LOC111089960 (protocadherin alpha-7) - Rat Genome Database

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Gene: LOC111089960 (protocadherin alpha-7) Canis lupus familiaris
Analyze
Symbol: LOC111089960 (Ensembl: PCDHA13)
Name: protocadherin alpha-7 (Ensembl:protocadherin alpha 13)
RGD ID: 13344706
Description: ENCODES a protein that exhibits calcium ion binding (inferred); INVOLVED IN serotonergic neuron axon guidance (ortholog); ASSOCIATED WITH autosomal dominant intellectual developmental disorder 31 (ortholog); familial adenomatous polyposis 1 (ortholog); genetic disease (ortholog); FOUND IN plasma membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: protocadherin alpha-10; protocadherin alpha-11; protocadherin alpha-12; protocadherin alpha-13; protocadherin alpha-C2
RGD Orthologs
Human
Mouse
Rat
Bonobo
Pig
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
NCBI Annotation Information: Annotation category: not annotated on reference assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1235,954,126 - 36,096,661 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl235,910,402 - 36,095,110 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha232,989,113 - 33,114,899 (+)NCBIDog10K_Boxer_Tasha
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Genomics

Comparative Map Data
LOC111089960
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1235,954,126 - 36,096,661 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl235,910,402 - 36,095,110 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha232,989,113 - 33,114,899 (+)NCBIDog10K_Boxer_Tasha
PCDHAC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,966,476 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,966,470 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,346,061 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,326,536 - 140,372,113 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,326,535 - 140,329,190NCBI
Celera5136,422,531 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,490,462 - 135,536,628 (+)NCBIHuRef
CHM1_15139,778,941 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,491,769 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdhac2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,276,731 - 37,320,716 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,276,556 - 37,320,710 (+)EnsemblGRCm39 Ensembl
GRCm381837,143,678 - 37,187,663 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,143,503 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,303,623 - 37,347,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,269,943 - 37,313,631 (+)NCBIMGSCv36mm8
MGSCv361837,331,075 - 37,374,763 (+)NCBIMGSCv36mm8
Cytogenetic Map18B3NCBI
cM Map1819.46NCBI
Pcdhac2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01830,172,740 - 30,215,896 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,881,386 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,884,685 - 29,928,030 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11829,911,330 - 29,954,676 (+)NCBI
Celera1828,509,807 - 28,552,754 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHAC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15142,445,483 - 142,448,709 (+)NCBIpanpan1.1PanPan1.1panPan2
LOC100621701
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2142,460,178 - 142,688,089 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12142,477,627 - 142,687,684 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22148,423,053 - 148,427,771 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in LOC111089960
1481 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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 11 2 12 5
Low 5 11 6 4 6 8 3 2
Below cutoff 5 6 5 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000009730   ⟹   ENSCAFP00000009032
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,944,005 - 36,094,633 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000009802   ⟹   ENSCAFP00000009100
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl236,047,517 - 36,095,110 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000061880   ⟹   ENSCAFP00000048257
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,992,220 - 36,094,633 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000065430   ⟹   ENSCAFP00000046242
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,986,731 - 36,094,633 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000068757   ⟹   ENSCAFP00000055188
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,917,810 - 36,094,633 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000070045   ⟹   ENSCAFP00000054585
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,979,281 - 36,094,633 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000071133   ⟹   ENSCAFP00000055860
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,992,220 - 36,094,935 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000072302   ⟹   ENSCAFP00000063194
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,925,084 - 36,094,633 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000083174   ⟹   ENSCAFP00000045922
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,910,402 - 36,094,633 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000089398   ⟹   ENSCAFP00000050710
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl235,962,220 - 36,094,633 (+)Ensembl
RefSeq Acc Id: XM_014107727   ⟹   XP_013963202
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1235,954,126 - 36,096,661 (+)NCBI
Dog10K_Boxer_Tasha232,989,113 - 33,114,899 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013963202 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCAFP00000009100.4
  ENSCAFP00000045922.2
  ENSCAFP00000046242.1
  ENSCAFP00000051293.2
  ENSCAFP00000054585.1
  ENSCAFP00000055188.1
  ENSCAFP00000055860.2
  ENSCAFP00000063194.1
Reference Protein Sequences
RefSeq Acc Id: XP_013963202   ⟸   XM_014107727
- Sequence:
RefSeq Acc Id: ENSCAFP00000054585   ⟸   ENSCAFT00000070045
RefSeq Acc Id: ENSCAFP00000045922   ⟸   ENSCAFT00000083174
RefSeq Acc Id: ENSCAFP00000009100   ⟸   ENSCAFT00000009802
RefSeq Acc Id: ENSCAFP00000009032   ⟸   ENSCAFT00000009730
RefSeq Acc Id: ENSCAFP00000055188   ⟸   ENSCAFT00000068757
RefSeq Acc Id: ENSCAFP00000063194   ⟸   ENSCAFT00000072302
RefSeq Acc Id: ENSCAFP00000046242   ⟸   ENSCAFT00000065430
RefSeq Acc Id: ENSCAFP00000050710   ⟸   ENSCAFT00000089398
RefSeq Acc Id: ENSCAFP00000055860   ⟸   ENSCAFT00000071133
RefSeq Acc Id: ENSCAFP00000048257   ⟸   ENSCAFT00000061880
Protein Domains
Cadherin


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000023033 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000009802.6 UniProtKB/TrEMBL
  ENSCAFT00000065430.2 UniProtKB/TrEMBL
  ENSCAFT00000065588.2 UniProtKB/TrEMBL
  ENSCAFT00000068757.2 UniProtKB/TrEMBL
  ENSCAFT00000070045.2 UniProtKB/TrEMBL
  ENSCAFT00000071133.2 UniProtKB/TrEMBL
  ENSCAFT00000072302.2 UniProtKB/TrEMBL
  ENSCAFT00000083174.2 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
NCBI Gene LOC111089960 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-1 UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-11 UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-12 UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-13 UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-3 UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-4 UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-C2 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin-like UniProtKB/TrEMBL
UniProt A0A8P0N8M5_CANLF UniProtKB/TrEMBL
  A0A8P0P413_CANLF UniProtKB/TrEMBL
  A0A8P0PBY6_CANLF UniProtKB/TrEMBL
  A0A8P0SZ39_CANLF UniProtKB/TrEMBL
  A0A8P0SZ99_CANLF UniProtKB/TrEMBL
  A0A8P0T3W4_CANLF UniProtKB/TrEMBL
  A0A8P0T7G0_CANLF UniProtKB/TrEMBL
  A0A8P0T832_CANLF UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-01-12 LOC111089960  protocadherin alpha-7  LOC111089960  protocadherin alpha-C2  Symbol and/or name change 5135510 APPROVED