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Report for CCDS28817.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
28817.2 Public Mus musculus 17 Vegfa 23 108 98 CCDS HistoryNCBI Gene:22339Re-query CCDS DB by CCDS ID:28817.2Re-query CCDS DB by GeneID:22339See the combined annotation on chromosome 17 in Sequence Viewer

Public Note for CCDS 28817.1
The coding region has been updated to start at an upstream non-AUG (CUG) translation start codon that is supported by conservation data. Experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620, supports the use of the equivalent CUG start codon in the human ortholog. Alternative translation initiation from a downstream AUG codon, which results in a shorter isoform with a predicted signal peptide, has also been shown for the human ortholog. Initiation from the alternative AUG codon in mouse would give rise to an isoform that is 178 aa shorter at the N-terminus. There is no experimental evidence showing the use of either start codon in mouse. Nonetheless, PMID:11731620 demonstrates the existence of the longer isoform in mouse by Western analysis with an N-terminal-specific antibody against the human protein.

Public since: CCDS release 2, NCBI annotation release 36.1, Ensembl annotation release 39

Review status: Reviewed (by CCDS collaboration)


Attributes
Non-AUG initiation codon

Sequence IDs included in CCDS 28817.2

Original Current Source Nucleotide ID Protein ID Status in CCDS Seq. Status Links
Original member Current member EBI ENSMUST00000167860.8 ENSMUSP00000131901.2 Accepted alive Link to Ensembl Transcript Viewer:ENSMUST00000167860.8Link to Ensembl Protein Viewer:ENSMUSP00000131901.2Re-query CCDS DB by Nucleotide ID:ENSMUST00000167860Re-query CCDS DB by Protein ID:ENSMUSP00000131901
Original member Current member NCBI NM_001025257.3 NP_001020428.2 Accepted alive Link to Nucleotide Sequence:NM_001025257.3Link to Protein Sequence:NP_001020428.2Re-query CCDS DB by Nucleotide ID:NM_001025257Re-query CCDS DB by Protein ID:NP_001020428Link to BLAST:NP_001020428.2

Chromosomal Locations for CCDS 28817.2

Assembly GRCm38.p6 (GCF_000001635.26)

On '-' strand of Chromosome 17 (NC_000083.6)
Genome Browser links: Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17See the combined annotation on chromosome 17 in Sequence Viewer

Chromosome Start Stop Links
17 46018858 46018879 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17
17 46024065 46024094 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17
17 46024444 46024520 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17
17 46025347 46025543 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17
17 46028351 46028399 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17
17 46031291 46031890 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17

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 (975 nt):
CTGACGGACAGACAGACAGACACCGCCCCCAGCCCCAGCGCCCACCTCCTCGCCGGCGGGCTGCCGACGG
TGGACGCGGCGGCGAGCCGCGAGGAACCGAAGCCCGCGCCCGGAGGCGGGGTGGAGGGGGTCGGGGCTCG
CGGGATTGCACGGAAACTTTTCGTCCAACTTCTGGGCTCTTCTCGCTCCGTAGTAGCCGTGGTCTGCGCC
GCAGGAGACAAACCGATCGGAGCTGGGAGAAGTGCTAGCTCGGGCCTGGAGAAGCCGGGGCCCGAGAAGA
GAGGGGAGGAAGAGAAGGAAGAGGAGAGGGGGCCGCAGTGGGCGCTCGGCTCTCAGGAGCCGAGCTCATG
GACGGGTGAGGCGGCCGTGTGCGCAGACAGTGCTCCAGCCGCGCGCGCGCCCCAGGCCCCGGCCCGGGCC
TCGGTTCCAGAAGGGAGAGGAGCCCGCCAAGGCGCGCAAGAGAGCGGGCTGCCTCGCAGTCCGAGCCGGA
GAGGGAGCGCGAGCCGCGCCGGCCCCGGACGGGCCTCCGAAACCATGAACTTTCTGCTCTCTTGGGTGCA
CTGGACCCTGGCTTTACTGCTGTACCTCCACCATGCCAAGTGGTCCCAGGCTGCACCCACGACAGAAGGA
GAGCAGAAGTCCCATGAAGTGATCAAGTTCATGGATGTCTACCAGCGAAGCTACTGCCGTCCGATTGAGA
CCCTGGTGGACATCTTCCAGGAGTACCCCGACGAGATAGAGTACATCTTCAAGCCGTCCTGTGTGCCGCT
GATGCGCTGTGCAGGCTGCTGTAACGATGAAGCCCTGGAGTGCGTGCCCACGTCAGAGAGCAACATCACC
ATGCAGATCATGCGGATCAAACCTCACCAAAGCCAGCACATAGGAGAGATGAGCTTCCTACAGCACAGCA
GATGTGAATGCAGACCAAAGAAAGACAGAACAAAGCCAGAAAAATGTGACAAGCCAAGGCGGTGA

Translation (324 aa):
MTDRQTDTAPSPSAHLLAGGLPTVDAAASREEPKPAPGGGVEGVGARGIARKLFVQLLGSSRSVVAVVCA
AGDKPIGAGRSASSGLEKPGPEKRGEEEKEEERGPQWALGSQEPSSWTGEAAVCADSAPAARAPQAPARA
SVPEGRGARQGAQESGLPRSPSRRGSASRAGPGRASETMNFLLSWVHWTLALLLYLHHAKWSQAAPTTEG
EQKSHEVIKFMDVYQRSYCRPIETLVDIFQEYPDEIEYIFKPSCVPLMRCAGCCNDEALECVPTSESNIT
MQIMRIKPHQSQHIGEMSFLQHSRCECRPKKDRTKPEKCDKPRR


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

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