Patz1 POZ (BTB) and AT hook containing zinc finger 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Patz1provided by RGD
Official Full Name: POZ (BTB) and AT hook containing zinc finger 1provided by RGD
Primary source: RGD:1308337
See related: EnsemblRapid:ENSRNOG00000018709 AllianceGenome:RGD:1308337
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: Zfp278; Znf278
Summary: Predicted to enable several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and ubiquitin protein ligase binding activity. Predicted to be involved in negative regulation of endothelial cell migration; regulation of gene expression; and regulation of immune system process. Predicted to act upstream of or within several processes, including T cell differentiation; male gonad development; and positive regulation of DNA-templated transcription. Predicted to be located in male germ cell nucleus. Predicted to be active in nucleoplasm. Orthologous to human PATZ1 (POZ/BTB and AT hook containing zinc finger 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 139.8), Thymus (RPKM 94.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14q21

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (82378226..82396679)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (78154590..78173032)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (83509763..83528898)

Chromosome 14 - NC_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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
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?

Together, these results suggest a novel mechanism regulating PATZ1 expression based on the upregulation of miR-29b expression induced by Ras oncogene.
Title: PATZ1 is a target of miR-29b that is induced by Ha-Ras oncogene in rat thyroid cells.

Submit: New GeneRIF Correction

General gene information

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Markers

RH141753 (e-PCR)
- UniSTS:223746

BE096205 (e-PCR)
- UniSTS:244004

BF418015 (e-PCR)
- UniSTS:249897

RH137686 (e-PCR)
- UniSTS:219773

RH143618 (e-PCR)
- UniSTS:232864

Patz1 (e-PCR), detects polymorphism
- UniSTS:547284

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within T cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within male gonad development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytokine production	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of immune system process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in male germ cell nucleus	ISO Inferred from Sequence Orthology more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: POZ-, AT hook-, and zinc finger-containing protein 1

Names: zinc finger protein 278

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_001107231.2 → NP_001100701.1 POZ-, AT hook-, and zinc finger-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_001100701.1

Status: VALIDATED

Description

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

Source sequence(s)

EV764152, JAXUCZ010000014

UniProtKB/TrEMBL

A6IK96, D3ZX15

Related

ENSRNOP00000025378.2, ENSRNOT00000025378.6

Conserved Domains (6) summary

COG5048
Location:357 → 408

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:357 → 377

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:561 → 582

ZF_C2H2; C2H2 Zn finger [structural motif]

cd18207
Location:14 → 162

BTB_POZ_ZBTB19_PATZ1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in POZ-, AT hook-, and zinc finger-containing protein 1 (PATZ1)

pfam15909
Location:382 → 461

zf-C2H2_8; C2H2-type zinc ribbon

pfam16637
Location:492 → 558

zf-C2H2_assoc3; Putative zinc-finger between two C2H2 zinc-fingers on Patz
NM_001277214.1 → NP_001264143.1 POZ-, AT hook-, and zinc finger-containing protein 1 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate exon in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

CK479676, JAXUCZ010000014

UniProtKB/TrEMBL

A0A0G2K420

Conserved Domains (5) summary

COG5048
Location:381 → 451

COG5048; FOG: Zn-finger [General function prediction only]

COG5189
Location:329 → 406

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:357 → 377

ZF_C2H2; C2H2 Zn finger [structural motif]

cd18207
Location:14 → 162

BTB_POZ_ZBTB19_PATZ1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in POZ-, AT hook-, and zinc finger-containing protein 1 (PATZ1)

pfam13912
Location:442 → 467

zf-C2H2_6; C2H2-type zinc finger
NM_001277215.1 → NP_001264144.1 POZ-, AT hook-, and zinc finger-containing protein 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

BC098801, JAXUCZ010000014

UniProtKB/TrEMBL

A0A0G2K2T7, Q4G032

Related

ENSRNOP00000073870.2, ENSRNOT00000081161.3

Conserved Domains (6) summary

smart00225
Location:42 → 159

BTB; Broad-Complex, Tramtrack and Bric a brac

COG5048
Location:357 → 408

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:357 → 377

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:357 → 377

zf-C2H2; Zinc finger, C2H2 type

pfam00651
Location:30 → 157

BTB; BTB/POZ domain

pfam13465
Location:369 → 394

zf-H2C2_2; Zinc-finger double domain

RNA

NR_102353.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) includes an alternate 5' terminal exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

DY318319, JAXUCZ010000014
NR_102354.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks several exons and includes alternate 5' and 3' terminal exons, compared to variant 1. This variant is represented as non-coding because the longest open reading frame is in a different frame compared to variant 1, and there is no support for the predicted protein encoded by this ORF.

Source sequence(s)

BC098801, DV728999, DY318319

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_086032.1 Reference GRCr8

Range

82378226..82396679

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006251292.5 → XP_006251354.1 POZ-, AT hook-, and zinc finger-containing protein 1 isoform X1

UniProtKB/TrEMBL

A0A0G2K420

Related

ENSRNOP00000072870.3, ENSRNOT00000082242.3

Conserved Domains (8) summary

smart00225
Location:42 → 159

BTB; Broad-Complex, Tramtrack and Bric a brac

COG4049
Location:600 → 635

COG4049; Uncharacterized protein, contains archaeal-type C2H2 Zn-finger [General function prediction only]

COG5048
Location:381 → 518

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:357 → 377

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00651
Location:30 → 157

BTB; BTB/POZ domain

pfam13465
Location:369 → 394

zf-H2C2_2; Zinc-finger double domain

pfam13912
Location:442 → 467

zf-C2H2_6; C2H2-type zinc finger

pfam16637
Location:536 → 604

zf-C2H2_assoc3; Putative zinc-finger between two C2H2 zinc-fingers on Patz
XM_063273186.1 → XP_063129256.1 POZ-, AT hook-, and zinc finger-containing protein 1 isoform X2

UniProtKB/TrEMBL

A0A0G2K6M4
XM_039092005.2 → XP_038947933.1 POZ-, AT hook-, and zinc finger-containing protein 1 isoform X2

UniProtKB/TrEMBL

A0A0G2K6M4

Conserved Domains (3) summary

COG5048
Location:357 → 408

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:357 → 377

ZF_C2H2; C2H2 Zn finger [structural motif]

cd18207
Location:14 → 162

BTB_POZ_ZBTB19_PATZ1; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in POZ-, AT hook-, and zinc finger-containing protein 1 (PATZ1)