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    SPECC1L sperm antigen with calponin homology and coiled-coil domains 1 like [ Homo sapiens (human) ]

    Gene ID: 23384, updated on 1-Mar-2024

    Summary

    Official Symbol
    SPECC1Lprovided by HGNC
    Official Full Name
    sperm antigen with calponin homology and coiled-coil domains 1 likeprovided by HGNC
    Primary source
    HGNC:HGNC:29022
    See related
    Ensembl:ENSG00000100014 MIM:614140; AllianceGenome:HGNC:29022
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TBHS; CYTSA; GBBB2; TBHS1; OBLFC1
    Summary
    This gene encodes a coiled-coil domain containing protein. The encoded protein may play a critical role in actin-cytoskeletal reorganization during facial morphogenesis. Mutations in this gene are a cause of oblique facial clefting-1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A read-through transcript composed of SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and the downstream ADORA2A (adenosine A2a receptor) gene sequence has been identified, but it is thought to be non-coding. [provided by RefSeq, Jun 2013]
    Expression
    Ubiquitous expression in testis (RPKM 21.3), thyroid (RPKM 13.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SPECC1L in Genome Data Viewer
    Location:
    22q11.23
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (24270831..24417738)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (24732441..24879351)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (24666799..24813706)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24655631-24656248 Neighboring gene SPECC1L-ADORA2A readthrough (NMD candidate) Neighboring gene POM121 transmembrane nucleoporin like 9, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24660235-24660965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18768 Neighboring gene BCR pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:24680125-24680630 Neighboring gene ribosomal protein S10 pseudogene 29 Neighboring gene Sharpr-MPRA regulatory region 3008 Neighboring gene Sharpr-MPRA regulatory region 3699 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:24712259-24712996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24734941-24735636 Neighboring gene uncharacterized LOC105372960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24804357-24804858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24804859-24805358 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24813636-24813812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24814323-24814932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24816151-24816760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24817371-24817980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24820284-24820935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24820936-24821586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24825428-24826389 Neighboring gene ADORA2A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24829365-24829914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24831043-24831543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13551 Neighboring gene adenosine A2a receptor Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24840685-24840876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18773 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24875502-24875689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24901494-24902032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24902033-24902569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18776 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24905414-24905687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18778 Neighboring gene beta-ureidopropionase 1

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Oculomaxillofacial dysostosis
    MedGen: C1838348 OMIM: 600251 GeneReviews: Not available
    Compare labs
    Teebi hypertelorism syndrome 1
    MedGen: CN306405 OMIM: 145420 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough SPECC1L-ADORA2A

    Readthrough gene: SPECC1L-ADORA2A, Included gene: ADORA2A

    Clone Names

    • KIAA0376

    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 actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in gap junction IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in microtubule organizing center IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in spindle IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    cytospin-A
    Names
    SPECC1-like protein
    cytokinesis and spindle organization A
    renal carcinoma antigen NY-REN-22

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_031915.3 RefSeqGene

      Range
      5002..151909
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001145468.4NP_001138940.4  cytospin-A isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AP000354, AP000355, KC877946
      Consensus CDS
      CCDS33619.1
      UniProtKB/Swiss-Prot
      B7Z758, F5H1H6, O15081, Q69YQ0
      UniProtKB/TrEMBL
      B2RMV2
      Related
      ENSP00000393363.1, ENST00000437398.5
      Conserved Domains (4) summary
      PHA03247
      Location:827992
      PHA03247; large tegument protein UL36; Provisional
      COG1196
      Location:500801
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd21199
      Location:10051116
      CH_CYTS; calponin homology (CH) domain found in the cytospin family
      pfam15921
      Location:172802
      CCDC158; Coiled-coil domain-containing protein 158
    2. NM_001254732.3NP_001241661.3  cytospin-A isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AP000354, AP000355, KC877946
      Consensus CDS
      CCDS58797.1
      UniProtKB/TrEMBL
      B2RMV2
      Related
      ENSP00000439633.1, ENST00000541492.1
      Conserved Domains (4) summary
      PHA03247
      Location:827992
      PHA03247; large tegument protein UL36; Provisional
      COG1196
      Location:500801
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam12128
      Location:176803
      DUF3584; Protein of unknown function (DUF3584)
      cl00030
      Location:9991078
      CH_SF; calponin homology (CH) domain superfamily
    3. NM_001254733.2NP_001241662.2  cytospin-A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AP000354, AP000355
      Conserved Domains (1) summary
      cd21199
      Location:71182
      CH_CYTS; calponin homology (CH) domain found in the cytospin family
    4. NM_015330.6NP_056145.5  cytospin-A isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AL832425, AP000354, BC013085, BC021132, BM126792, HY105216
      Consensus CDS
      CCDS33619.1
      UniProtKB/Swiss-Prot
      B7Z758, F5H1H6, O15081, Q69YQ0
      UniProtKB/TrEMBL
      B2RMV2
      Related
      ENSP00000325785.8, ENST00000314328.14
      Conserved Domains (4) summary
      PHA03247
      Location:827992
      PHA03247; large tegument protein UL36; Provisional
      COG1196
      Location:500801
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd21199
      Location:10051116
      CH_CYTS; calponin homology (CH) domain found in the cytospin family
      pfam15921
      Location:172802
      CCDC158; Coiled-coil domain-containing protein 158

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      24270831..24417738
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      24732441..24879351
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)