Patj PATJ, crumbs cell polarity complex component [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Patjprovided by MGI
Official Full Name: PATJ, crumbs cell polarity complex componentprovided by MGI
Primary source: MGI:MGI:1277960
See related: Ensembl:ENSMUSG00000061859 AllianceGenome:MGI:1277960
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Cipp; Inadl
Summary: This gene encodes a multivalent PDZ domain protein, which is expressed exclusively in brain and kidney. This protein selectively interacts with inward rectifier K+ (Kir) family members, N-methyl-D-aspartate receptor subunits, neurexins and neuroligins, as well as cell surface molecules enriched in synaptic membranes. Thus, this protein may serve as a scaffold that brings structurally diverse but functionally connected proteins into close proximity at the synapse. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in cerebellum adult (RPKM 10.7), large intestine adult (RPKM 4.4) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 C6; 4 45.6 cM

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (98283803..98607840)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (98395560..98719603)

Chromosome 4 - NC_000070.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PATJ and MPDZ are required for trophectoderm lineage specification in early mouse embryos.
Title: PATJ and MPDZ are required for trophectoderm lineage specification in early mouse embryos.
Data show taht channel-interacting PDZ protein, 'CIPP', interacts with proteins involved in cytoskeletal dynamics, in particular, with the small G-protein effector IRSp53
Title: Channel-interacting PDZ protein, 'CIPP', interacts with proteins involved in cytoskeletal dynamics.
analysis of structures of tetrameric L27 domain complexes formed by mLin-2/mLin-7 and Patj/Pals1 scaffold proteins
Title: A unified assembly mode revealed by the structures of tetrameric L27 domain complexes formed by mLin-2/mLin-7 and Patj/Pals1 scaffold proteins.
Data show that MUPP1 interacts with angiomotin (Amot), JEAP/Amot-like 1 and MASCOT/Amot-like 2, and that all the Amot/JEAP family proteins also interacted with Patj, a close relative of MUPP1.
Title: Molecular characterization of angiomotin/JEAP family proteins: interaction with MUPP1/Patj and their endogenous properties.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

d5rat25 (e-PCR)
- UniSTS:122126

D4Mit28 (e-PCR), detects polymorphism
- UniSTS:130070

AW743107 (e-PCR)
- UniSTS:207643

AF060539 (e-PCR)
- UniSTS:159260

px-50g7 (e-PCR)
- UniSTS:257891

38.MMHAP42FLE5.seq (e-PCR)
- UniSTS:124279

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

D4Mit246 (e-PCR), detects polymorphism
- UniSTS:130032

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in establishment of apical/basal cell polarity	ISS Inferred from Sequence or Structural Similarity more info
involved_in tight junction assembly	IBA Inferred from Biological aspect of Ancestor 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	IDA Inferred from Direct Assay more info	PubMed
located_in apical part of cell	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation 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
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of subapical complex	IDA Inferred from Direct Assay more info	PubMed
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: PALS1-associated tight junction protein; channel-interacting PDZ domain protein; channel-interacting PDZ domain-containing protein; inactivation no after-potential D-like protein; novel ankyrin-repeat 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_001005784.1 → NP_001005784.1 inaD-like protein isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks multiple 3' exons but has an alternate 3' segment, as compared to variant 1. The encoded isoform (2) has a much shorter and distinct C-terminus, as compared to isoform 1.

Source sequence(s)

AK050545, AK077268, AL671229, CD547724, CK340630

UniProtKB/Swiss-Prot

Q63ZW7

Conserved Domains (3) summary

pfam09045
Location:8 → 65

L27_2; L27_2

smart00228
Location:685 → 774

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) ...
NM_001005787.1 → NP_001005787.1 inaD-like protein isoform 4

See identical proteins and their annotated locations for NP_001005787.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks multiple 5' exons and two 3' exons but has an alternate 5' exon and an alternate 3' segment, as compared to variant 1. The encoded isoform (4) has shorter and distinct N- and C-termini, as compared to isoform 1.

Source sequence(s)

BC037607, BU851730, BY105808

Consensus CDS

CCDS18377.1

UniProtKB/Swiss-Prot

Q63ZW7

Related

ENSMUSP00000030290.8, ENSMUST00000030290.8

Conserved Domains (3) summary

smart00228
Location:247 → 332

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

cd00992
Location:485 → 569

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:231 → 246

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
NM_001355177.1 → NP_001342106.1 inaD-like protein isoform 5

Status: REVIEWED

Source sequence(s)

AK044043, AK050545, AK077268, AL670941, AL671229, BB617492, BM900173

Conserved Domains (2) summary

smart00228
Location:617 → 702

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

cd00992
Location:855 → 940

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) ...
NM_007704.2 → NP_031730.1 inaD-like protein isoform 3

See identical proteins and their annotated locations for NP_031730.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks multiple 5' exons but has an alternate 5' exon, as compared to variant 1. The encoded isoform (3) has a much shorter and distinct N-terminus, as compared to isoform 1.

Source sequence(s)

AL670941, AV287690, BC037607, BU851730, BY105808

Consensus CDS

CCDS18376.1

UniProtKB/Swiss-Prot

Q63ZW7

Related

ENSMUSP00000099854.4, ENSMUST00000102792.10

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:231 → 246

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
NM_172696.2 → NP_766284.2 inaD-like protein isoform 1

See identical proteins and their annotated locations for NP_766284.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AK044043, AK050545, AK077268, AL670941, BB617492, CK340630

Consensus CDS

CCDS18375.1

UniProtKB/Swiss-Prot

A2ADS7, O70471, Q5PRG3, Q63ZW7, Q6P6J1, Q80YR8, Q8BPB9

UniProtKB/TrEMBL

A0A571BEG7, A2ADL9

Related

ENSMUSP00000049176.4, ENSMUST00000041284.10

Conserved Domains (4) summary

smart00228
Location:1469 → 1554

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

cd00992
Location:1707 → 1792

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:1453 → 1468

MPDZ_u10; Unstructured region 10 on multiple PDZ protein

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

98283803..98607840

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006502704.4 → XP_006502767.1 inaD-like protein isoform X3

UniProtKB/TrEMBL

A0A571BEG7

Conserved Domains (3) summary

smart00228
Location:1445 → 1530

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

cd00992
Location:1683 → 1768

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_006502705.4 → XP_006502768.1 inaD-like protein isoform X4

UniProtKB/TrEMBL

A0A571BEG7

Related

ENSMUSP00000102649.2, ENSMUST00000107034.8

Conserved Domains (4) summary

smart00228
Location:1242 → 1327

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

cd00992
Location:1679 → 1764

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:1453 → 1468

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
XM_006502699.4 → XP_006502762.1 inaD-like protein isoform X1

See identical proteins and their annotated locations for XP_006502762.1

UniProtKB/Swiss-Prot

A2ADS7, O70471, Q5PRG3, Q63ZW7, Q6P6J1, Q80YR8, Q8BPB9

UniProtKB/TrEMBL

A0A571BEG7, A2ADL9

Conserved Domains (4) summary

smart00228
Location:1469 → 1554

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

cd00992
Location:1707 → 1792

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:1453 → 1468

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
XM_006502700.4 → XP_006502763.1 inaD-like protein isoform X1

See identical proteins and their annotated locations for XP_006502763.1

UniProtKB/Swiss-Prot

A2ADS7, O70471, Q5PRG3, Q63ZW7, Q6P6J1, Q80YR8, Q8BPB9

UniProtKB/TrEMBL

A0A571BEG7, A2ADL9

Conserved Domains (4) summary

smart00228
Location:1469 → 1554

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

cd00992
Location:1707 → 1792

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:1453 → 1468

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
XM_006502702.4 → XP_006502765.1 inaD-like protein isoform X2

See identical proteins and their annotated locations for XP_006502765.1

UniProtKB/TrEMBL

A0A571BEG7

Conserved Domains (4) summary

smart00228
Location:1460 → 1545

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

cd00992
Location:1698 → 1783

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:2 → 56

L27_2

pfam16667
Location:1444 → 1459

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
XM_006502703.4 → XP_006502766.1 inaD-like protein isoform X2

See identical proteins and their annotated locations for XP_006502766.1

UniProtKB/TrEMBL

A0A571BEG7

Conserved Domains (4) summary

smart00228
Location:1460 → 1545

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

cd00992
Location:1698 → 1783

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:2 → 56

L27_2

pfam16667
Location:1444 → 1459

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
XM_006502701.1 → XP_006502764.1 inaD-like protein isoform X1

See identical proteins and their annotated locations for XP_006502764.1

UniProtKB/Swiss-Prot

A2ADS7, O70471, Q5PRG3, Q63ZW7, Q6P6J1, Q80YR8, Q8BPB9

UniProtKB/TrEMBL

A0A571BEG7, A2ADL9

Conserved Domains (4) summary

smart00228
Location:1469 → 1554

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

cd00992
Location:1707 → 1792

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:1453 → 1468

MPDZ_u10; Unstructured region 10 on multiple PDZ protein
XM_006502707.4 → XP_006502770.1 inaD-like protein isoform X5

Conserved Domains (3) summary

smart00228
Location:243 → 328

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

cd00992
Location:481 → 566

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:227 → 242

MPDZ_u10; Unstructured region 10 on multiple PDZ protein