Human Gene LIN7C (ENST00000278193.7) from GENCODE V44
  Description: Homo sapiens lin-7 homolog C, crumbs cell polarity complex component (LIN7C), mRNA. (from RefSeq NM_018362)
Gencode Transcript: ENST00000278193.7
Gencode Gene: ENSG00000148943.12
Transcript (Including UTRs)
   Position: hg38 chr11:27,494,418-27,506,769 Size: 12,352 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr11:27,498,649-27,506,752 Size: 8,104 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:27,494,418-27,506,769)mRNA (may differ from genome)Protein (197 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LIN7C_HUMAN
DESCRIPTION: RecName: Full=Protein lin-7 homolog C; Short=Lin-7C; AltName: Full=Mammalian lin-seven protein 3; Short=MALS-3; AltName: Full=Vertebrate lin-7 homolog 3; Short=Veli-3;
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.
SUBUNIT: Forms two exclusive ternary complexes with CASK and APBA1 or CASKIN1 (By similarity). 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. Interacts with HTR4 (By similarity). Forms a tripartite complex composed of DLG1, MPP7 and LIN7 (LIN7A or LIN7C). Interacts with MAPK12 (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein. Basolateral cell membrane; Peripheral membrane protein. Cell junction (By similarity). Cell junction, synapse, postsynaptic cell membrane, postsynaptic density; Peripheral membrane protein (By similarity). Cell junction, tight junction (By similarity). Cell junction, synapse, synaptosome (By similarity). Note=Enriched in synaptosomes and at epithelial cell-cell junctions (By similarity). Mainly basolateral in renal epithelial cells.
DOMAIN: The kinase interacting site is required for proper delivery of ERBB2 to the basolateral membrane (By similarity).
DOMAIN: The PDZ domain regulates endocytosis and recycling of the receptor at the membrane (By similarity).
DOMAIN: The L27 domain mediates interaction with CASK and is involved in the formation of multimeric complexes and the association of LIN7 to membranes (By similarity).
SIMILARITY: Belongs to the lin-7 family.
SIMILARITY: Contains 1 L27 domain.
SIMILARITY: Contains 1 PDZ (DHR) domain.

-  Primer design for this transcript
 

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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.01 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 298.23 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR 0.00170.000 Picture PostScript Text
3' UTR -954.104231-0.226 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004172 - L27
IPR014775 - L27_C
IPR017365 - Lin-7_homologue
IPR001478 - PDZ

Pfam Domains:
PF02828 - L27 domain
PF00595 - PDZ domain (Also known as DHR or GLGF)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3LRA - X-ray


ModBase Predicted Comparative 3D Structure on Q9NUP9
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl WormBase 
Protein SequenceProtein SequenceProtein Sequence Protein Sequence 
AlignmentAlignmentAlignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008092 cytoskeletal protein binding
GO:0019904 protein domain specific binding
GO:0030165 PDZ domain binding
GO:0097016 L27 domain binding

Biological Process:
GO:0002011 morphogenesis of an epithelial sheet
GO:0006887 exocytosis
GO:0007269 neurotransmitter secretion
GO:0015031 protein transport
GO:0045199 maintenance of epithelial cell apical/basal polarity
GO:1903361 protein localization to basolateral plasma membrane

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005923 bicellular tight junction
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016323 basolateral plasma membrane
GO:0030054 cell junction
GO:0043005 neuron projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0097025 MPP7-DLG1-LIN7 complex
GO:0098793 presynapse


-  Descriptions from all associated GenBank mRNAs
  BC039459 - Homo sapiens lin-7 homolog C (C. elegans), mRNA (cDNA clone IMAGE:5312672).
AF090900 - Homo sapiens clone HQ0189 PRO0189 mRNA, complete cds.
AK025540 - Homo sapiens cDNA: FLJ21887 fis, clone HEP03135, highly similar to AF090900 Homo sapiens clone HQ0189 PRO0189 mRNA.
BC053907 - Homo sapiens lin-7 homolog C (C. elegans), mRNA (cDNA clone MGC:61447 IMAGE:6502685), complete cds.
AL833601 - Homo sapiens mRNA; cDNA DKFZp686G0667 (from clone DKFZp686G0667).
JD054073 - Sequence 35097 from Patent EP1572962.
JD388958 - Sequence 369982 from Patent EP1572962.
JD457528 - Sequence 438552 from Patent EP1572962.
JD247709 - Sequence 228733 from Patent EP1572962.
JD368346 - Sequence 349370 from Patent EP1572962.
JD413915 - Sequence 394939 from Patent EP1572962.
JD388957 - Sequence 369981 from Patent EP1572962.
JD457527 - Sequence 438551 from Patent EP1572962.
JD523082 - Sequence 504106 from Patent EP1572962.
JD293448 - Sequence 274472 from Patent EP1572962.
JD234208 - Sequence 215232 from Patent EP1572962.
JD367664 - Sequence 348688 from Patent EP1572962.
JD051819 - Sequence 32843 from Patent EP1572962.
AK002077 - Homo sapiens cDNA FLJ11215 fis, clone PLACE1008000, weakly similar to CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110.
JD314495 - Sequence 295519 from Patent EP1572962.
JD563003 - Sequence 544027 from Patent EP1572962.
BC009774 - Homo sapiens lin-7 homolog C (C. elegans), mRNA (cDNA clone IMAGE:4132182).
JD236223 - Sequence 217247 from Patent EP1572962.
JD302514 - Sequence 283538 from Patent EP1572962.
JD053358 - Sequence 34382 from Patent EP1572962.
JD285203 - Sequence 266227 from Patent EP1572962.
AK223156 - Homo sapiens mRNA for lin-7 homolog C variant, clone: LNG03068.
JD223404 - Sequence 204428 from Patent EP1572962.
JD434241 - Sequence 415265 from Patent EP1572962.
JD490734 - Sequence 471758 from Patent EP1572962.
JD082046 - Sequence 63070 from Patent EP1572962.
JD286400 - Sequence 267424 from Patent EP1572962.
JD533472 - Sequence 514496 from Patent EP1572962.
JD229066 - Sequence 210090 from Patent EP1572962.
JD521814 - Sequence 502838 from Patent EP1572962.
JD360034 - Sequence 341058 from Patent EP1572962.
KJ894188 - Synthetic construct Homo sapiens clone ccsbBroadEn_03582 LIN7C gene, encodes complete protein.
AB385247 - Synthetic construct DNA, clone: pF1KB9493, Homo sapiens LIN7C gene for lin-7 homolog C, complete cds, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NUP9 (Reactome details) participates in the following event(s):

R-HSA-5336443 LIN7, CASK and APBA1 bind
R-HSA-6794352 NRXNs binds CASK tripartite complex
R-HSA-212676 Dopamine Neurotransmitter Release Cycle
R-HSA-112310 Neurotransmitter release cycle
R-HSA-6794361 Neurexins and neuroligins
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000278193.1, ENST00000278193.2, ENST00000278193.3, ENST00000278193.4, ENST00000278193.5, ENST00000278193.6, LIN7C_HUMAN, MALS3, NM_018362, Q9NUP9, uc001mrl.1, uc001mrl.2, uc001mrl.3, uc001mrl.4, uc001mrl.5, VELI3
UCSC ID: ENST00000278193.7
RefSeq Accession: NM_018362
Protein: Q9NUP9 (aka LIN7C_HUMAN)
CCDS: CCDS7864.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.