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 CCDS25096.2 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
25096.2 Reviewed, update pending Mus musculus 11 Sdf2 23 108 98 CCDS HistoryNCBI Gene:20316Re-query CCDS DB by CCDS ID:25096.2Re-query CCDS DB by GeneID:20316See the combined annotation on chromosome 11 in Sequence Viewer

Public Note for CCDS 25096.2
The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript data. The updated start codon is only conserved in mouse and rat, and it has a weak Kozak signal. It is possible that ribosomal leaky scanning may allow the better conserved downstream start codon to be used some of the time. There is no experimental evidence indicating which start codon is preferentially used in vivo.

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

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


Attributes
CDS uses downstream AUG

Sequence IDs included in CCDS 25096.2

Original Current Source Nucleotide ID Protein ID Status in CCDS Seq. Status Links
Original member Current member EBI ENSMUST00000002133.8 ENSMUSP00000002133.8 Accepted alive Link to Ensembl Transcript Viewer:ENSMUST00000002133.8Link to Ensembl Protein Viewer:ENSMUSP00000002133.8Re-query CCDS DB by Nucleotide ID:ENSMUST00000002133Re-query CCDS DB by Protein ID:ENSMUSP00000002133
Original member NCBI NM_009143.3 NP_033169.3 Updated not alive Link to Nucleotide Sequence:NM_009143.3Link to Protein Sequence:NP_033169.3Re-query CCDS DB by Nucleotide ID:NM_009143Re-query CCDS DB by Protein ID:NP_033169
Current member NCBI NM_009143.4 NP_033169.4 Pending alive Link to Nucleotide Sequence:NM_009143.4Link to Protein Sequence:NP_033169.4Re-query CCDS DB by Nucleotide ID:NM_009143Re-query CCDS DB by Protein ID:NP_033169Link to BLAST:NP_033169.4

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_033169.4 211 Q9DCT5 211 100% 0 0

Chromosomal Locations for CCDS 25096.2

Assembly GRCm38.p6 (GCF_000001635.26)

On '+' strand of Chromosome 11 (NC_000077.6)
Genome Browser links: Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 11Link to Ensembl Genome Browser on chromosome 11See the combined annotation on chromosome 11 in Sequence Viewer

Chromosome Start Stop Links
11 78245996 78246170 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 11Link to Ensembl Genome Browser on chromosome 11
11 78251016 78251212 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 11Link to Ensembl Genome Browser on chromosome 11
11 78254851 78255138 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 11Link to Ensembl Genome Browser on chromosome 11

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.

Nucleotide Sequence (660 nt):
ATGATTAGTTCTCTCGGATCTAGGATGGCTGTCTTGTCGCTTCTGTTGTTGGGTGGTTTGTGGAGCGCTG
TGGGAGCGTCCAACATGGCTGTCGTTACTTGCGGCTCCGTGGTGAAGCTACTCAATACACGCCACAATGT
CCGACTGCATTCTCACGACGTGCGCTATGGGTCAGGTAGTGGGCAGCAGTCAGTGACAGGTGTGACCTCT
GTGGATGACAGCAACAGTTACTGGAGGATACGGGGGAAGACAGCCACAGTGTGTGAAAGGGGAACCCCCA
TCAAATGCGGGCAGCCCATCCGTCTGACACACATCAACACAGGTCGAAACCTGCACAGCCACCATTTCAC
TTCACCTCTCTCTGGAAACCAGGAAGTGAGTGCCTTTGGCGAAGAAGGTGAAGGCGACTATCTGGATGAC
TGGACAGTGCTCTGTAATGGACCTTACTGGGTTAGAGATGGTGAGGTGAGGTTCAAACATTCTTCCACTG
ACGTACTGCTGTCTGTCACAGGAGAACAGTACGGACGACCCATAAGTGGACAAAAAGAGGTACATGGTAT
GGCCCAGCCAAGTCAGAACAACTACTGGAAGGCCATGGAAGGCATCTTCATGAAGCCCAGTGAGTTGCTG
AGGGCAGAGGTCCATCATGCAGAGCTGTGA

Translation (219 aa):
MISSLGSRMAVLSLLLLGGLWSAVGASNMAVVTCGSVVKLLNTRHNVRLHSHDVRYGSGSGQQSVTGVTS
VDDSNSYWRIRGKTATVCERGTPIKCGQPIRLTHINTGRNLHSHHFTSPLSGNQEVSAFGEEGEGDYLDD
WTVLCNGPYWVRDGEVRFKHSSTDVLLSVTGEQYGRPISGQKEVHGMAQPSQNNYWKAMEGIFMKPSELL
RAEVHHAEL


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