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    C2orf49 chromosome 2 open reading frame 49 [ Homo sapiens (human) ]

    Gene ID: 79074, updated on 14-Nov-2024

    Summary

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    Official Symbol
    C2orf49provided by HGNC
    Official Full Name
    chromosome 2 open reading frame 49provided by HGNC
    Primary source
    HGNC:HGNC:28772
    See related
    Ensembl:ENSG00000135974 AllianceGenome:HGNC:28772
    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
    Also known as
    asw
    Summary
    Predicted to be involved in embryonic morphogenesis. Located in nucleoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 7.4), endometrium (RPKM 6.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C2orf49 in Genome Data Viewer
    Location:
    2q12.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (105337540..105385899)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (105798730..105846677)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (105953997..105965668)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:105866724-105867602 Neighboring gene transforming growth factor beta receptor associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16313 Neighboring gene Sharpr-MPRA regulatory region 6730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16315 Neighboring gene C2orf49 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:105985867-105986368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:105986369-105986868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16316 Neighboring gene four and a half LIM domains 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:106015289-106016111 Neighboring gene NANOG hESC enhancer GRCh37_chr2:106043866-106044367 Neighboring gene uncharacterized LOC105373529 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:106093757-106093969 Neighboring gene VISTA enhancer hs2590 Neighboring gene uncharacterized LOC105375311

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

    Bibliography

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    Related articles in PubMed

    1. Novel gene ashwin functions in Xenopus cell survival and anteroposterior patterning. Patil SS, et al. Dev Dyn, 2006 Jul. PMID 16680723
    2. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. Popow J, et al. Nature, 2014 Jul 3. PMID 24870230, Free PMC Article
    3. EML3 is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase. Tegha-Dunghu J, et al. J Cell Sci, 2008 May 15. PMID 18445686
    4. The pseudophosphatase STYX targets the F-box of FBXW7 and inhibits SCFFBXW7 function. Reiterer V, et al. EMBO J, 2017 Feb 1. PMID 28007894, Free PMC Article
    5. A catalogue of putative HIV-1 protease host cell substrates. Impens F, et al. Biol Chem, 2012 Sep. PMID 22944692

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, chromosome 2 open reading frame 49, is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
    retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human chromosome 2 open reading frame 49 (C2orf49; Ashwin) at amino acid residues 29-30 by the HIV-1 protease PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC5509, FLJ45759

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in embryonic morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of tRNA-splicing ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of tRNA-splicing ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of tRNA-splicing ligase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ashwin

    NCBI Reference Sequences (RefSeq)

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    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_001286537.2 → NP_001273466.1  ashwin isoform 2

      See identical proteins and their annotated locations for NP_001273466.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal segment but maintains the reading frame compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC012360, AK304268, BQ003369
      Consensus CDS
      CCDS74550.1
      UniProtKB/TrEMBL
      C9J4K0
      Related
      ENSP00000386361.1, ENST00000410049.1
      Conserved Domains (1) summary
      pfam15323
      Location:13 → 190
      Ashwin; Developmental protein

    2. NM_024093.3 → NP_076998.1  ashwin isoform 1

      See identical proteins and their annotated locations for NP_076998.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC012360, BC001310, BQ003369
      Consensus CDS
      CCDS2068.1
      UniProtKB/Swiss-Prot
      B3KXN3, B4E2G9, Q9BVC5
      Related
      ENSP00000258457.2, ENST00000258457.7
      Conserved Domains (1) summary
      pfam15323
      Location:13 → 232
      Ashwin; Developmental protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      105337540..105385899
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445805.1 → XP_047301761.1  ashwin isoform X1

      UniProtKB/Swiss-Prot
      B3KXN3, B4E2G9, Q9BVC5

    2. XM_017004892.3 → XP_016860381.2  ashwin isoform X2

      UniProtKB/TrEMBL
      C9J4K0

    3. XM_024453135.2 → XP_024308903.1  ashwin isoform X1

      UniProtKB/Swiss-Prot
      B3KXN3, B4E2G9, Q9BVC5
      Related
      ENSP00000520835.1, ENST00000718457.1
      Conserved Domains (1) summary
      pfam15323
      Location:13 → 232
      Ashwin; Developmental protein

    4. XM_024453136.2 → XP_024308904.2  ashwin isoform X2

      UniProtKB/TrEMBL
      C9J4K0

    RNA

    1. XR_007081585.1 RNA Sequence

    2. XR_007081586.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      105798730..105846677
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343847.1 → XP_054199822.1  ashwin isoform X1

      UniProtKB/Swiss-Prot
      B3KXN3, B4E2G9, Q9BVC5

    2. XM_054343848.1 → XP_054199823.1  ashwin isoform X1

      UniProtKB/Swiss-Prot
      B3KXN3, B4E2G9, Q9BVC5

    3. XM_054343850.1 → XP_054199825.1  ashwin isoform X2

      UniProtKB/TrEMBL
      C9J4K0

    4. XM_054343849.1 → XP_054199824.1  ashwin isoform X2

      UniProtKB/TrEMBL
      C9J4K0

    RNA

    1. XR_008486513.1 RNA Sequence

    2. XR_008486514.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BVC5.1 GenPept UniProtKB/Swiss-Prot:Q9BVC5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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