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Report for CCDS6370.1 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
6370.1 Public Homo sapiens 8 SLA 24 110 108 CCDS HistoryNCBI Gene:6503Re-query CCDS DB by CCDS ID:6370.1Re-query CCDS DB by GeneID:6503See the combined annotation on chromosome 8 in Sequence Viewer

Public Note for CCDS 6370.1
This CCDS represents a 276 aa protein that is encoded by NM_001045556.2, which is based on BX648382.1 and several locally supporting ESTs. However, it should be noted that NM_001045556.2 contains an upstream translation start codon at nts 504-506, as used in the NM_001045557.2 variant which encodes a 293 aa protein. The use of this upstream start codon in NM_001045556.2 would result in only a 15 aa ORF with a stop codon in the second exon. The short length of this upstream ORF may allow escape from nonsense-mediated mRNA decay (NMD) and translation reinitiation at the downstream start codon (nts 833-835) to encode the represented 276 aa protein, or alternatively, the weak Kozak signal at the upstream start codon may enable leaky scanning by the translation machinery and subsequent use of the downstream start codon. The 276 aa protein is consistent with reports in the literature, including PMIDs:7543898, 8825655 and 9660183. Variants encoding both the longer and shorter isoforms are also present in mouse (NM_001029841.3 and NM_009192.2, respectively).

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 6370.1

Original Current Source Nucleotide ID Protein ID MANE Status in CCDS Seq. Status Links
Original member Current member EBI ENST00000338087.10 ENSP00000337548.5 MANE Select Accepted alive Link to Ensembl Transcript Viewer:ENST00000338087.10Link to Ensembl Protein Viewer:ENSP00000337548.5Re-query CCDS DB by Nucleotide ID:ENST00000338087Re-query CCDS DB by Protein ID:ENSP00000337548
Original member Current member NCBI NM_001045556.3 NP_001039021.1 MANE Select Accepted alive Link to Nucleotide Sequence:NM_001045556.3Link to Protein Sequence:NP_001039021.1Re-query CCDS DB by Nucleotide ID:NM_001045556Re-query CCDS DB by Protein ID:NP_001039021Link to BLAST:NP_001039021.1

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_001039021.1 276 Q13239-1 276 100% 0 0

Chromosomal Locations for CCDS 6370.1

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 133038524 133038737 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 133039998 133040130 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 133044984 133045115 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 133047830 133047933 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 133049902 133049988 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 133050816 133050915 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 8Link to Ensembl Genome Browser on chromosome 8
8 133060100 133060160 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 (831 nt):
ATGGGAAACAGCATGAAATCCACCCCTGCGCCTGCCGAGAGGCCCCTGCCCAACCCGGAGGGACTGGATA
GCGACTTCCTTGCCGTGCTAAGTGACTACCCGTCTCCTGACATCAGCCCCCCGATATTCCGCCGAGGGGA
GAAACTGCGTGTGATTTCTGATGAAGGGGGCTGGTGGAAAGCTATTTCTCTTAGCACTGGTCGAGAGAGT
TACATCCCTGGAATATGTGTGGCCAGAGTTTACCATGGCTGGCTGTTTGAGGGCCTGGGCAGAGACAAGG
CCGAGGAGCTGCTGCAGCTGCCAGACACAAAGGTCGGCTCCTTCATGATCAGAGAGAGTGAGACCAAGAA
AGGGTTTTACTCACTGTCGGTGAGACACAGGCAGGTAAAGCATTACCGCATTTTCCGTCTGCCCAACAAC
TGGTACTACATTTCCCCGAGGCTCACCTTCCAGTGCCTGGAGGACCTGGTGAACCACTATTCTGAGGTGG
CTGATGGCCTGTGCTGTGTGCTCACCACGCCCTGCCTGACACAAAGCACGGCTGCCCCAGCAGTGAGGGC
CTCCAGCTCACCTGTCACCTTGCGTCAGAAGACTGTGGACTGGAGGAGAGTGTCCAGACTGCAGGAGGAC
CCCGAGGGAACAGAGAACCCGCTTGGGGTAGACGAGTCCCTTTTCAGCTATGGCCTTCGAGAGAGCATTG
CCTCTTACCTGTCCCTGACCAGTGAGGACAACACCTCCTTTGATCGAAAGAAGAAAAGCATCTCCCTGAT
GTATGGTGGCAGCAAGAGAAAGAGCTCATTCTTCTCATCACCACCTTACTTTGAGGACTAG

Translation (276 aa):
MGNSMKSTPAPAERPLPNPEGLDSDFLAVLSDYPSPDISPPIFRRGEKLRVISDEGGWWKAISLSTGRES
YIPGICVARVYHGWLFEGLGRDKAEELLQLPDTKVGSFMIRESETKKGFYSLSVRHRQVKHYRIFRLPNN
WYYISPRLTFQCLEDLVNHYSEVADGLCCVLTTPCLTQSTAAPAVRASSSPVTLRQKTVDWRRVSRLQED
PEGTENPLGVDESLFSYGLRESIASYLSLTSEDNTSFDRKKKSISLMYGGSKRKSSFFSSPPYFED


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 Links to:   History report
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 Re-query CCDS DB by:   CCDS ID
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 Genome Browser Links:   Ensembl Genome Browser
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