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

Gene ID: 55084, updated on 2-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
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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 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
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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

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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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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