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    SMCO2 single-pass membrane protein with coiled-coil domains 2 [ Homo sapiens (human) ]

    Gene ID: 341346, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SMCO2provided by HGNC
    Official Full Name
    single-pass membrane protein with coiled-coil domains 2provided by HGNC
    Primary source
    HGNC:HGNC:34448
    See related
    Ensembl:ENSG00000165935 AllianceGenome:HGNC:34448
    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
    C12orf70
    Summary
    Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See SMCO2 in Genome Data Viewer
    Location:
    12p11.23
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (27423316..27502185)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (27294986..27373856)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (27599669..27655118)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902905 Neighboring gene serine/threonine kinase 38 like Neighboring gene uncharacterized LOC124902906 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4311 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27082 Neighboring gene basic helix-loop-helix ARNT like 2 Neighboring gene BMAL2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:27589181-27589746 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:27627037-27628236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:27631436-27631936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:27675956-27676557 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:27677161-27677761 Neighboring gene arginyl-tRNA synthetase 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6146 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:27701742-27702941 Neighboring gene PPFIA binding protein 1 Neighboring gene Sharpr-MPRA regulatory region 6326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4312 Neighboring gene chromosome 12 open reading frame 71B, pseudogene Neighboring gene MRPS35 divergent transcript Neighboring gene RAB15 effector protein

    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
    • 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. The finished DNA sequence of human chromosome 12. Scherer SE, et al. Nature, 2006 Mar 16. PMID 16541075
    2. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    single-pass membrane and coiled-coil domain-containing protein 2

    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_001145010.3 → NP_001138482.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_001138482.1

      Status: VALIDATED

      Source sequence(s)
      AC068794
      Consensus CDS
      CCDS44852.1
      UniProtKB/Swiss-Prot
      A6NFE2
      UniProtKB/TrEMBL
      J3KNC3
      Related
      ENSP00000298876.4, ENST00000298876.8
      Conserved Domains (1) summary
      pfam14992
      Location:12 → 342
      TMCO5; TMCO5 family

    2. NM_001387218.3 → NP_001374147.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC068794
      Consensus CDS
      CCDS91667.1
      UniProtKB/TrEMBL
      A0A8V8TM60
      Related
      ENSP00000513681.1, ENST00000698358.1
      Conserved Domains (1) summary
      pfam14992
      Location:75 → 213
      TMCO5; TMCO5 family

    3. NM_001395208.2 → NP_001382137.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC068794
      Consensus CDS
      CCDS44852.1
      UniProtKB/Swiss-Prot
      A6NFE2
      UniProtKB/TrEMBL
      J3KNC3
      Related
      ENSP00000441688.1, ENST00000535986.2
      Conserved Domains (1) summary
      pfam14992
      Location:12 → 342
      TMCO5; TMCO5 family

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      27423316..27502185
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428776.1 → XP_047284732.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X2

    2. XM_047428775.1 → XP_047284731.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NFE2
      Conserved Domains (1) summary
      pfam14992
      Location:12 → 342
      TMCO5; TMCO5 family

    3. XM_017019254.2 → XP_016874743.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X3

      Conserved Domains (1) summary
      pfam14992
      Location:91 → 263
      TMCO5; TMCO5 family

    4. XM_011520636.3 → XP_011518938.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X4

      Conserved Domains (1) summary
      pfam14992
      Location:13 → 176
      TMCO5; TMCO5 family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      27294986..27373856
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371935.1 → XP_054227910.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X2

    2. XM_054371934.1 → XP_054227909.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      A6NFE2

    3. XM_054371936.1 → XP_054227911.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X3

    4. XM_054371938.1 → XP_054227913.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X4

    5. XM_054371937.1 → XP_054227912.1  single-pass membrane and coiled-coil domain-containing protein 2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NFE2.2 GenPept UniProtKB/Swiss-Prot:A6NFE2

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