LIN7B (lin-7 homolog B, crumbs cell polarity complex component) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: LIN7B (lin-7 homolog B, crumbs cell polarity complex component) Homo sapiens
Analyze
Symbol: LIN7B
Name: lin-7 homolog B, crumbs cell polarity complex component
RGD ID: 734321
HGNC Page HGNC
Description: Enables protein domain specific binding activity. Predicted to be involved in maintenance of epithelial cell apical/basal polarity; neurotransmitter secretion; and protein localization to basolateral plasma membrane. Predicted to be located in plasma membrane. Predicted to be part of MPP7-DLG1-LIN7 complex. Predicted to be active in basolateral plasma membrane; cell-cell junction; and synapse; INTERACTS WITH 17beta-hydroxy-5alpha-androstan-3-one; 2-hydroxypropanoic acid; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: hLin7B; hVeli2; lin-7 homolog B; lin-7-a; LIN-7B; MALS-2; MALS2; mammalian lin-seven protein 2; veli-2; VELI2; vertebrate lin-7 homolog 2
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1949,114,324 - 49,118,460 (+)EnsemblGRCh38hg38GRCh38
GRCh381949,114,339 - 49,118,464 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371949,617,627 - 49,621,717 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361954,309,430 - 54,313,529 (+)NCBINCBI36hg18NCBI36
Build 341954,309,429 - 54,313,529NCBI
Celera1946,484,840 - 46,488,937 (+)NCBI
Cytogenetic Map19q13.33NCBI
HuRef1945,993,785 - 45,997,881 (+)NCBIHuRef
CHM1_11949,619,736 - 49,623,829 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9753324   PMID:10341223   PMID:11742811   PMID:12151522   PMID:12477932   PMID:12975309   PMID:14596909   PMID:14960569   PMID:15024025   PMID:15317815   PMID:16192269   PMID:16192277  
PMID:16473877   PMID:16979770   PMID:17237226   PMID:18286632   PMID:19460752   PMID:20720508   PMID:21873635   PMID:22658674   PMID:25196215   PMID:26186194   PMID:28514442   PMID:31091453  
PMID:32296183  


Genomics

Comparative Map Data
LIN7B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1949,114,324 - 49,118,460 (+)EnsemblGRCh38hg38GRCh38
GRCh381949,114,339 - 49,118,464 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371949,617,627 - 49,621,717 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361954,309,430 - 54,313,529 (+)NCBINCBI36hg18NCBI36
Build 341954,309,429 - 54,313,529NCBI
Celera1946,484,840 - 46,488,937 (+)NCBI
Cytogenetic Map19q13.33NCBI
HuRef1945,993,785 - 45,997,881 (+)NCBIHuRef
CHM1_11949,619,736 - 49,623,829 (+)NCBICHM1_1
Lin7b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39745,017,315 - 45,019,988 (-)NCBIGRCm39mm39
GRCm39 Ensembl745,017,315 - 45,020,007 (-)Ensembl
GRCm38745,367,891 - 45,370,564 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl745,367,891 - 45,370,583 (-)EnsemblGRCm38mm10GRCm38
MGSCv37752,623,261 - 52,625,934 (-)NCBIGRCm37mm9NCBIm37
MGSCv36745,235,933 - 45,238,606 (-)NCBImm8
Celera740,823,918 - 40,826,591 (-)NCBICelera
Cytogenetic Map7B3NCBI
Lin7b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2195,846,888 - 95,849,628 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl195,846,243 - 95,849,977 (-)Ensembl
Rnor_6.01101,358,313 - 101,361,439 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1101,358,396 - 101,360,971 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01102,421,965 - 102,425,037 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4195,838,781 - 95,841,356 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1195,916,891 - 95,919,467 (-)NCBI
Celera190,103,272 - 90,105,847 (-)NCBICelera
Cytogenetic Map1q22NCBI
Lin7b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555591,611,004 - 1,614,320 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555591,610,924 - 1,613,736 (-)NCBIChiLan1.0ChiLan1.0
LIN7B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11955,045,557 - 55,055,761 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1955,047,704 - 55,055,761 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01946,125,272 - 46,129,450 (+)NCBIMhudiblu_PPA_v0panPan3
LIN7B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11107,332,623 - 107,336,099 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1107,332,623 - 107,336,302 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1107,332,623 - 107,336,302 (-)NCBICanFam3.1canFam3CanFam3.1
ROS_Cfam_1.01107,857,485 - 107,860,971 (-)NCBI
UMICH_Zoey_3.11107,525,392 - 107,528,877 (-)NCBI
UNSW_CanFamBas_1.01107,171,615 - 107,175,101 (-)NCBI
UU_Cfam_GSD_1.01108,007,220 - 108,010,706 (-)NCBI
Lin7b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934921,441,132 - 21,444,484 (+)NCBI
SpeTri2.0NW_0049366643,059,365 - 3,062,674 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIN7B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl654,309,535 - 54,313,138 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1654,309,552 - 54,313,138 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2650,015,309 - 50,018,898 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LIN7B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1642,337,437 - 42,341,865 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607322,230,042 - 22,234,175 (+)NCBIVero_WHO_p1.0
Lin7b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248324,965,537 - 4,968,574 (-)NCBIHetGla_female_1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1448
Count of miRNA genes:717
Interacting mature miRNAs:818
Transcripts:ENST00000221459, ENST00000391864, ENST00000465141, ENST00000469137, ENST00000474252, ENST00000486217, ENST00000595200
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 873 1298 849 86 123 17 2848 1384 2939 49 924 771 70 34 2229
Low 1563 1664 876 537 1769 447 1505 812 788 369 525 839 102 1 1170 559 4 1
Below cutoff 2 26 1 49 2 1 7 1 6 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000221459   ⟹   ENSP00000221459
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1949,114,370 - 49,118,460 (+)Ensembl
RefSeq Acc Id: ENST00000391864   ⟹   ENSP00000375737
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1949,114,324 - 49,118,460 (+)Ensembl
RefSeq Acc Id: ENST00000465141
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1949,116,118 - 49,117,995 (+)Ensembl
RefSeq Acc Id: ENST00000469137
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1949,114,466 - 49,118,460 (+)Ensembl
RefSeq Acc Id: ENST00000474252
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1949,115,226 - 49,118,059 (+)Ensembl
RefSeq Acc Id: ENST00000486217   ⟹   ENSP00000474643
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1949,114,424 - 49,115,489 (+)Ensembl
RefSeq Acc Id: ENST00000595200   ⟹   ENSP00000472804
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1949,114,409 - 49,118,015 (+)Ensembl
RefSeq Acc Id: NM_001308419   ⟹   NP_001295348
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381949,114,370 - 49,118,460 (+)NCBI
CHM1_11949,619,736 - 49,623,829 (+)NCBI
Sequence:
RefSeq Acc Id: NM_022165   ⟹   NP_071448
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381949,114,370 - 49,118,460 (+)NCBI
GRCh371949,617,618 - 49,621,717 (+)RGD
Build 361954,309,430 - 54,313,529 (+)NCBI Archive
Celera1946,484,840 - 46,488,937 (+)RGD
HuRef1945,993,785 - 45,997,881 (+)ENTREZGENE
CHM1_11949,619,736 - 49,623,829 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006723323   ⟹   XP_006723386
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381949,114,341 - 49,118,460 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017027131   ⟹   XP_016882620
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381949,114,339 - 49,118,464 (+)NCBI
Sequence:
RefSeq Acc Id: XR_243950
RefSeq Status:
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381949,114,341 - 49,118,460 (+)NCBI
GRCh371949,617,618 - 49,621,717 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_071448   ⟸   NM_022165
- Peptide Label: isoform 1
- UniProtKB: Q9HAP6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006723386   ⟸   XM_006723323
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001295348   ⟸   NM_001308419
- Peptide Label: isoform 2
- UniProtKB: Q9HAP6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016882620   ⟸   XM_017027131
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSP00000472804   ⟸   ENST00000595200
RefSeq Acc Id: ENSP00000375737   ⟸   ENST00000391864
RefSeq Acc Id: ENSP00000221459   ⟸   ENST00000221459
RefSeq Acc Id: ENSP00000474643   ⟸   ENST00000486217
Protein Domains
L27   PDZ

Promoters
RGD ID:13205077
Promoter ID:EPDNEW_H26119
Type:initiation region
Name:LIN7B_1
Description:lin-7 homolog B, crumbs cell polarity complex component
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381949,114,375 - 49,114,435EPDNEW
RGD ID:6795748
Promoter ID:HG_KWN:30516
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000391864,   NM_022165,   OTTHUMT00000258982,   OTTHUMT00000258983,   OTTHUMT00000258985
Position:
Human AssemblyChrPosition (strand)Source
Build 361954,309,371 - 54,310,122 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19q13.33-13.43(chr19:47908540-58539965)x3 copy number gain See cases [RCV000052914] Chr19:47908540..58539965 [GRCh38]
Chr19:48411797..59051332 [GRCh37]
Chr19:53103609..63743144 [NCBI36]
Chr19:19q13.33-13.43
pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47929575-58572206)x3 copy number gain See cases [RCV000052915] Chr19:47929575..58572206 [GRCh38]
Chr19:48432832..59083573 [GRCh37]
Chr19:53124644..63775385 [NCBI36]
Chr19:19q13.33-13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic|uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19q13.33(chr19:49556215-49651042)x1 copy number loss not provided [RCV000752727] Chr19:49556215..49651042 [GRCh37]
Chr19:19q13.33
benign
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19q13.31-13.42(chr19:44738088-53621561)x3 copy number gain not provided [RCV001007050] Chr19:44738088..53621561 [GRCh37]
Chr19:19q13.31-13.42
pathogenic
NM_022165.3(LIN7B):c.603-8C>G single nucleotide variant not provided [RCV000961212] Chr19:49118344 [GRCh38]
Chr19:49621601 [GRCh37]
Chr19:19q13.33
benign
GRCh37/hg19 19q13.33(chr19:49600909-51366070)x3 copy number gain not provided [RCV000847250] Chr19:49600909..51366070 [GRCh37]
Chr19:19q13.33
uncertain significance
null single nucleotide variant not provided [RCV001693330] Chr19:49114449 [GRCh38]
Chr19:49617706 [GRCh37]
Chr19:19q13.33
benign
GRCh37/hg19 19q13.32-13.42(chr19:47939842-54626871) copy number gain not provided [RCV001249294] Chr19:47939842..54626871 [GRCh37]
Chr19:19q13.32-13.42
not provided
GRCh37/hg19 19q13.33-13.43(chr19:48463931-57095254)x3 copy number gain not provided [RCV001259944] Chr19:48463931..57095254 [GRCh37]
Chr19:19q13.33-13.43
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17788 AgrOrtholog
COSMIC LIN7B COSMIC
Ensembl Genes ENSG00000104863 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000221459 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000375737 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000472804 UniProtKB/TrEMBL
  ENSP00000474643 UniProtKB/TrEMBL
Ensembl Transcript ENST00000221459 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000391864 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000486217 UniProtKB/TrEMBL
  ENST00000595200 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot
GTEx ENSG00000104863 GTEx
HGNC ID HGNC:17788 ENTREZGENE
Human Proteome Map LIN7B Human Proteome Map
InterPro L27_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L27_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  L27_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIN7 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
KEGG Report hsa:64130 UniProtKB/Swiss-Prot
NCBI Gene 64130 ENTREZGENE
OMIM 612331 OMIM
Pfam L27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot
PharmGKB PA134914453 PharmGKB
PIRSF Lin-7_homologue UniProtKB/Swiss-Prot
PROSITE L27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot
SMART L27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF101288 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50156 UniProtKB/Swiss-Prot
UniProt LIN7B_HUMAN UniProtKB/Swiss-Prot
  M0R2U1_HUMAN UniProtKB/TrEMBL
  Q9HAP6 ENTREZGENE
  S4R3R4_HUMAN UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-29 LIN7B  lin-7 homolog B, crumbs cell polarity complex component    lin-7 homolog B (C. elegans)  Symbol and/or name change 5135510 APPROVED