Patj PATJ, crumbs cell polarity complex component [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Patjprovided by RGD
Official Full Name: PATJ, crumbs cell polarity complex componentprovided by RGD
Primary source: RGD:1565362
See related: EnsemblRapid:ENSRNOG00000007551 AllianceGenome:RGD:1565362
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Inadl; Inadl2; RGD1565362
Summary: Predicted to be involved in several processes, including establishment of apical/basal cell polarity; positive regulation of epithelial cell migration; and tight junction assembly. Part of protein-containing complex. Orthologous to human PATJ (PATJ crumbs cell polarity complex component). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 164.7), Lung (RPKM 92.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q33

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (118177557..118480301)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (113061985..113364807)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (117038548..117340308)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the crystal structure of a 4-L27 domain-containing heterotrimer derived from the tripartite complex Patj/Pals1/Mals2
Title: Structure of an L27 domain heterotrimer from cell polarity complex Patj/Pals1/Mals2 reveals mutually independent L27 domain assembly mode.

Submit: New GeneRIF Correction

General gene information

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Markers

d5rat25 (e-PCR)
- UniSTS:122126

RH143216 (e-PCR)
- UniSTS:232463

AU049786 (e-PCR)
- UniSTS:146232

RH142079 (e-PCR)
- UniSTS:224069

UniSTS:234969 (e-PCR)
- UniSTS:234969

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in establishment of apical/basal cell polarity	ISO Inferred from Sequence Orthology more info
involved_in establishment of apical/basal cell polarity	ISS Inferred from Sequence or Structural Similarity more info
involved_in microtubule organizing center organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of epithelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in regulation of microtubule cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in tight junction assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in tight junction assembly	ISO Inferred from Sequence Orthology more info
involved_in tight junction assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in apical part of cell	IBA Inferred from Biological aspect of Ancestor more info
is_active_in apical part of cell	ISO Inferred from Sequence Orthology more info
located_in apical part of cell	ISO Inferred from Sequence Orthology more info
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
located_in apical plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in bicellular tight junction	IBA Inferred from Biological aspect of Ancestor more info
located_in bicellular tight junction	ISO Inferred from Sequence Orthology more info
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cell junction	ISO Inferred from Sequence Orthology more info
located_in centriolar satellite	IEA Inferred from Electronic Annotation more info
located_in centriolar satellite	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of subapical complex	ISO Inferred from Sequence Orthology more info
located_in tight junction	ISO Inferred from Sequence Orthology more info
located_in tight junction	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: inaD-like protein

Names: InaD-like 2; PDZ domain protein; channel-interacting PDZ domain-containing protein; pals1-associated tight junction protein; protein associated to tight junctions

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_080398.1 → NP_536323.1 inaD-like protein

See identical proteins and their annotated locations for NP_536323.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

F1MAD2

UniProtKB/TrEMBL

A0A8I6AG04

Related

ENSRNOP00000010211.6, ENSRNOT00000010211.10

Conserved Domains (5) summary

smart00228
Location:1471 → 1556

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

COG0793
Location:391 → 511

CtpA; C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones]

cd00992
Location:1709 → 1794

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam09045
Location:8 → 65

L27_2

pfam16667
Location:1400 → 1470

MPDZ_u10; Unstructured region 10 on multiple PDZ protein

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

118177557..118480301

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109186.2 → XP_038965114.1 inaD-like protein isoform X1

UniProtKB/TrEMBL

A0A8I5ZMD2, A0A8I6AG04

Related

ENSRNOP00000079221.1, ENSRNOT00000095175.2

Conserved Domains (4) summary

smart00228
Location:1244 → 1329

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

COG0793
Location:391 → 511

CtpA; C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones]

cd00992
Location:1731 → 1816

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam09045
Location:8 → 65

L27_2
XM_039109188.2 → XP_038965116.1 inaD-like protein isoform X4

UniProtKB/TrEMBL

A0A8I6AG04

Related

ENSRNOP00000077045.2, ENSRNOT00000101438.2

Conserved Domains (4) summary

smart00228
Location:1244 → 1329

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

COG0793
Location:391 → 511

CtpA; C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones]

cd00992
Location:1681 → 1766

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam09045
Location:8 → 65

L27_2
XM_063287101.1 → XP_063143171.1 inaD-like protein isoform X3
XM_063287102.1 → XP_063143172.1 inaD-like protein isoform X5

UniProtKB/TrEMBL

A0A8I5ZJD2

Related

ENSRNOP00000105981.1, ENSRNOT00000165802.1
XM_063287100.1 → XP_063143170.1 inaD-like protein isoform X2
XM_008763915.4 → XP_008762137.1 inaD-like protein isoform X6

Conserved Domains (3) summary

pfam09045
Location:8 → 65

L27_2; L27_2

smart00228
Location:684 → 773

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:248 → 325

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
XM_008763916.4 → XP_008762138.1 inaD-like protein isoform X8

See identical proteins and their annotated locations for XP_008762138.1

UniProtKB/TrEMBL

A0A8I6GME4

Related

ENSRNOP00000097148.1, ENSRNOT00000103328.2

Conserved Domains (3) summary

smart00228
Location:247 → 332

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:485 → 570

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam16667
Location:176 → 246

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
XM_063287103.1 → XP_063143173.1 inaD-like protein isoform X7