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C11orf49 chromosome 11 open reading frame 49 [ Homo sapiens (human) ]

Gene ID: 79096, updated on 7-Oct-2019

Summary

Official Symbol
C11orf49provided by HGNC
Official Full Name
chromosome 11 open reading frame 49provided by HGNC
Primary source
HGNC:HGNC:28720
See related
Ensembl:ENSG00000149179
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Ubiquitous expression in brain (RPKM 7.9), skin (RPKM 5.2) and 25 other tissues See more
Orthologs

Genomic context

See C11orf49 in Genome Data Viewer
Location:
11p11.2
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (46936524..47164385)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (46958240..47185932)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene cytoskeleton associated protein 5 Neighboring gene small nucleolar RNA, C/D box 67 Neighboring gene LRP4 antisense RNA 1 Neighboring gene LDL receptor related protein 4 Neighboring gene ATPase Asna1 pseudogene Neighboring gene uncharacterized LOC107984329 Neighboring gene ADP ribosylation factor GTPase activating protein 2 Neighboring gene ribosomal protein S20 pseudogene 26 Neighboring gene protein kinase C and casein kinase substrate in neurons 3 Neighboring gene microRNA 6745

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Phenotypes

NHGRI GWAS Catalog

Description
Genetic predictors of fibrin D-dimer levels in healthy adults.
NHGRI GWA Catalog
Two new susceptibility loci 1q24.2 and 11p11.2 confer risk to severe acne.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC4707, FLJ22210

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001003676.2NP_001003676.1  UPF0705 protein C11orf49 isoform 1

    See identical proteins and their annotated locations for NP_001003676.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks the 3' splice junction, compared to variant 2. The resulting isoform (1) is C-terminal truncated, compared to isoform 2.
    Source sequence(s)
    BC052291, DA487960
    Consensus CDS
    CCDS41641.1
    UniProtKB/Swiss-Prot
    Q9H6J7
    Related
    ENSP00000378844.2, ENST00000395460.6
  2. NM_001003677.3NP_001003677.1  UPF0705 protein C11orf49 isoform 2

    See identical proteins and their annotated locations for NP_001003677.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (2).
    Source sequence(s)
    BC013988, DA487960
    Consensus CDS
    CCDS31480.1
    UniProtKB/Swiss-Prot
    Q9H6J7
    Related
    ENSP00000367878.3, ENST00000378615.7
  3. NM_001003678.3NP_001003678.1  UPF0705 protein C11orf49 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an alternate 3' terminal exon, compared to variant 2. The resulting isoform (4) has a shorter and distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AC090589, BU728094, CK724853, DB027437
    Consensus CDS
    CCDS31479.1
    UniProtKB/Swiss-Prot
    Q9H6J7
    Related
    ENSP00000367881.2, ENST00000378618.6
  4. NM_001278222.1NP_001265151.1  UPF0705 protein C11orf49 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 5' coding region which results in an upstream start codon, and has an alternate splice site in the 3' coding region, compared to variant 2. The resulting isoform (5) has a distinct N-terminus and lacks an internal segment in the C-terminal region, compared to isoform 2.
    Source sequence(s)
    AK300813, BI763384, DA487960
    UniProtKB/TrEMBL
    B4DUV7
  5. NM_024113.5NP_077018.1  UPF0705 protein C11orf49 isoform 3

    See identical proteins and their annotated locations for NP_077018.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the 3' coding region, compared to variant 2. The resulting isoform (3) lacks an internal segment in the C-terminal region, compared to isoform 2.
    Source sequence(s)
    BC001860
    Consensus CDS
    CCDS7925.1
    UniProtKB/Swiss-Prot
    Q9H6J7
    Related
    ENSP00000278460.7, ENST00000278460.11

RNA

  1. NR_103471.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) has an additional exon in the 5' region and lacks an alternate segment in the 3' region, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK316318, BC009455, DA374145
  2. NR_103472.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) lacks an exon in the 5' region and a segment in the 3' region, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK293609, BC001860, BI763384, DA487960
    Related
    ENST00000525895.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    46936524..47164385
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520364.2XP_011518666.1  UPF0705 protein C11orf49 isoform X1

  2. XM_017018281.1XP_016873770.1  UPF0705 protein C11orf49 isoform X6

  3. XM_017018279.1XP_016873768.1  UPF0705 protein C11orf49 isoform X6

  4. XM_017018278.1XP_016873767.1  UPF0705 protein C11orf49 isoform X6

  5. XM_017018282.1XP_016873771.1  UPF0705 protein C11orf49 isoform X7

    UniProtKB/TrEMBL
    B4DUV7
  6. XM_011520365.3XP_011518667.1  UPF0705 protein C11orf49 isoform X4

  7. XM_006718315.2XP_006718378.1  UPF0705 protein C11orf49 isoform X2

  8. XM_017018277.2XP_016873766.1  UPF0705 protein C11orf49 isoform X5

  9. XM_017018276.2XP_016873765.1  UPF0705 protein C11orf49 isoform X3

  10. XM_017018280.1XP_016873769.1  UPF0705 protein C11orf49 isoform X6

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