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Report for CCDS47209.1 (current version)

CCDS Status Species Chrom. Gene CCDS Release NCBI Annotation Release Ensembl Annotation Release Links
47209.1 Public Homo sapiens 5 IL6ST 24 110 108 CCDS HistoryNCBI Gene:3572Re-query CCDS DB by CCDS ID:47209.1Re-query CCDS DB by GeneID:3572See the combined annotation on chromosome 5 in Sequence Viewer

Public Note for CCDS 47209.1
This CCDS ID represents the gp130-RAPS isoform described in PMIDs: 10880057 and 16646038. This variant is supported by the transcript AB015706.1. It should be noted that this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID:10880057 using an antibody specific for the distinct C-terminus of this isoform. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this isoform.

Public since: CCDS release 6, NCBI annotation release 37.1, Ensembl annotation release 55

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


Attributes
Nonsense-mediated decay (NMD) candidate

Sequence IDs included in CCDS 47209.1

Original Current Source Nucleotide ID Protein ID MANE Status in CCDS Seq. Status Links
Original member Current member EBI ENST00000522633.2 ENSP00000435399.1 Accepted alive Link to Ensembl Transcript Viewer:ENST00000522633.2Link to Ensembl Protein Viewer:ENSP00000435399.1Re-query CCDS DB by Nucleotide ID:ENST00000522633Re-query CCDS DB by Protein ID:ENSP00000435399
Original member Current member NCBI NM_175767.3 NP_786943.1 Accepted alive Link to Nucleotide Sequence:NM_175767.3Link to Protein Sequence:NP_786943.1Re-query CCDS DB by Nucleotide ID:NM_175767Re-query CCDS DB by Protein ID:NP_786943Link to BLAST:NP_786943.1

RefSeq Length Related UniProtKB/SwissProt Length Identity Gaps Mismatches
NP_786943.1 329 P40189-2 329 100% 0 0

Chromosomal Locations for CCDS 47209.1

Assembly GRCh38.p14 (GCF_000001405.40)

On '-' strand of Chromosome 5 (NC_000005.10)
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 55956219 55956235 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 55960402 55960561 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 55963352 55963506 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 55964146 55964312 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 55968276 55968396 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 55969550 55969855 Link to NCBI NucleotideLink to UCSC Genome Browser on chromosome 5Link to Ensembl Genome Browser on chromosome 5
5 55976215 55976278 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.

Nucleotide Sequence (990 nt):
ATGTTGACGTTGCAGACTTGGCTAGTGCAAGCCTTGTTTATTTTCCTCACCACTGAATCTACAGGTGAAC
TTCTAGATCCATGTGGTTATATCAGTCCTGAATCTCCAGTTGTACAACTTCATTCTAATTTCACTGCAGT
TTGTGTGCTAAAGGAAAAATGTATGGATTATTTTCATGTAAATGCTAATTACATTGTCTGGAAAACAAAC
CATTTTACTATTCCTAAGGAGCAATATACTATCATAAACAGAACAGCATCCAGTGTCACCTTTACAGATA
TAGCTTCATTAAATATTCAGCTCACTTGCAACATTCTTACATTCGGACAGCTTGAACAGAATGTTTATGG
AATCACAATAATTTCAGGCTTGCCTCCAGAAAAACCTAAAAATTTGAGTTGCATTGTGAACGAGGGGAAG
AAAATGAGGTGTGAGTGGGATGGTGGAAGGGAAACACACTTGGAGACAAACTTCACTTTAAAATCTGAAT
GGGCAACACACAAGTTTGCTGATTGCAAAGCAAAACGTGACACCCCCACCTCATGCACTGTTGATTATTC
TACTGTGTATTTTGTCAACATTGAAGTCTGGGTAGAAGCAGAGAATGCCCTTGGGAAGGTTACATCAGAT
CATATCAATTTTGATCCTGTATATAAAGTGAAGCCCAATCCGCCACATAATTTATCAGTGATCAACTCAG
AGGAACTGTCTAGTATCTTAAAATTGACATGGACCAACCCAAGTATTAAGAGTGTTATAATACTAAAATA
TAACATTCAATATAGGACCAAAGATGCCTCAACTTGGAGCCAGATTCCTCCTGAAGACACAGCATCCACC
CGATCTTCATTCACTGTCCAAGACCTTAAACCTTTTACAGAATATGTGTTTAGGATTCGCTGTATGAAGG
AAGATGGTAAGGGATACTGGAGTGACTGGAGTGAAGAAGCAAGTGGGATCACCTATGAAGATAACATTGC
CTCCTTTTGA

Translation (329 aa):
MLTLQTWLVQALFIFLTTESTGELLDPCGYISPESPVVQLHSNFTAVCVLKEKCMDYFHVNANYIVWKTN
HFTIPKEQYTIINRTASSVTFTDIASLNIQLTCNILTFGQLEQNVYGITIISGLPPEKPKNLSCIVNEGK
KMRCEWDGGRETHLETNFTLKSEWATHKFADCKAKRDTPTSCTVDYSTVYFVNIEVWVEAENALGKVTSD
HINFDPVYKVKPNPPHNLSVINSEELSSILKLTWTNPSIKSVIILKYNIQYRTKDASTWSQIPPEDTAST
RSSFTVQDLKPFTEYVFRIRCMKEDGKGYWSDWSEEASGITYEDNIASF


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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