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Report for CCDS47398.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
47398.2 Public Homo sapiens 6 POU5F1 24 110 108 CCDS HistoryNCBI Gene:5460Re-query CCDS DB by CCDS ID:47398.2Re-query CCDS DB by GeneID:5460See the combined annotation on chromosome 6 in Sequence Viewer

Public Note for CCDS 47398.1
The coding region has been updated to shorten the N-terminus to one that is more supported by available transcript data and publication evidence. The update uses a non-AUG (CUG) start codon, which was shown to be the predominant start codon in studies in PMID:19489092. The transcript also has two other potential start codons, which are used less frequently: an upstream and polymorphic AUG start codon, which can produce a 265 aa isoform, and a downstream AUG start codon, which can produce a 164 aa isoform. The upstream AUG is not present in the GRCh37 primary assembly, where it appears as AGG versus AUG. This is a valid polymorphism (reference SNP 3130932), as described in PMIDs 1408763 and 19489092. This polymorphic start codon has a weak Kozak signal, and therefore in AUG-containing alleles, leaky scanning by ribosomes may occur to allow preferential initiation at the downstream CUG start codon. The isoform derived from the CUG start codon is the only one detected endogenously in studies in PMID:19489092.

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

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


Attributes
Non-AUG initiation codon

Sequence IDs included in CCDS 47398.2

Original Current Source Nucleotide ID Protein ID MANE Status in CCDS Seq. Status Links
Original member Current member EBI ENST00000606567.6 ENSP00000475880.2 Accepted alive Link to Ensembl Transcript Viewer:ENST00000606567.6Link to Ensembl Protein Viewer:ENSP00000475880.2Re-query CCDS DB by Nucleotide ID:ENST00000606567Re-query CCDS DB by Protein ID:ENSP00000475880
Original member Current member NCBI NM_001173531.3 NP_001167002.1 Accepted alive Link to Nucleotide Sequence:NM_001173531.3Link to Protein Sequence:NP_001167002.1Re-query CCDS DB by Nucleotide ID:NM_001173531Re-query CCDS DB by Protein ID:NP_001167002Link to BLAST:NP_001167002.1
Original member Current member NCBI NM_203289.6 NP_976034.4 Accepted alive Link to Nucleotide Sequence:NM_203289.6Link to Protein Sequence:NP_976034.4Re-query CCDS DB by Nucleotide ID:NM_203289Re-query CCDS DB by Protein ID:NP_976034Link to BLAST:NP_976034.4

Chromosomal Locations for CCDS 47398.2

Assembly GRCh38.p14 (GCF_000001405.40)

On '-' strand of Chromosome 6 (NC_000006.12)
Genome Browser links: Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6See the combined annotation on chromosome 6 in Sequence Viewer

Chromosome Start Stop Links
6 31164601 31164867 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 31165128 31165286 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 31165571 31165701 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 31165927 31165942 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6

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. This works on the replacement symbol in the Translation Exceptions section also.

Translation Exceptions:
replace the symbol L (codon CTG) with M at amino acid position 1

Nucleotide Sequence (573 nt):
CTGGGGGTTCTATTTGGGAAGGTATTCAGCCAAACGACCATCTGCCGCTTTGAGGCTCTGCAGCTTAGCT
TCAAGAACATGTGTAAGCTGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAACAATGAAAATCT
TCAGGAGATATGCAAAGCAGAAACCCTCGTGCAGGCCCGAAAGAGAAAGCGAACCAGTATCGAGAACCGA
GTGAGAGGCAACCTGGAGAATTTGTTCCTGCAGTGCCCGAAACCCACACTGCAGCAGATCAGCCACATCG
CCCAGCAGCTTGGGCTCGAGAAGGATGTGGTCCGAGTGTGGTTCTGTAACCGGCGCCAGAAGGGCAAGCG
ATCAAGCAGCGACTATGCACAACGAGAGGATTTTGAGGCTGCTGGGTCTCCTTTCTCAGGGGGACCAGTG
TCCTTTCCTCTGGCCCCAGGGCCCCATTTTGGTACCCCAGGCTATGGGAGCCCTCACTTCACTGCACTGT
ACTCCTCGGTCCCTTTCCCTGAGGGGGAAGCCTTTCCCCCTGTCTCCGTCACCACTCTGGGCTCTCCCAT
GCATTCAAACTGA

Translation (190 aa):
MGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENR
VRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPV
SFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPVSVTTLGSPMHSN


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

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