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Report for CCDS4907.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
4907.2 Public Homo sapiens 6 VEGFA 24 110 108 CCDS HistoryNCBI Gene:7422Re-query CCDS DB by CCDS ID:4907.2Re-query CCDS DB by GeneID:7422See the combined annotation on chromosome 6 in Sequence Viewer

Public Note for CCDS 4907.1
The coding region has been updated to start at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. Most of the publicly available long mRNAs at this locus do not extend far enough 5' to include the CUG start codon, including M27281.1 which supports this variant. However, BC058855.1, several unspliced partial transcripts and the aforementioned publications all support transcription initiation further upstream. Hence, this CCDS representation includes the extended 5' CDS. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55009.1.

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

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


Attributes
Non-AUG initiation codon

Sequence IDs included in CCDS 4907.2

Original Current Source Nucleotide ID Protein ID MANE Status in CCDS Seq. Status Links
Original member Current member EBI ENST00000672860.3 ENSP00000500082.3 MANE Select Accepted alive Link to Ensembl Transcript Viewer:ENST00000672860.3Link to Ensembl Protein Viewer:ENSP00000500082.3Re-query CCDS DB by Nucleotide ID:ENST00000672860Re-query CCDS DB by Protein ID:ENSP00000500082
Original member Current member NCBI NM_003376.6 NP_003367.4 MANE Select Accepted alive Link to Nucleotide Sequence:NM_003376.6Link to Protein Sequence:NP_003367.4Re-query CCDS DB by Nucleotide ID:NM_003376Re-query CCDS DB by Protein ID:NP_003367Link to BLAST:NP_003367.4

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_003367.4 395 P15692-13 395 100% 0 0

Chromosomal Locations for CCDS 4907.2

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 43770707 43771312 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 43774341 43774392 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 43777469 43777665 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 43778460 43778536 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 43778889 43778918 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 43780732 43780803 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 43781956 43782087 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 6Link to Ensembl Genome Browser on chromosome 6
6 43784541 43784562 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 (1188 nt):
CTGACGGACAGACAGACAGACACCGCCCCCAGCCCCAGCTACCACCTCCTCCCCGGCCGGCGGCGGACAG
TGGACGCGGCGGCGAGCCGCGGGCAGGGGCCGGAGCCCGCGCCCGGAGGCGGGGTGGAGGGGGTCGGGGC
TCGCGGCGTCGCACTGAAACTTTTCGTCCAACTTCTGGGCTGTTCTCGCTTCGGAGGAGCCGTGGTCCGC
GCGGGGGAAGCCGAGCCGAGCGGAGCCGCGAGAAGTGCTAGCTCGGGCCGGGAGGAGCCGCAGCCGGAGG
AGGGGGAGGAGGAAGAAGAGAAGGAAGAGGAGAGGGGGCCGCAGTGGCGACTCGGCGCTCGGAAGCCGGG
CTCATGGACGGGTGAGGCGGCGGTGTGCGCAGACAGTGCTCCAGCCGCGCGCGCTCCCCAGGCCCTGGCC
CGGGCCTCGGGCCGGGGAGGAAGAGTAGCTCGCCGAGGCGCCGAGGAGAGCGGGCCGCCCCACAGCCCGA
GCCGGAGAGGGAGCGCGAGCCGCGCCGGCCCCGGTCGGGCCTCCGAAACCATGAACTTTCTGCTGTCTTG
GGTGCATTGGAGCCTTGCCTTGCTGCTCTACCTCCACCATGCCAAGTGGTCCCAGGCTGCACCCATGGCA
GAAGGAGGAGGGCAGAATCATCACGAAGTGGTGAAGTTCATGGATGTCTATCAGCGCAGCTACTGCCATC
CAATCGAGACCCTGGTGGACATCTTCCAGGAGTACCCTGATGAGATCGAGTACATCTTCAAGCCATCCTG
TGTGCCCCTGATGCGATGCGGGGGCTGCTGCAATGACGAGGGCCTGGAGTGTGTGCCCACTGAGGAGTCC
AACATCACCATGCAGATTATGCGGATCAAACCTCACCAAGGCCAGCACATAGGAGAGATGAGCTTCCTAC
AGCACAACAAATGTGAATGCAGACCAAAGAAAGATAGAGCAAGACAAGAAAAAAAATCAGTTCGAGGAAA
GGGAAAGGGGCAAAAACGAAAGCGCAAGAAATCCCGGTATAAGTCCTGGAGCGTTCCCTGTGGGCCTTGC
TCAGAGCGGAGAAAGCATTTGTTTGTACAAGATCCGCAGACGTGTAAATGTTCCTGCAAAAACACAGACT
CGCGTTGCAAGGCGAGGCAGCTTGAGTTAAACGAACGTACTTGCAGATGTGACAAGCCGAGGCGGTGA

Translation (395 aa):
MTDRQTDTAPSPSYHLLPGRRRTVDAAASRGQGPEPAPGGGVEGVGARGVALKLFVQLLGCSRFGGAVVR
AGEAEPSGAARSASSGREEPQPEEGEEEEEKEEERGPQWRLGARKPGSWTGEAAVCADSAPAARAPQALA
RASGRGGRVARRGAEESGPPHSPSRRGSASRAGPGRASETMNFLLSWVHWSLALLLYLHHAKWSQAAPMA
EGGGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEES
NITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKDRARQEKKSVRGKGKGQKRKRKKSRYKSWSVPCGPC
SERRKHLFVQDPQTCKCSCKNTDSRCKARQLELNERTCRCDKPRR


Links Key
 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
  NCBI Sequence Viewer
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