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

Gene ID: 341346, updated on 3-Apr-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 integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
12p11.23
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (27423316..27502185)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (27294986..27373856)
105.20220307 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)

Genotypes

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_2023_10

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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