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    SOBP sine oculis binding protein homolog [ Homo sapiens (human) ]

    Gene ID: 55084, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SOBPprovided by HGNC
    Official Full Name
    sine oculis binding protein homologprovided by HGNC
    Primary source
    HGNC:HGNC:29256
    See related
    Ensembl:ENSG00000112320 MIM:613667; AllianceGenome:HGNC:29256
    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
    JXC1; MRAMS
    Summary
    The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]
    Expression
    Broad expression in brain (RPKM 6.2), ovary (RPKM 3.5) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SOBP in Genome Data Viewer
    Location:
    6q21
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107490117..107661306)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108669050..108840201)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (107811321..107982510)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene decaprenyl diphosphate synthase subunit 2 Neighboring gene ribosomal protein S24 pseudogene 12 Neighboring gene uncharacterized LOC124901366 Neighboring gene MPRA-validated peak6006 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:107780809-107781730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17441 Neighboring gene NANOG hESC enhancer GRCh37_chr6:107906855-107907747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925473-107925974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925975-107926474 Neighboring gene Sharpr-MPRA regulatory region 6907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107978733-107979310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107979311-107979887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107989710-107990210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107990211-107990711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107994533-107995032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107995930-107996511 Neighboring gene uncharacterized LOC124901367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107996512-107997092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17443 Neighboring gene Scm polycomb group protein like 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24908

    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. circSOBP Inhibits Bladder Cancer Proliferation and Metastasis by Regulating the miR-200a-3p/PTEN Axis and Participating in the Immune Response. Zhang Y, et al. Cell Transplant, 2023 Jan-Dec. PMID 37026617, Free PMC Article
    2. Recurrent intragenic exon rearrangements of SOBP and AUTS2 in non-Hodgkin B-cell lymphoma. Matsumoto Y, et al. Int J Hematol, 2020 Jan. PMID 31686349
    3. Identification of MEG8/miR-378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis. Lei J, et al. Cancer Med, 2021 Apr. PMID 33742531, Free PMC Article
    4. SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system. Birk E, et al. Am J Hum Genet, 2010 Nov 12. PMID 21035105, Free PMC Article
    5. Novel circular RNA circSOBP governs amoeboid migration through the regulation of the miR-141-3p/MYPT1/p-MLC2 axis in prostate cancer. Chao F, et al. Clin Transl Med, 2021 Mar. PMID 33784000, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. circSOBP Inhibits Bladder Cancer Proliferation and Metastasis by Regulating the miR-200a-3p/PTEN Axis and Participating in the Immune Response.
      Title: circSOBP Inhibits Bladder Cancer Proliferation and Metastasis by Regulating the miR-200a-3p/PTEN Axis and Participating in the Immune Response.
    2. Novel circular RNA circSOBP governs amoeboid migration through the regulation of the miR-141-3p/MYPT1/p-MLC2 axis in prostate cancer.
      Title: Novel circular RNA circSOBP governs amoeboid migration through the regulation of the miR-141-3p/MYPT1/p-MLC2 axis in prostate cancer.
    3. Identification of MEG8/miR-378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis.
      Title: Identification of MEG8/miR-378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis.
    4. The intragenic exon rearrangements (IERs) involved in SOBP (6q21) exon 2 and 3 and AUTS2 (7q11.22) exon 2-4 were the molecular lesions specific to tumors and were frequently detected in non-Hodgkin B cell lymphoma (B-NHL) samples. These IERs constitute novel genetic alterations of B-NHL, which might be associated with tumorigenesis and be useful as genetic biological markers.
      Title: Recurrent intragenic exon rearrangements of SOBP and AUTS2 in non-Hodgkin B-cell lymphoma.
    5. This study shows mutated SOBP involvement in syndromic and nonsyndromic ID with psychosis in humans.
      Title: SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    Associated conditions

    Description Tests
    Intellectual disability, anterior maxillary protrusion, and strabismus
    MedGen: C3150924 OMIM: 613671 GeneReviews: Not available
    		Compare labs

    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

    Clone Names

    • FLJ10159

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SUMO polymer binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in animal organ development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cochlea development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cognition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in inner ear morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sine oculis-binding protein homolog
    Names
    jackson circler protein 1

    NCBI Reference Sequences (RefSeq)

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    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_028200.2 RefSeqGene

      Range
      5005..176194
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018013.4 → NP_060483.3  sine oculis-binding protein homolog

      See identical proteins and their annotated locations for NP_060483.3

      Status: REVIEWED

      Source sequence(s)
      AL096816, AL121957, BC014859, BC113966, BM684094, BX442875
      Consensus CDS
      CCDS43488.1
      UniProtKB/Swiss-Prot
      A7XYQ1, B0QZ12, Q5BJD4, Q8N2B2
      Related
      ENSP00000318900.5, ENST00000317357.10
      Conserved Domains (1) summary
      pfam15279
      Location:224 → 524
      SOBP; Sine oculis-binding 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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      107490117..107661306
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535920.3 → XP_011534222.1  sine oculis-binding protein homolog isoform X1

      See identical proteins and their annotated locations for XP_011534222.1

      Conserved Domains (1) summary
      pfam15279
      Location:275 → 575
      SOBP; Sine oculis-binding protein

    2. XM_047418962.1 → XP_047274918.1  sine oculis-binding protein homolog isoform X2

    3. XM_047418963.1 → XP_047274919.1  sine oculis-binding protein homolog isoform X3

      UniProtKB/Swiss-Prot
      A7XYQ1, B0QZ12, Q5BJD4, Q8N2B2

    4. XM_047418964.1 → XP_047274920.1  sine oculis-binding protein homolog isoform X4

    5. XM_047418965.1 → XP_047274921.1  sine oculis-binding protein homolog isoform X5

    6. XM_047418968.1 → XP_047274924.1  sine oculis-binding protein homolog isoform X6

    7. XM_047418967.1 → XP_047274923.1  sine oculis-binding protein homolog isoform X5

    8. XM_047418966.1 → XP_047274922.1  sine oculis-binding protein homolog isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      108669050..108840201
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355763.1 → XP_054211738.1  sine oculis-binding protein homolog isoform X1

    2. XM_054355764.1 → XP_054211739.1  sine oculis-binding protein homolog isoform X2

    3. XM_054355765.1 → XP_054211740.1  sine oculis-binding protein homolog isoform X3

    4. XM_054355766.1 → XP_054211741.1  sine oculis-binding protein homolog isoform X4

    5. XM_054355767.1 → XP_054211742.1  sine oculis-binding protein homolog isoform X5

    6. XM_054355769.1 → XP_054211744.1  sine oculis-binding protein homolog isoform X6

    7. XM_054355768.1 → XP_054211743.1  sine oculis-binding protein homolog isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A7XYQ1.2 GenPept UniProtKB/Swiss-Prot:A7XYQ1

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