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    SIPA1L3 signal induced proliferation associated 1 like 3 [ Homo sapiens (human) ]

    Gene ID: 23094, updated on 5-Mar-2024

    Summary

    Official Symbol
    SIPA1L3provided by HGNC
    Official Full Name
    signal induced proliferation associated 1 like 3provided by HGNC
    Primary source
    HGNC:HGNC:23801
    See related
    Ensembl:ENSG00000105738 MIM:616655; AllianceGenome:HGNC:23801
    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
    SPAL3; SPAR3; CTRCT45
    Summary
    This gene belongs to the signal induced proliferation associated 1 family of genes, which encode GTPase-activating proteins specific for the GTP-binding protein Rap1. Rap1 has been implicated in regulation of cell adhesion, cell polarity, and organization of the cytoskeleton. Like other members of the family, the protein encoded by this gene contains RapGAP and PDZ domains. In addition, this protein contains a C-terminal leucine zipper domain. This gene is proposed to function in epithelial cell morphogenesis and establishment or maintenance of polarity. Consistently, expression of the protein in cell culture showed localization to cell-cell borders in apical regions, and downregulation of the gene in 3D Caco2 cell culture resulted in abnormal cell polarity and morphogenesis. Allelic variants of this gene have been associated with congenital cataracts in humans. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in small intestine (RPKM 6.9), duodenum (RPKM 6.5) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SIPA1L3 in Genome Data Viewer
    Location:
    19q13.13-q13.2
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (37907208..38208369)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (40709260..41010527)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (38397848..38699009)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372395 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38353930-38354430 Neighboring gene uncharacterized LOC107985301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38405529-38406394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38406395-38407260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14560 Neighboring gene WD repeat domain 87 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38423536-38424198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10561 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38453618-38454118 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38472499-38473000 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38479003-38479508 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38479509-38480014 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38480015-38480522 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38480523-38481028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38481029-38481534 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:38489623-38490822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38494121-38494652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38503265-38503837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38515553-38516056 Neighboring gene uncharacterized LOC105372396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38516057-38516560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38527685-38528186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14567 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:38538329-38539077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38542997-38543498 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38546196-38546766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38561125-38561626 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38561627-38562126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38565075-38565574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38572086-38572639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38602551-38603168 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38609967-38610170 Neighboring gene MPRA-validated peak3469 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38620740-38621240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38621241-38621741 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38623222-38623722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38634171-38635020 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38648368-38648546 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38656938-38657140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38661080-38661641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38666131-38666631 Neighboring gene small nucleolar RNA, C/D box 152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38693513-38694196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38700253-38701236 Neighboring gene RNA, 7SL, cytoplasmic 663, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:38707788-38708987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38709595-38710094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38718119-38718889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38729145-38729644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38734884-38735760 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38746806-38746993 Neighboring gene double PHD fingers 1 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 14A

    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?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in epithelial cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in epithelial cell morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in establishment of epithelial cell polarity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in establishment of epithelial cell polarity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in eye development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in hematopoietic progenitor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of small GTPase mediated signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    located_in apical part of cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in apical plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in stress fiber IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in tricellular tight junction IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    signal-induced proliferation-associated 1-like protein 3
    Names
    SIPA1-like protein 3
    SPA-1-like protein 3
    spine-associated RapGAP 3

    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_046730.1 RefSeqGene

      Range
      4988..306149
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015073.3NP_055888.1  signal-induced proliferation-associated 1-like protein 3

      See identical proteins and their annotated locations for NP_055888.1

      Status: REVIEWED

      Source sequence(s)
      AC011465, AC011479, AC016582, AI560928, BC150620, BM193478
      Consensus CDS
      CCDS33007.1
      UniProtKB/Swiss-Prot
      O60292, Q2TV87
      Related
      ENSP00000222345.4, ENST00000222345.11
      Conserved Domains (3) summary
      cd00992
      Location:9661036
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam02145
      Location:641821
      Rap_GAP; Rap/ran-GAP
      pfam11881
      Location:14771726
      SPAR_C; C-terminal domain of SPAR protein

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      37907208..38208369
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438486.1XP_047294442.1  signal-induced proliferation-associated 1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      O60292, Q2TV87
    2. XM_017026518.3XP_016882007.1  signal-induced proliferation-associated 1-like protein 3 isoform X2

      Conserved Domains (3) summary
      cd00992
      Location:9661036
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam02145
      Location:641821
      Rap_GAP; Rap/ran-GAP
      pfam11881
      Location:14771725
      SPAR_C; C-terminal domain of SPAR protein
    3. XM_047438490.1XP_047294446.1  signal-induced proliferation-associated 1-like protein 3 isoform X3

    4. XM_047438489.1XP_047294445.1  signal-induced proliferation-associated 1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      O60292, Q2TV87
    5. XM_047438487.1XP_047294443.1  signal-induced proliferation-associated 1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      O60292, Q2TV87
    6. XM_011526657.3XP_011524959.1  signal-induced proliferation-associated 1-like protein 3 isoform X1

      See identical proteins and their annotated locations for XP_011524959.1

      UniProtKB/Swiss-Prot
      O60292, Q2TV87
      Conserved Domains (3) summary
      cd00992
      Location:9661036
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam02145
      Location:641821
      Rap_GAP; Rap/ran-GAP
      pfam11881
      Location:14771726
      SPAR_C; C-terminal domain of SPAR protein
    7. XM_047438488.1XP_047294444.1  signal-induced proliferation-associated 1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      O60292, Q2TV87

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      40709260..41010527
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320310.1XP_054176285.1  signal-induced proliferation-associated 1-like protein 3 isoform X2

    2. XM_054320311.1XP_054176286.1  signal-induced proliferation-associated 1-like protein 3 isoform X3

    3. XM_054320308.1XP_054176283.1  signal-induced proliferation-associated 1-like protein 3 isoform X1

      UniProtKB/TrEMBL
      B2RWP0
    4. XM_054320309.1XP_054176284.1  signal-induced proliferation-associated 1-like protein 3 isoform X1

      UniProtKB/TrEMBL
      B2RWP0