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Aliases for LIN7B Gene

Aliases for LIN7B Gene

  • Lin-7 Homolog B, Crumbs Cell Polarity Complex Component 2 3 5
  • Mammalian Lin-Seven Protein 2 3 4
  • Vertebrate Lin-7 Homolog 2 3 4
  • Veli-2 3 4
  • MALS-2 3 4
  • HLin7B 3 4
  • HVeli2 3 4
  • MALS2 3 4
  • VELI2 3 4
  • Lin-7 Homolog B (C. Elegans) 2
  • Protein Lin-7 Homolog B 3
  • LIN-7B 3
  • Lin-7B 4

External Ids for LIN7B Gene

Previous GeneCards Identifiers for LIN7B Gene

  • GC19P050275
  • GC19P049985
  • GC19P054293
  • GC19P054309
  • GC19P054275
  • GC19P049618
  • GC19P045993
  • GC19P049623
  • GC19P049627

Summaries for LIN7B Gene

GeneCards Summary for LIN7B Gene

LIN7B (Lin-7 Homolog B, Crumbs Cell Polarity Complex Component) is a Protein Coding gene. Diseases associated with LIN7B include Retinitis Pigmentosa 24. Among its related pathways are Transmission across Chemical Synapses and Signaling by Rho GTPases. Gene Ontology (GO) annotations related to this gene include protein domain specific binding and L27 domain binding. An important paralog of this gene is LIN7C.

UniProtKB/Swiss-Prot for LIN7B Gene

  • Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells. May increase the amplitude of ASIC3 acid-evoked currents by stabilizing the channel at the cell surface (By similarity).

Gene Wiki entry for LIN7B Gene

Additional gene information for LIN7B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIN7B Gene

Genomics for LIN7B Gene

GeneHancer (GH) Regulatory Elements for LIN7B Gene

Promoters and enhancers for LIN7B 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
GH19J049113 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 663.3 +0.2 155 2.2 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZBTB7B SLC30A9 POLR2B LIN7B CGB8 SNRNP70 NTF4 CGB7 KCNA7 C19orf73
GH19J049148 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.4 +35.9 35905 4.4 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 PPFIA3 TRPM4 SNRNP70 PRR12 GRWD1 PIH1D1 SNORD35A ALDH16A1 RPL13A PTOV1-AS2
GH19J049117 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 12.2 +4.5 4484 2.9 CLOCK FEZF1 DMAP1 SLC30A9 ZNF213 ZNF143 SP3 NFYC ZNF610 GLIS1 C19orf73 PPFIA3 NUP62 SNRNP70 ENSG00000269321 IRF3 PRR12 PTOV1-AS2 SNORD35A SNORD35B
GH19J049142 Promoter/Enhancer 1.5 Ensembl ENCODE dbSUPER 13.2 +28.5 28493 1.1 HDGF PKNOX1 ATF1 SIN3A RFX5 GLIS2 FOS ATF7 CREM ZBTB2 PPFIA3 C19orf73 LIN7B SNRNP70 NTF4 CGB7 KCNA7 SLC6A16 CD37 CCDC155
GH19J049145 Enhancer 1.4 Ensembl ENCODE dbSUPER 12.6 +32.1 32058 1.6 CLOCK ATF1 ARNT ARID4B SIN3A ETS1 ZNF121 GLIS2 ZNF143 ATF7 SNRNP70 PPFIA3 PRR12 C19orf73 LIN7B KCNA7 NTF4 CGB7 SLC6A16 CD37
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIN7B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LIN7B gene promoter:
  • PPAR-gamma2
  • PPAR-gamma1
  • PPAR-alpha
  • Pax-5
  • RelA
  • NF-kappaB
  • NF-kappaB1
  • NF-1
  • NF-1/L
  • GATA-3

Genomic Locations for LIN7B Gene

Genomic Locations for LIN7B Gene
chr19:49,114,324-49,118,460
(GRCh38/hg38)
Size:
4,137 bases
Orientation:
Plus strand
chr19:49,617,581-49,621,717
(GRCh37/hg19)
Size:
4,137 bases
Orientation:
Plus strand

Genomic View for LIN7B Gene

Genes around LIN7B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIN7B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIN7B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIN7B Gene

Proteins for LIN7B Gene

  • Protein details for LIN7B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HAP6-LIN7B_HUMAN
    Recommended name:
    Protein lin-7 homolog B
    Protein Accession:
    Q9HAP6

    Protein attributes for LIN7B Gene

    Size:
    207 amino acids
    Molecular mass:
    22896 Da
    Quaternary structure:
    • Forms two exclusive ternary complexes with CASK and APBA1 or CASKIN1. Can also interact with other modular proteins containing protein-protein interaction domains like MPP5, MPP6, MPP7, DLG1, DLG2 and DLG3 through its L27 domain. Interacts with DLG4 and GRIN2B as well as CDH1 and CTNNB1, the channels KCNJ12/Kir2.2, KCNJ4/Kir2.3 and probably KCNJ2/Kir2.1 and SLC6A12/BGT-1 via its PDZ domain. The association of LIN7A with cadherin and beta-catenin is calcium-dependent, occurs at synaptic junctions and requires the actin cytoskeleton. Interacts with EGFR, ERBB2, ERBB3 and ERBB4 with both PDZ and KID domains. Associates with KIF17 via APBA1 (By similarity). Interacts with ASIC3. Interacts with TOPK. Interacts with RTKN.

    Three dimensional structures from OCA and Proteopedia for LIN7B Gene

    Alternative splice isoforms for LIN7B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIN7B Gene

Post-translational modifications for LIN7B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LIN7B Gene

No data available for DME Specific Peptides for LIN7B Gene

Domains & Families for LIN7B Gene

Gene Families for LIN7B Gene

Protein Domains for LIN7B Gene

Suggested Antigen Peptide Sequences for LIN7B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HAP6

UniProtKB/Swiss-Prot:

LIN7B_HUMAN :
  • The kinase interacting site is required for proper delivery of ERBB2 to the basolateral membrane.
  • Belongs to the lin-7 family.
Domain:
  • The kinase interacting site is required for proper delivery of ERBB2 to the basolateral membrane.
  • The PDZ domain regulates endocytosis and recycling of the receptor at the membrane.
  • The L27 domain mediates interaction with CASK and is involved in the formation of multimeric complexes and the association of LIN7 to membranes.
Family:
  • Belongs to the lin-7 family.
genes like me logo Genes that share domains with LIN7B: view

Function for LIN7B Gene

Molecular function for LIN7B Gene

UniProtKB/Swiss-Prot Function:
Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells. May increase the amplitude of ASIC3 acid-evoked currents by stabilizing the channel at the cell surface (By similarity).

Gene Ontology (GO) - Molecular Function for LIN7B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11742811
GO:0019904 protein domain specific binding IPI 17237226
GO:0030165 PDZ domain binding IEA --
GO:0097016 L27 domain binding IBA --
genes like me logo Genes that share ontologies with LIN7B: view
genes like me logo Genes that share phenotypes with LIN7B: view

Animal Models for LIN7B Gene

MGI Knock Outs for LIN7B:

Animal Model Products

CRISPR Products

miRNA for LIN7B Gene

miRTarBase miRNAs that target LIN7B

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIN7B

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LIN7B Gene

Localization for LIN7B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIN7B Gene

Cell membrane; Peripheral membrane protein. Basolateral cell membrane; Peripheral membrane protein. Cell junction. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density; Peripheral membrane protein. Cell junction, tight junction. Cell junction, synapse, synaptosome. Note=Enriched in synaptosomes and at epithelial cell-cell junctions (By similarity). Mainly basolateral in renal epithelial cells. {ECO:0000250}.

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 LIN7B gene
Compartment Confidence
plasma membrane 5
cytosol 3

Gene Ontology (GO) - Cellular Components for LIN7B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005911 cell-cell junction IBA,IEA --
GO:0005923 bicellular tight junction IEA --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with LIN7B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LIN7B Gene

Pathways & Interactions for LIN7B Gene

genes like me logo Genes that share pathways with LIN7B: view

Gene Ontology (GO) - Biological Process for LIN7B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IEA --
GO:0007269 neurotransmitter secretion TAS,IEA --
GO:0015031 protein transport IEA --
GO:0045199 maintenance of epithelial cell apical/basal polarity IBA --
GO:1903361 protein localization to basolateral plasma membrane IBA --
genes like me logo Genes that share ontologies with LIN7B: view

No data available for SIGNOR curated interactions for LIN7B Gene

Drugs & Compounds for LIN7B Gene

(1) Drugs for LIN7B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with LIN7B: view

Transcripts for LIN7B Gene

mRNA/cDNA for LIN7B Gene

(4) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(4) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LIN7B Gene

Lin-7 homolog B (C. elegans):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIN7B

Alternative Splicing Database (ASD) splice patterns (SP) for LIN7B Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7
SP1: - - - - -
SP2: - -
SP3: - -
SP4: -
SP5:

Relevant External Links for LIN7B Gene

GeneLoc Exon Structure for
LIN7B
ECgene alternative splicing isoforms for
LIN7B

Expression for LIN7B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIN7B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LIN7B Gene

This gene is overexpressed in Brain (36.1), Fetal ovary (18.2), and Testis (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LIN7B Gene



Protein tissue co-expression partners for LIN7B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LIN7B Gene:

LIN7B

SOURCE GeneReport for Unigene cluster for LIN7B Gene:

Hs.221737

Evidence on tissue expression from TISSUES for LIN7B Gene

  • Nervous system(4.4)
  • Kidney(4.2)
genes like me logo Genes that share expression patterns with LIN7B: view

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 LIN7B Gene

Orthologs for LIN7B Gene

This gene was present in the common ancestor of animals.

Orthologs for LIN7B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LIN7B 34
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LIN7B 34 33
  • 92.11 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LIN7B 34 33
  • 91.71 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lin7b 33
  • 87.6 (n)
mouse
(Mus musculus)
Mammalia Lin7b 16 34 33
  • 87.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 68 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia LIN7B 34
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lin7b 33
  • 76.33 (n)
zebrafish
(Danio rerio)
Actinopterygii lin7b 34 33
  • 74.72 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.824 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005858 33
  • 70.39 (n)
fruit fly
(Drosophila melanogaster)
Insecta veli 34 33
  • 67.18 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lin-7 34 33
  • 60.71 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10352 34
  • 75 (a)
OneToMany
Species where no ortholog for LIN7B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 LIN7B Gene

ENSEMBL:
Gene Tree for LIN7B (if available)
TreeFam:
Gene Tree for LIN7B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIN7B: view image

Paralogs for LIN7B Gene

Paralogs for LIN7B Gene

(9) SIMAP similar genes for LIN7B Gene using alignment to 3 proteins:

  • LIN7B_HUMAN
  • M0R2U1_HUMAN
  • S4R3R4_HUMAN
genes like me logo Genes that share paralogs with LIN7B: view

Variants for LIN7B Gene

Sequence variations from dbSNP and Humsavar for LIN7B Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000029134 -- 49,118,920(+) C/G/T downstream_transcript_variant
rs1000095052 -- 49,114,286(+) G/A upstream_transcript_variant
rs1000139660 -- 49,116,985(+) C/T intron_variant
rs1001098124 -- 49,112,942(+) C/T upstream_transcript_variant
rs1001434132 -- 49,113,408(+) G/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LIN7B Gene

Variant ID Type Subtype PubMed ID
dgv3619n100 CNV gain 25217958
dgv3620n100 CNV gain 25217958
dgv3621n100 CNV gain 25217958
esv1011024 CNV deletion 20482838
esv2760526 CNV gain 21179565
nsv1060108 CNV gain 25217958
nsv833857 CNV loss 17160897
nsv833859 CNV loss 17160897
nsv9739 CNV gain+loss 18304495

Variation tolerance for LIN7B Gene

Residual Variation Intolerance Score: 42.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.35; 7.68% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIN7B Gene

Human Gene Mutation Database (HGMD)
LIN7B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIN7B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIN7B Gene

Disorders for LIN7B Gene

MalaCards: The human disease database

(1) MalaCards diseases for LIN7B Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 24
  • rp24
- elite association - COSMIC cancer census association via MalaCards
Search LIN7B in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LIN7B

genes like me logo Genes that share disorders with LIN7B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIN7B Gene

Publications for LIN7B Gene

  1. Identification of a cell polarity-related protein, Lin-7B, as a binding partner for a Rho effector, Rhotekin, and their possible interaction in neurons. (PMID: 16979770) Sudo K … Nagata K (Neuroscience research 2006) 3 4 22 58
  2. The stardust family protein MPP7 forms a tripartite complex with LIN7 and DLG1 that regulates the stability and localization of DLG1 to cell junctions. (PMID: 17237226) Bohl J … Vande Pol SB (The Journal of biological chemistry 2007) 3 4 58
  3. PSD-95 and Lin-7b interact with acid-sensing ion channel-3 and have opposite effects on H+- gated current. (PMID: 15317815) Hruska-Hageman AM … Welsh MJ (The Journal of biological chemistry 2004) 3 4 58
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58
  5. Basolateral membrane expression of the Kir 2.3 channel is coordinated by PDZ interaction with Lin-7/CASK complex. (PMID: 11742811) Olsen O … Welling PA (American journal of physiology. Cell physiology 2002) 3 4 58

Products for LIN7B Gene

Sources for LIN7B Gene

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