Aliases for IGSF9B Gene

Aliases for IGSF9B Gene

  • Immunoglobulin Superfamily Member 9B 2 3 4 5
  • MIR4697 Host Gene (Non-Protein Coding) 2 3
  • Protein Turtle Homolog B 3 4
  • LINC00947 2 3
  • KIAA1030 2 4
  • Long Intergenic Non-Protein Coding RNA 947 3
  • Immunoglobulin Superfamily, Member 9B 2
  • MIR4697 Host Gene 2
  • MIR4697HG 3
  • LOC283174 2
  • IGSF9B 5
  • IgSF9B 4

External Ids for IGSF9B Gene

Previous HGNC Symbols for IGSF9B Gene

  • MIR4697HG

Previous GeneCards Identifiers for IGSF9B Gene

  • GC11M133291
  • GC11M133785
  • GC11M129739
  • GC11M133908
  • GC11M133897
  • GC11M133915

Summaries for IGSF9B Gene

GeneCards Summary for IGSF9B Gene

IGSF9B (Immunoglobulin Superfamily Member 9B) is a Protein Coding gene. Diseases associated with IGSF9B include Ovarian Cancer. Gene Ontology (GO) annotations related to this gene include kinase binding. An important paralog of this gene is IGSF9.

UniProtKB/Swiss-Prot Summary for IGSF9B Gene

  • Transmembrane protein which is abundantly expressed in interneurons, where it may regulate inhibitory synapse development. May mediate homophilic cell adhesion.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IGSF9B Gene

Genomics for IGSF9B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for IGSF9B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J133955 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 267 +0.5 543 3.3 SP1 NR2C1 ETS1 ZIC2 MBD2 CTBP1 KLF9 YY1 SMARCA5 SP2 IGSF9B lnc-JAM3-10 HSALNG0088348 lnc-JAM3-6 SPATA19
GH11J133946 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 26.6 +9.3 9343 2.7 CTCF ZIC2 SIN3A REST ZNF341 EBF1 RAD21 BHLHE40 ELF1 MIER2 IGSF9B HSALNG0088348 lnc-JAM3-6 SPATA19
GH11J134032 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 15.8 -79.3 -79284 8 MCM7 ZIC2 SIN3A ZNF521 VEZF1 ZNF341 GABPA GABPB1 KLF9 SP2 ENSG00000254648 IGSF9B JAM3 GLB1L3 LINC02731
GH11J133950 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 18.7 +5.7 5687 2.8 ZIC2 ZNF341 KLF9 YY1 ZFP37 MAX GLIS1 SP7 TRIM28 ZNF366 IGSF9B lnc-JAM3-6 HSALNG0088348 SPATA19
GH11J133944 Promoter/Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 21 +11.6 11621 1.5 EGR1 EGR2 CHD2 ZFHX2 KLF17 IGSF9B NCAPD3 HSALNG0088348 lnc-JAM3-6 SPATA19
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IGSF9B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for IGSF9B

Top Transcription factor binding sites by QIAGEN in the IGSF9B gene promoter:
  • Brachyury
  • E47
  • Hand1
  • HNF-4alpha1
  • HNF-4alpha2
  • ITF-2
  • Nkx2-5
  • RREB-1
  • RSRFC4
  • Tal-1beta

Genomic Locations for IGSF9B Gene

Latest Assembly
chr11:133,896,438-133,956,968
(GRCh38/hg38)
Size:
60,531 bases
Orientation:
Minus strand

Previous Assembly
chr11:133,766,333-133,826,863
(GRCh37/hg19 by Entrez Gene)
Size:
60,531 bases
Orientation:
Minus strand

chr11:133,778,459-133,826,880
(GRCh37/hg19 by Ensembl)
Size:
48,422 bases
Orientation:
Minus strand

Genomic View for IGSF9B Gene

Genes around IGSF9B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IGSF9B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IGSF9B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IGSF9B Gene

Proteins for IGSF9B Gene

  • Protein details for IGSF9B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPX0-TUTLB_HUMAN
    Recommended name:
    Protein turtle homolog B
    Protein Accession:
    Q9UPX0
    Secondary Accessions:
    • G5EA26

    Protein attributes for IGSF9B Gene

    Size:
    1349 amino acids
    Molecular mass:
    147089 Da
    Quaternary structure:
    • Found in a complex with MAGI2 and NLGN2, where it interacts with MAGI2 (via PDZ 5 and PDZ 6 domains).

    Alternative splice isoforms for IGSF9B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for IGSF9B Gene

Post-translational modifications for IGSF9B Gene

  • N-glycosylated and sialylated. Not significantly O-glycosylated.
  • Glycosylation at Asn241, Asn258, and Asn624
  • Modification sites at PhosphoSitePlus

Other Protein References for IGSF9B Gene

No data available for DME Specific Peptides for IGSF9B Gene

Domains & Families for IGSF9B Gene

Gene Families for IGSF9B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for IGSF9B Gene

Suggested Antigen Peptide Sequences for IGSF9B Gene

GenScript: Design optimal peptide antigens:
  • Immunoglobulin superfamily member 9B (TUTLB_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UPX0

UniProtKB/Swiss-Prot:

TUTLB_HUMAN :
  • Belongs to the immunoglobulin superfamily. Turtle family.
Family:
  • Belongs to the immunoglobulin superfamily. Turtle family.
genes like me logo Genes that share domains with IGSF9B: view

Function for IGSF9B Gene

Molecular function for IGSF9B Gene

UniProtKB/Swiss-Prot Function:
Transmembrane protein which is abundantly expressed in interneurons, where it may regulate inhibitory synapse development. May mediate homophilic cell adhesion.

Phenotypes From GWAS Catalog for IGSF9B Gene

Gene Ontology (GO) - Molecular Function for IGSF9B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with IGSF9B: view

Phenotypes for IGSF9B Gene

genes like me logo Genes that share phenotypes with IGSF9B: view

Animal Models for research

  • Taconic Biosciences Mouse Models for IGSF9B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IGSF9B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for IGSF9B Gene

Localization for IGSF9B Gene

Subcellular locations from UniProtKB/Swiss-Prot for IGSF9B Gene

Cell junction, synapse, postsynaptic cell membrane. Single-pass type I membrane protein. Cell junction, synapse, postsynaptic density.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IGSF9B gene
Compartment Confidence
plasma membrane 4
nucleus 3
extracellular 1
cytoskeleton 1
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for IGSF9B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with IGSF9B: view

Pathways & Interactions for IGSF9B Gene

PathCards logo

SuperPathways for IGSF9B Gene

No Data Available

Interacting Proteins for IGSF9B Gene

Gene Ontology (GO) - Biological Process for IGSF9B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with IGSF9B: view

No data available for Pathways by source and SIGNOR curated interactions for IGSF9B Gene

Drugs & Compounds for IGSF9B Gene

No Compound Related Data Available

Transcripts for IGSF9B Gene

mRNA/cDNA for IGSF9B Gene

3 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IGSF9B

Alternative Splicing Database (ASD) splice patterns (SP) for IGSF9B Gene

No ASD Table

Relevant External Links for IGSF9B Gene

GeneLoc Exon Structure for
IGSF9B

Expression for IGSF9B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for IGSF9B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for IGSF9B Gene

This gene is overexpressed in Frontal cortex (45.1) and Retina (23.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for IGSF9B Gene



Protein tissue co-expression partners for IGSF9B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for IGSF9B

SOURCE GeneReport for Unigene cluster for IGSF9B Gene:

Hs.204121

Evidence on tissue expression from TISSUES for IGSF9B Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with IGSF9B: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IGSF9B Gene

Orthologs for IGSF9B Gene

This gene was present in the common ancestor of animals.

Orthologs for IGSF9B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia IGSF9B 30 31
  • 97.58 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia IGSF9B 30 31
  • 91.34 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Igsf9b 30
  • 89.88 (n)
Cow
(Bos Taurus)
Mammalia IGSF9B 30 31
  • 89.49 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Igsf9b 30 17 31
  • 89.46 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia IGSF9B 31
  • 87 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia IGSF9B 31
  • 67 (a)
OneToOne
Chicken
(Gallus gallus)
Aves IGSF9B 30 31
  • 81.68 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia IGSF9B 31
  • 78 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia igsf9b 30
  • 69.08 (n)
Zebrafish
(Danio rerio)
Actinopterygii igsf9bb 30 31
  • 70.08 (n)
OneToMany
igsf9ba 31
  • 64 (a)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13476 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG16857 31
  • 26 (a)
ManyToMany
tutl 31
  • 21 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea igcm-2 31
  • 25 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 39 (a)
OneToMany
Species where no ortholog for IGSF9B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for IGSF9B Gene

ENSEMBL:
Gene Tree for IGSF9B (if available)
TreeFam:
Gene Tree for IGSF9B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for IGSF9B: view image

Paralogs for IGSF9B Gene

(5) SIMAP similar genes for IGSF9B Gene using alignment to 4 proteins:

  • TUTLB_HUMAN
  • E9PRP3_HUMAN
  • G5EA26_HUMAN
  • H0YDP1_HUMAN
genes like me logo Genes that share paralogs with IGSF9B: view

Variants for IGSF9B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for IGSF9B Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs113797769 Likely Benign: not provided 133,920,248(-) G/A
NM_001277285.3(IGSF9B):c.3477C>T (p.Gly1159=)
SYNONYMOUS
rs148045307 Benign: not provided 133,919,890(-) C/T
NM_001277285.3(IGSF9B):c.3835G>A (p.Ala1279Thr)
MISSENSE
rs182620767 Benign: not provided 133,931,561(-) G/T
NM_001277285.3(IGSF9B):c.1260C>A (p.Pro420=)
SYNONYMOUS
rs199538394 Likely Benign: not provided 133,920,180(-) C/T
NM_001277285.3(IGSF9B):c.3545G>A (p.Arg1182Gln)
MISSENSE
rs77730320 Benign: not provided 133,921,088(-) G/A
NM_001277285.3(IGSF9B):c.2637C>T (p.Phe879=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for IGSF9B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for IGSF9B Gene

Variant ID Type Subtype PubMed ID
dgv1301n100 CNV gain 25217958
dgv727e59 CNV duplication 20981092
dgv728e59 CNV duplication 20981092
esv2745307 CNV deletion 23290073
esv2745309 CNV deletion 23290073
esv2745310 CNV deletion 23290073
esv275426 CNV gain+loss 21479260
nsv1051677 CNV gain 25217958
nsv1051677 CNV gain 25217958
nsv1070997 CNV deletion 25765185
nsv1110200 CNV duplication 24896259
nsv468900 CNV loss 19166990
nsv468900 CNV loss 19166990
nsv556595 CNV loss 21841781
nsv556595 CNV loss 21841781
nsv826144 CNV gain 20364138
nsv826145 CNV loss 20364138
nsv826146 CNV gain 20364138
nsv952765 CNV deletion 24416366
nsv952765 CNV deletion 24416366
nsv952766 CNV deletion 24416366

Variation tolerance for IGSF9B Gene

Residual Variation Intolerance Score: 2.07% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.82; 58.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IGSF9B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
IGSF9B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IGSF9B Gene

Disorders for IGSF9B Gene

MalaCards: The human disease database

(1) MalaCards diseases for IGSF9B Gene - From: LNC and COP

Disorder Aliases PubMed IDs
ovarian cancer
  • ovarian cancer, somatic
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for IGSF9B

genes like me logo Genes that share disorders with IGSF9B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for IGSF9B Gene

Publications for IGSF9B Gene

  1. Long Noncoding RNA MIR4697HG Promotes Cell Growth and Metastasis in Human Ovarian Cancer. (PMID: 28168162) Zhang LQ … Zhao LP (Analytical cellular pathology (Amsterdam) 2017) 3 74
  2. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 3 4
  3. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3
  4. Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course. (PMID: 30217166) Gil-Varea E … Comabella M (Journal of neuroinflammation 2018) 3
  5. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. (PMID: 28611215) Fei T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2017) 3

Products for IGSF9B Gene

Sources for IGSF9B Gene