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Report for CCDS28818.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
28818.2 Public Mus musculus 17 Vegfa 21 106 86 CCDS HistoryNCBI Gene:22339Re-query CCDS DB by CCDS ID:28818.2Re-query CCDS DB by GeneID:22339See the combined annotation on chromosome 17 in Sequence Viewer

Public Note for CCDS 28818.1
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 RefSeq, Havana and CCDS collaboration)


Attributes
Non-AUG initiation codon

Sequence IDs included in CCDS 28818.2

Original Current Source Nucleotide ID Protein ID Status in CCDS Seq. Status Links
Original member Current member EBI,WTSI ENSMUST00000071648 ENSMUSP00000071575 Accepted alive Link to Ensembl Transcript Viewer:ENSMUST00000071648Link to Ensembl Protein Viewer:ENSMUSP00000071575Re-query CCDS DB by Nucleotide ID:ENSMUST00000071648Re-query CCDS DB by Protein ID:ENSMUSP00000071575
Original member Current member EBI,WTSI OTTMUST00000039102 OTTMUSP00000017463 Accepted alive Link to Vega Transcript Viewer:OTTMUST00000039102Link to Vega Protein Viewer:OTTMUSP00000017463Re-query CCDS DB by Nucleotide ID:OTTMUST00000039102Re-query CCDS DB by Protein ID:OTTMUSP00000017463
Original member Current member NCBI NM_009505.4 NP_033531.3 Accepted alive Link to Nucleotide Sequence:NM_009505.4Link to Protein Sequence:NP_033531.3Re-query CCDS DB by Nucleotide ID:NM_009505Re-query CCDS DB by Protein ID:NP_033531Link to BLAST:NP_033531.3

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_033531.3 368 Q00731-6 368 100% 0 0

Chromosomal Locations for CCDS 28818.2

Assembly GRCm38.p4 (GCF_000001635.24)

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 17Link to Vega 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 17Link to Vega Genome Browser on chromosome 17
17 46020991 46021122 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 17Link to Ensembl Genome Browser on chromosome 17Link to Vega 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 17Link to Vega 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 17Link to Vega 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 17Link to Vega 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 17Link to Vega 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 17Link to Vega 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 (1107 nt):
CTGACGGACAGACAGACAGACACCGCCCCCAGCCCCAGCGCCCACCTCCTCGCCGGCGGGCTGCCGACGG
TG
GACGCGGCGGCGAGCCGCGAGGAACCGAAGCCCGCGCCCGGAGGCGGGGTGGAGGGGGTCGGGGCTCG
C
GGGATTGCACGGAAACTTTTCGTCCAACTTCTGGGCTCTTCTCGCTCCGTAGTAGCCGTGGTCTGCGCC
GCA
GGAGACAAACCGATCGGAGCTGGGAGAAGTGCTAGCTCGGGCCTGGAGAAGCCGGGGCCCGAGAAGA
GA
GGGGAGGAAGAGAAGGAAGAGGAGAGGGGGCCGCAGTGGGCGCTCGGCTCTCAGGAGCCGAGCTCATG
G
ACGGGTGAGGCGGCCGTGTGCGCAGACAGTGCTCCAGCCGCGCGCGCGCCCCAGGCCCCGGCCCGGGCC
TCG
GTTCCAGAAGGGAGAGGAGCCCGCCAAGGCGCGCAAGAGAGCGGGCTGCCTCGCAGTCCGAGCCGGA
GA
GGGAGCGCGAGCCGCGCCGGCCCCGGACGGGCCTCCGAAACCATGAACTTTCTGCTCTCTTGGGTGCA
C
TGGACCCTGGCTTTACTGCTGTACCTCCACCATGCCAAGTGGTCCCAGGCTGCACCCACGACAGAAGGA
GAG
CAGAAGTCCCATGAAGTGATCAAGTTCATGGATGTCTACCAGCGAAGCTACTGCCGTCCGATTGAGA
CC
CTGGTGGACATCTTCCAGGAGTACCCCGACGAGATAGAGTACATCTTCAAGCCGTCCTGTGTGCCGCT
G
ATGCGCTGTGCAGGCTGCTGTAACGATGAAGCCCTGGAGTGCGTGCCCACGTCAGAGAGCAACATCACC
ATG
CAGATCATGCGGATCAAACCTCACCAAAGCCAGCACATAGGAGAGATGAGCTTCCTACAGCACAGCA
GA
TGTGAATGCAGACCAAAGAAAGACAGAACAAAGCCAGAAAATCACTGTGAGCCTTGTTCAGAGCGGAG
A
AAGCATTTGTTTGTCCAAGATCCGCAGACGTGTAAATGTTCCTGCAAAAACACAGACTCGCGTTGCAAG
GCG
AGGCAGCTTGAGTTAAACGAACGTACTTGCAGATGTGACAAGCCAAGGCGGTGA


Translation (368 aa):
MTDRQTDTAPSPSAHLLAGGLPTVDAAASREEPKPAPGGGVEGVGARGIARKLFVQLLGSSRSVVAVVCA
A
GDKPIGAGRSASSGLEKPGPEKRGEEEKEEERGPQWALGSQEPSSWTGEAAVCADSAPAARAPQAPARA
S
VPEGRGARQGAQESGLPRSPSRRGSASRAGPGRASETMNFLLSWVHWTLALLLYLHHAK
WSQAAPTTEG
E
QKSHE
VIKFMDVYQRSYCRPIETLVDIFQEYPDEIEYIFKPSCVPLMRCAGCCNDEALECVPTSESNIT
M
Q
IMRIKPHQSQHIGEMSFLQHSRCECRPKKDRTKPENHCEPCSERRKHLFVQDPQTCKCSCKNTDSRCK
A
RQLELNERTC
RCDKPRR



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