LIN7C (lin-7 homolog C, crumbs cell polarity complex component) - Rat Genome Database

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Gene: LIN7C (lin-7 homolog C, crumbs cell polarity complex component) Sus scrofa
Analyze
Symbol: LIN7C
Name: lin-7 homolog C, crumbs cell polarity complex component
RGD ID: 14266286
Description: ENCODES a protein that exhibits PDZ domain binding (ortholog); INVOLVED IN neurotransmitter secretion (ortholog); ASSOCIATED WITH genetic disease (ortholog); intellectual disability (ortholog); FOUND IN cell-cell junction (ortholog); glutamatergic synapse (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: protein lin-7 homolog C
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl232,845,208 - 32,856,322 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1232,844,928 - 32,855,166 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2235,428,346 - 35,438,699 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
LIN7C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl232,845,208 - 32,856,322 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1232,844,928 - 32,855,166 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2235,428,346 - 35,438,699 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIN7C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381127,494,418 - 27,506,769 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1127,494,418 - 27,506,769 (-)EnsemblGRCh38hg38GRCh38
GRCh371127,515,965 - 27,528,316 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361127,472,699 - 27,484,879 (-)NCBINCBI36Build 36hg18NCBI36
Build 341127,472,699 - 27,484,879NCBI
Celera1127,661,655 - 27,674,034 (-)NCBICelera
Cytogenetic Map11p14.1NCBI
HuRef1127,214,688 - 27,227,063 (-)NCBIHuRef
CHM1_11127,515,302 - 27,527,664 (-)NCBICHM1_1
T2T-CHM13v2.01127,634,869 - 27,647,239 (-)NCBIT2T-CHM13v2.0
Lin7c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392109,721,205 - 109,731,348 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2109,721,198 - 109,731,348 (+)EnsemblGRCm39 Ensembl
GRCm382109,890,878 - 109,900,937 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2109,890,853 - 109,901,003 (+)EnsemblGRCm38mm10GRCm38
MGSCv372109,731,035 - 109,741,094 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362109,691,717 - 109,701,776 (+)NCBIMGSCv36mm8
Celera2111,051,913 - 111,061,966 (+)NCBICelera
Cytogenetic Map2E3NCBI
cM Map256.65NCBI
Lin7c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83116,859,425 - 116,872,363 (+)NCBIGRCr8
mRatBN7.2396,406,800 - 96,417,779 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl396,406,813 - 96,417,728 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx399,967,159 - 99,974,467 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03108,566,119 - 108,573,427 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03106,329,474 - 106,336,786 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03101,010,923 - 101,018,235 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3101,010,899 - 101,018,433 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03107,611,032 - 107,618,344 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4395,327,942 - 95,335,254 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1395,224,369 - 95,231,682 (+)NCBI
Celera395,431,335 - 95,438,647 (+)NCBICelera
Cytogenetic Map3q34NCBI
Lin7c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554766,650,106 - 6,658,817 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554766,650,539 - 6,658,811 (-)NCBIChiLan1.0ChiLan1.0
LIN7C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2929,705,210 - 29,717,388 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11129,705,738 - 29,717,917 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01127,458,735 - 27,471,068 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11127,361,291 - 27,373,440 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1127,361,301 - 27,373,440 (-)Ensemblpanpan1.1panPan2
Lin7c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494736,572,620 - 36,582,951 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365405,727,435 - 5,737,924 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365405,727,463 - 5,736,696 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIN7C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1137,598,442 - 37,610,568 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl137,598,475 - 37,606,392 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038134,908,426 - 134,920,431 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lin7c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476617,161,179 - 17,167,073 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476617,159,205 - 17,167,119 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LIN7C
230 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 4 3 5 2 23 2 3 3
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000022243   ⟹   ENSSSCP00000027907
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,845,208 - 32,856,322 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000060576   ⟹   ENSSSCP00000044489
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,847,805 - 32,852,391 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000067448   ⟹   ENSSSCP00000070487
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,848,265 - 32,856,322 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000070067   ⟹   ENSSSCP00000061975
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,847,534 - 32,852,391 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000072257   ⟹   ENSSSCP00000063356
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,845,208 - 32,856,322 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000083286   ⟹   ENSSSCP00000061549
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,847,382 - 32,856,322 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000093576   ⟹   ENSSSCP00000075559
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,845,208 - 32,852,391 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000099435   ⟹   ENSSSCP00000078893
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl232,845,208 - 32,855,658 (+)Ensembl
RefSeq Acc Id: XM_003122904   ⟹   XP_003122952
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1232,844,928 - 32,855,166 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_003122952   ⟸   XM_003122904
- UniProtKB: F2Z5M5 (UniProtKB/TrEMBL),   A0A8D0YQY9 (UniProtKB/TrEMBL),   A0A8D0YNY8 (UniProtKB/TrEMBL),   A0A8D1GJU0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000061549   ⟸   ENSSSCT00000083286
RefSeq Acc Id: ENSSSCP00000044489   ⟸   ENSSSCT00000060576
RefSeq Acc Id: ENSSSCP00000061975   ⟸   ENSSSCT00000070067
RefSeq Acc Id: ENSSSCP00000027907   ⟸   ENSSSCT00000022243
RefSeq Acc Id: ENSSSCP00000063356   ⟸   ENSSSCT00000072257
RefSeq Acc Id: ENSSSCP00000070487   ⟸   ENSSSCT00000067448
RefSeq Acc Id: ENSSSCP00000078893   ⟸   ENSSSCT00000099435
RefSeq Acc Id: ENSSSCP00000075559   ⟸   ENSSSCT00000093576
Protein Domains
L27   PDZ


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000022806 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005011813 UniProtKB/TrEMBL
  ENSSSCG00025067985 UniProtKB/TrEMBL
  ENSSSCG00035010196 UniProtKB/TrEMBL
  ENSSSCG00040041122 UniProtKB/TrEMBL
  ENSSSCG00045004870 UniProtKB/TrEMBL
  ENSSSCG00050015949 UniProtKB/TrEMBL
  ENSSSCG00055013041 UniProtKB/TrEMBL
  ENSSSCG00060057939 UniProtKB/TrEMBL
  ENSSSCG00065014002 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000022243 ENTREZGENE
  ENSSSCT00000022243.3 UniProtKB/TrEMBL
  ENSSSCT00000060576.2 UniProtKB/TrEMBL
  ENSSSCT00000067448.2 UniProtKB/TrEMBL
  ENSSSCT00000072257.1 UniProtKB/TrEMBL
  ENSSSCT00000083286.1 UniProtKB/TrEMBL
  ENSSSCT00000093576.1 UniProtKB/TrEMBL
  ENSSSCT00000099435.1 UniProtKB/TrEMBL
  ENSSSCT00005018383.1 UniProtKB/TrEMBL
  ENSSSCT00005018606.1 UniProtKB/TrEMBL
  ENSSSCT00025093553.1 UniProtKB/TrEMBL
  ENSSSCT00035012750.1 UniProtKB/TrEMBL
  ENSSSCT00035012766.1 UniProtKB/TrEMBL
  ENSSSCT00040055352.1 UniProtKB/TrEMBL
  ENSSSCT00045008075.1 UniProtKB/TrEMBL
  ENSSSCT00050021707.1 UniProtKB/TrEMBL
  ENSSSCT00055025800.1 UniProtKB/TrEMBL
  ENSSSCT00060079010.1 UniProtKB/TrEMBL
  ENSSSCT00065018633.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
  L27 domain UniProtKB/TrEMBL
InterPro L27_C UniProtKB/TrEMBL
  L27_dom UniProtKB/TrEMBL
  L27_dom_sf UniProtKB/TrEMBL
  LIN7 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
KEGG Report ssc:100518294 UniProtKB/TrEMBL
NCBI Gene LIN7C ENTREZGENE
PANTHER PROTEIN LIN-7 HOMOLOG UniProtKB/TrEMBL
  PROTEIN LIN-7 HOMOLOG C UniProtKB/TrEMBL
Pfam L27 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
PIRSF Lin-7_homologue UniProtKB/TrEMBL
PROSITE L27 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
SMART L27 UniProtKB/TrEMBL
  PDZ UniProtKB/TrEMBL
Superfamily-SCOP SSF101288 UniProtKB/TrEMBL
  SSF50156 UniProtKB/TrEMBL
UniProt A0A5G2QBW9_PIG UniProtKB/TrEMBL
  A0A5G2QHL3_PIG UniProtKB/TrEMBL
  A0A5G2R043_PIG UniProtKB/TrEMBL
  A0A8D0YNY8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0YQY9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1GJU0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1GP87_PIG UniProtKB/TrEMBL
  A0A8W4FB90_PIG UniProtKB/TrEMBL
  A0A8W4FI44_PIG UniProtKB/TrEMBL
  F2Z5M5 ENTREZGENE
UniProt Secondary A0A287AKE5 UniProtKB/TrEMBL
  F2Z5M5 UniProtKB/TrEMBL
VGNC ID VGNC:89732 ENTREZGENE