000446099.1 Accepted alive Link to Ensembl Transcript Viewer:ENST00000399794.6Link to Ensembl Protein Viewer:ENSP00000446099.1Re-query CCDS DB by Nucleotide ID:ENST00000399794Re-query CCDS DB by Protein ID:ENSP00000446099
Original member Current member EBI ENST00000652648.1 ENSP00000498248.1 MANE Select Accepted alive Link to Ensembl Transcript Viewer:ENST00000652648.1Link to Ensembl Protein Viewer:ENSP00000498248.1Re-query CCDS DB by Nucleotide ID:ENST00000652648Re-query CCDS DB by Protein ID:ENSP00000498248
Original member Current member NCBI NM_001162536.3 NP_001156008.1 MANE Select Accepted alive Link to Nucleotide Sequence:NM_001162536.3Link to Protein Sequence:NP_001156008.1Re-query CCDS DB by Nucleotide ID:NM_001162536Re-query CCDS DB by Protein ID:NP_001156008Link to BLAST:NP_001156008.1
Original member Current member NCBI NM_019610.6 NP_062556.2 Accepted alive Link to Nucleotide Sequence:NM_019610.6Link to Protein Sequence:NP_062556.2Re-query CCDS DB by Nucleotide ID:NM_019610Re-query CCDS DB by Protein ID:NP_062556Link to BLAST:NP_062556.2

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_001156008.1 390 Q96E39 390 100% 0 0
NP_062556.2 390 Q96E39 390 100% 0 0

Chromosomal Locations for CCDS 716.1

Assembly GRCh38.p14 (GCF_000001405.40)

On '-' strand of Chromosome 1 (NC_000001.11)
Genome Browser links: Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 1Link to Ensembl Genome Browser on chromosome 1See the combined annotation on chromosome 1 in Sequence Viewer

Chromosome Start Stop Links
1 88982654 88983826 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 1Link to Ensembl Genome Browser on chromosome 1

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 (1173 nt):
ATGGTTGAAGCAGATCGCCCAGGAAAGCTCTTCATTGGTGGGCTTAATACGGAAACAAATGAGAAAGCTC
TTGAAACAGTATTTGGCAAATATGGACGAATAGTGGAAGTACTCTTGATAAAAGACCGTGAAACCAACAA
ATCAAGAGGATTTGCTTTTGTCACCTTTGAAAGCCCAGCAGACGCTAAGGATGCAGCCAGAGACATGAAT
GGAAAGTCATTAGATGGAAAAGCCATCAAGGTGGAACAAGCCACCAAACCATCATTTGAAAGAGGTAGAC
ATGGACCGCCCCCACCTCCAAGAAGTAGAGGTCCTCCAAGAGGTTTTGGAGCTGGAAGAGGAGGAAGTGG
AGGAACCAGGGGACCTCCTTCACGAGGAGGACACATGGATGATGGTGGATATTCCATGAATTTTAACATG
AGTTCTTCCAGGGGACCACTCCCAGTAAAAAGAGGACCACCACCAAGAAGTGGGGGTCCTTCTCCTAAGA
GATCTGCACCTTCAGGACTAGTTCGCAGCAGCAGTGGAATGGGAGGAAGAGCTCCTCTATCACGTGGAAG
AGATAGTTATGGAGGTCCACCTCGAAGGGAACCGCTCCCCTCTCGTAGAGATGTTTATTTGTCCCCAAGA
GATGATGGGTATTCTACTAAAGACAGCTATTCAAGCAGAGATTACCCAAGTTCTCGTGATACAAGAGATT
ATGCACCACCACCACGAGATTATACTTACCGTGATTATGGTCATTCCAGTTCACGTGATGACTATCCATC
AAGAGGCTATGGCGATAGAGATGGATATGGTCGTGATCGTGACTATTCAGATCATCCAAGTGGAGGTTCC
TACAGAGATTCATATGAGAGTTATGGTAACTCACGTAGTGCTCCACTTACACGAGGGCCCCCGCCATCTT
ATGGTGGAAGCAGTCGCTATGATGATTATAGCAGCTCACGTGATGGATATGGTGGAAGTCGAGACAGTTA
CTCAAGCAGCCGAAGTGATCTCTACTCAAGTTGTGACAGGGTTGGCAGACAAGAAAGAGGGCTTCCCCCT
TCTGTAGAAAGGGGGTACCCTTCTTCACGTGATTCCTACAGCAGTTCAAGCCGCGGAGCACCAAGAGGTG
CTGGCCCTGGAGGAAGCCGATCTGATAGAGGGGGAGGCAGAAGCAGATACTAG

Translation (390 aa):
MVEADRPGKLFIGGLNTETNEKALETVFGKYGRIVEVLLIKDRETNKSRGFAFVTFESPADAKDAARDMN
GKSLDGKAIKVEQATKPSFERGRHGPPPPPRSRGPPRGFGAGRGGSGGTRGPPSRGGHMDDGGYSMNFNM
SSSRGPLPVKRGPPPRSGGPSPKRSAPSGLVRSSSGMGGRAPLSRGRDSYGGPPRREPLPSRRDVYLSPR
DDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYGDRDGYGRDRDYSDHPSGGS
YRDSYESYGNSRSAPLTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSCDRVGRQERGLPP
SVERGYPSSRDSYSSSSRGAPRGAGPGGSRSDRGGGRSRY


Links Key
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 Genome Browser Links:   Ensembl Genome Browser
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