NCBI CCDS banner
PubMed Entrez Gene BLAST OMIM
  

CCDS
Home
FTP
Process
Releases & Statistics

Collaborators
EBI
HGNC
MGI
NCBI

Contact Us
email CCDS

Genome Displays

Ensembl
NCBI
UCSC
VEGA

Related Resources
Gene
HomoloGene
MANE
RefSeq

Report for CCDS19873.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
19873.2 Public Mus musculus 5 Gtf3a 23 108 98 CCDS HistoryNCBI Gene:66596Re-query CCDS DB by CCDS ID:19873.2Re-query CCDS DB by GeneID:66596See the combined annotation on chromosome 5 in Sequence Viewer

Public Note for CCDS 19873.1
The coding region has been updated to start at a non-AUG (CUG) translation start codon that is conserved in several mammalian species. This non-AUG start site has not been experimentally tested in any system, but the resulting protein is consistent in size with the purified human ortholog described in PMID:8063702, and the update adds several additional zinc finger domains, which are described for this protein in PMID:11814676. Use of the non-AUG start site is also supported by the presence of strong secondary structure and a downstream hairpin that may promote ribosome stalling and non-AUG translation initiation, which is suggested for non-AUG initiation in PMID:2236042.

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 19873.2

Original Current Source Nucleotide ID Protein ID Status in CCDS Seq. Status Links
Original member Current member EBI ENSMUST00000146511.7 ENSMUSP00000119607.1 Accepted alive Link to Ensembl Transcript Viewer:ENSMUST00000146511.7Link to Ensembl Protein Viewer:ENSMUSP00000119607.1Re-query CCDS DB by Nucleotide ID:ENSMUST00000146511Re-query CCDS DB by Protein ID:ENSMUSP00000119607
Original member Current member EBI ENSMUST00000233741.1 ENSMUSP00000156679.1 Accepted alive Link to Ensembl Transcript Viewer:ENSMUST00000233741.1Link to Ensembl Protein Viewer:ENSMUSP00000156679.1Re-query CCDS DB by Nucleotide ID:ENSMUST00000233741Re-query CCDS DB by Protein ID:ENSMUSP00000156679
Original member Current member NCBI NM_025652.3 NP_079928.2 Accepted alive Link to Nucleotide Sequence:NM_025652.3Link to Protein Sequence:NP_079928.2Re-query CCDS DB by Nucleotide ID:NM_025652Re-query CCDS DB by Protein ID:NP_079928Link to BLAST:NP_079928.2

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_079928.2 364 Q8VHT7 364 100% 0 0

Chromosomal Locations for CCDS 19873.2

Assembly GRCm38.p6 (GCF_000001635.26)

On '+' strand of Chromosome 5 (NC_000071.6)
Genome Browser links: Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5See the combined annotation on chromosome 5 in Sequence Viewer

Chromosome Start Stop Links
5 146948781 146948975 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146950533 146950633 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146951187 146951283 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146951874 146951962 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146952727 146952800 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146953227 146953307 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146953848 146954077 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146955124 146955183 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 146955368 146955535 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5

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 (1095 nt):
CTGGAGCCGCGGGTGTCAGTCGCGGAAGCGGTGTCGTCGCTGACCATCGCGGATGCGTTCGTCGGGGCCT
GTGAGGGCCCCGCGCCGCCGCGCCCCGCGCTGCCCAGCAGGTTCATCTGCTCCTTTCCCGACTGCAGCGC
CAGTTACAACAAAGCCTGGAAGCTAGACGCGCACCTATGCAAACACACGGGGGAGAGGCCATTTGTTTGC
GACTATGAGGGCTGTGGCAAGGCCTTCATCAGAGACTACCATCTGAGCCGGCATGTCCTGATTCACACCG
GGGAAAAGCCGTTTGTTTGTGCAGATGATGGCTGTAATCAGAAATTCAACACAAAATCAAACTTGAAGAA
ACACATTGAACGCAAACATGGAAACCCACAAAAACAGTATGTGTGCAGTTATGAGGGTTGCAAGAAGGCC
TTTAAGAAGCACCAGCAGCTGAGAACCCATCAGTGCCAGCACACCAGCGAGCCGCTCTTCAGGTGTACCC
ACGAGGGATGCGGGAAGCACTTTGCCTCGCCCAGCAGGCTGAAACGGCATGGGAAAGTTCACGAGGGCTA
CCTGTGTCAAAAGGGATGTTCTTTCATGGGAAAAACGTGGACAGAGCTCCTGAAACACATGAGAGAAGCC
CATAAAGAGGACATAACCTGCAATGTATGTCAGAGGATGTTCAAGCGCAGAGATTACCTTAAGCAGCACA
TGAAGACTCACGCCCCGGAAAGGGATGTGTACCGCTGTCCGCGGCAAGGCTGCGGAAGAACCTACACAAC
CGTGTTCAACCTGCAGAGCCACATTCTCTCCTTCCACGAGGAAAAGCGCCCATTTGTGTGTGAGCACGCT
GGCTGTGGCAAGACATTCGCAATGAAACAGAGTCTCATGAGGCACAGTGTCGTGCACGATCCCGACAAGA
AGAGGATGAAGCTCAAAGTAAGAGCCCCTCGGGAGAGACGCAGCTTGGCCTCTCGCCTCAGTGGGTACTT
CCCTCCTAAGAGGAAACAAGAGCCCGACTACTCCTTGCCTAACGCCAGCGCAGAGTCCAGCAGCAGCCCA
GAGGCCCAGCTGCCCCCGCCAGCCGCCTTACTCACTGTCTGCTAG

Translation (364 aa):
MEPRVSVAEAVSSLTIADAFVGACEGPAPPRPALPSRFICSFPDCSASYNKAWKLDAHLCKHTGERPFVC
DYEGCGKAFIRDYHLSRHVLIHTGEKPFVCADDGCNQKFNTKSNLKKHIERKHGNPQKQYVCSYEGCKKA
FKKHQQLRTHQCQHTSEPLFRCTHEGCGKHFASPSRLKRHGKVHEGYLCQKGCSFMGKTWTELLKHMREA
HKEDITCNVCQRMFKRRDYLKQHMKTHAPERDVYRCPRQGCGRTYTTVFNLQSHILSFHEEKRPFVCEHA
GCGKTFAMKQSLMRHSVVHDPDKKRMKLKVRAPRERRSLASRLSGYFPPKRKQEPDYSLPNASAESSSSP
EAQLPPPAALLTVC


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

Disclaimer | Write to the Help Desk
NCBI | NLM | NIH