PAX5 paired box 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PAX5provided by HGNC
Official Full Name: paired box 5provided by HGNC
Primary source: HGNC:HGNC:8619
See related: Ensembl:ENSG00000196092 MIM:167414; AllianceGenome:HGNC:8619
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ALL3; BSAP; PAX-5
Summary: This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. Paired box transcription factors are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. This gene encodes the B-cell lineage specific activator protein that is expressed at early, but not late stages of B-cell differentiation. Its expression has also been detected in developing CNS and testis and so the encoded protein may also play a role in neural development and spermatogenesis. This gene is located at 9p13, which is involved in t(9;14)(p13;q32) translocations recurring in small lymphocytic lymphomas of the plasmacytoid subtype, and in derived large-cell lymphomas. This translocation brings the potent E-mu enhancer of the IgH gene into close proximity of the PAX5 promoter, suggesting that the deregulation of transcription of this gene contributes to the pathogenesis of these lymphomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Expression: Biased expression in lymph node (RPKM 16.7), spleen (RPKM 9.5) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9p13.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (36833269..37034268, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (36856835..37057984, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (36833266..37034265, complement)

Chromosome 9 - NC_000009.12 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms.
Title: EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms.
PAX5 fusion genes in acute lymphoblastic leukemia: A literature review.
Title: PAX5 fusion genes in acute lymphoblastic leukemia: A literature review.
FOXO1 and PAX5 Rearrangement in Alveolar Rhabdomyosarcoma in Saudi Pediatric Patients.
Title: FOXO1 and PAX5 Rearrangement in Alveolar Rhabdomyosarcoma in Saudi Pediatric Patients.
PAX5 aberrant expression incorporated in MIPI-SP risk scoring system exhibits additive value in mantle cell lymphoma.
Title: PAX5 aberrant expression incorporated in MIPI-SP risk scoring system exhibits additive value in mantle cell lymphoma.
Functional damaging germline variants in ETV6, IKZF1, PAX5 and RUNX1 predisposing to B-cell precursor acute lymphoblastic leukemia.
Title: Functional damaging germline variants in ETV6, IKZF1, PAX5 and RUNX1 predisposing to B-cell precursor acute lymphoblastic leukemia.
Type 2 diabetes candidate genes, including PAX5, cause impaired insulin secretion in human pancreatic islets.
Title: Type 2 diabetes candidate genes, including PAX5, cause impaired insulin secretion in human pancreatic islets.
PAX5/ITGAX Contributed to the Progression of Atherosclerosis by Regulation of B Differentiation via TNF-alpha Signaling Pathway.
Title: PAX5/ITGAX Contributed to the Progression of Atherosclerosis by Regulation of B Differentiation via TNF-α Signaling Pathway.
PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia.
Title: PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia.
DNA hypermethylation of CADM1, PAX5, WT1, RARbeta, and PAX6 genes in oropharyngeal cancer associated with human papillomavirus.
Title: DNA hypermethylation of CADM1, PAX5, WT1, RARβ, and PAX6 genes in oropharyngeal cancer associated with human papillomavirus.
The utility of PAX8 in comparison with PAX5 immunohistochemical staining in the diagnosis of Hodgkin lymphoma.
Title: The utility of PAX8 in comparison with PAX5 immunohistochemical staining in the diagnosis of Hodgkin lymphoma.

Submit: New GeneRIF Correction See all GeneRIFs (172)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Leukemia, acute lymphoblastic, susceptibility to, 3 MedGen: C3809874 OMIM: 615545 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2022-05-24) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2022-05-24) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association study of intelligence: additive effects of novel brain expressed genes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide scan for loci of adolescent obesity and their relationship with blood pressure. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9S772 (e-PCR), detects polymorphism
- UniSTS:149269

STS-M96944 (e-PCR)
- UniSTS:38956

D9S1968 (e-PCR)
- UniSTS:25392

PAX5_1027 (e-PCR)
- UniSTS:277555

PAX5_V277 (e-PCR)
- UniSTS:277555

SHGC-143721 (e-PCR)
- UniSTS:184896

PMC133916P3 (e-PCR)
- UniSTS:270688

Pax5 (e-PCR), detects polymorphism
- UniSTS:265581

NoName (e-PCR)
- UniSTS:485486

Pax5 (e-PCR), detects polymorphism
- UniSTS:463216

Pax5 (e-PCR), detects polymorphism
- UniSTS:256447

Pax5 (e-PCR), detects polymorphism
- UniSTS:502731

GDB:373099 (e-PCR)
- UniSTS:156894

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in B cell differentiation	TAS Traceable Author Statement more info	PubMed
involved_in adult behavior	IEA Inferred from Electronic Annotation more info
involved_in anatomical structure development	IBA Inferred from Biological aspect of Ancestor more info
involved_in cerebral cortex development	IEA Inferred from Electronic Annotation more info
involved_in embryonic cranial skeleton morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in lateral ventricle development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: paired box protein Pax-5

Names: B-cell lineage specific activator; paired box homeotic gene 5; paired domain gene 5; transcription factor PAX 5

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.

Genomic

NG_033894.1 RefSeqGene

Range

5212..206211

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1384

mRNA and Protein(s)

NM_001280547.2 → NP_001267476.1 paired box protein Pax-5 isoform 2

See identical proteins and their annotated locations for NP_001267476.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, AY463954

Consensus CDS

CCDS65047.1

UniProtKB/Swiss-Prot

Q02548

Related

ENSP00000367083.2, ENST00000377852.7

Conserved Domains (2) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:279 → 355

Pax2_C; Paired-box protein 2 C terminal
NM_001280548.2 → NP_001267477.1 paired box protein Pax-5 isoform 3

See identical proteins and their annotated locations for NP_001267477.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, AY463955

Consensus CDS

CCDS65048.1

UniProtKB/Swiss-Prot

Q02548

Related

ENSP00000367084.2, ENST00000377853.6

Conserved Domains (2) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:279 → 341

Pax2_C; Paired-box protein 2 C terminal
NM_001280549.2 → NP_001267478.1 paired box protein Pax-5 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two consecutive exons in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, AY463956

Consensus CDS

CCDS65045.1

UniProtKB/TrEMBL

E7EQT0

Related

ENSP00000429637.1, ENST00000523241.6

Conserved Domains (1) summary

smart00351
Location:16 → 140

PAX; Paired Box domain
NM_001280550.2 → NP_001267479.1 paired box protein Pax-5 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks three consecutive exons in the 3' coding, which results in a frameshift, compared to variant 1. The encoded isoform (5) has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, AY463957

Consensus CDS

CCDS65044.1

UniProtKB/TrEMBL

E7ERW5

Related

ENSP00000429291.1, ENST00000520154.6

Conserved Domains (1) summary

smart00351
Location:16 → 140

PAX; Paired Box domain
NM_001280551.2 → NP_001267480.1 paired box protein Pax-5 isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks several exons and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (6) is shorter, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, FJ626410, FJ626420

Consensus CDS

CCDS65039.1

UniProtKB/TrEMBL

E7ES87

Related

ENSP00000429197.1, ENST00000523145.5

Conserved Domains (1) summary

cl21459
Location:1 → 34

HTH; Helix-turn-helix domains
NM_001280552.2 → NP_001267481.1 paired box protein Pax-5 isoform 7

See identical proteins and their annotated locations for NP_001267481.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks two consecutive in-frame exons in the 3' coding region, compared to variant 1. The encoded isoform (7) is shorter, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, FJ626421

Consensus CDS

CCDS65046.1

UniProtKB/Swiss-Prot

Q02548

Related

ENSP00000367078.2, ENST00000377847.6

Conserved Domains (1) summary

smart00351
Location:16 → 140

PAX; Paired Box domain
NM_001280553.2 → NP_001267482.1 paired box protein Pax-5 isoform 8

See identical proteins and their annotated locations for NP_001267482.1

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks two alternate exons in the central and 3' coding region, compared to variant 1. The encoded isoform (8) is shorter, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, FJ626423

Consensus CDS

CCDS65042.1

UniProtKB/Swiss-Prot

Q02548

Related

ENSP00000430773.1, ENST00000520281.5

Conserved Domains (2) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:236 → 298

Pax2_C; Paired-box protein 2 C terminal
NM_001280554.2 → NP_001267483.1 paired box protein Pax-5 isoform 9

See identical proteins and their annotated locations for NP_001267483.1

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (9) is shorter, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, FJ626422

Consensus CDS

CCDS65043.1

UniProtKB/Swiss-Prot

Q02548

Related

ENSP00000412188.1, ENST00000414447.5

Conserved Domains (2) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:236 → 347

Pax2_C; Paired-box protein 2 C terminal
NM_001280555.2 → NP_001267484.1 paired box protein Pax-5 isoform 10

See identical proteins and their annotated locations for NP_001267484.1

Status: REVIEWED

Description

Transcript Variant: This variant (10) lacks two alternate exons in the central and 3' coding region, compared to variant 1. The encoded isoform (10) is shorter, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, FJ626424, M96944

Consensus CDS

CCDS65041.1

UniProtKB/Swiss-Prot

Q02548

Related

ENSP00000404687.1, ENST00000446742.5

Conserved Domains (2) summary

pfam12403
Location:213 → 290

Pax2_C; Paired-box protein 2 C terminal

cl21459
Location:16 → 80

HTH; Helix-turn-helix domains
NM_001280556.2 → NP_001267485.1 paired box protein Pax-5 isoform 11

See identical proteins and their annotated locations for NP_001267485.1

Status: REVIEWED

Description

Transcript Variant: This variant (11) lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (11) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AL161781, AL450267, M96944

Consensus CDS

CCDS65040.1

UniProtKB/TrEMBL

E7ERK2

Related

ENSP00000429359.1, ENST00000522003.5

Conserved Domains (2) summary

pfam12403
Location:171 → 281

Pax2_C; Paired-box protein 2 C terminal

cl21459
Location:1 → 34

HTH; Helix-turn-helix domains
NM_016734.3 → NP_057953.1 paired box protein Pax-5 isoform 1

See identical proteins and their annotated locations for NP_057953.1

Status: REVIEWED

Description

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

Source sequence(s)

AL161781, AL450267, M96944

Consensus CDS

CCDS6607.1

UniProtKB/Swiss-Prot

A3QVP7, C0KTF6, C0KTF7, C0KTF8, C0KTF9, C0KTG0, O75933, Q02548, Q5SFM2, Q6S728, Q6S729, Q6S730, Q6S731, Q6S732

Related

ENSP00000350844.4, ENST00000358127.9

Conserved Domains (2) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:279 → 389

Pax2_C; Paired-box protein 2 C terminal

RNA

NR_103999.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (12) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL161781, AL450267, AY463953
NR_104000.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (13) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL161781, AL450267, FJ626425