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PAX5 paired box 5 [ Homo sapiens (human) ]

Gene ID: 5079, updated on 28-Oct-2018

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; Vega:OTTHUMG00000019907
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
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

Genomic context

See PAX5 in Genome Data Viewer
Location:
9p13.2
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (36833275..37034479, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (36833272..37034476, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene maternal embryonic leucine zipper kinase Neighboring gene uncharacterized LOC105376030 Neighboring gene microRNA 4475 Neighboring gene microRNA 4540 Neighboring gene enhancer in intron 7 of PAX5 Neighboring gene microRNA 4476 Neighboring gene uncharacterized LOC105376032 Neighboring gene uncharacterized LOC105376031 Neighboring gene PAX5 promoter region Neighboring gene ribosomal protein L32 pseudogene 21 Neighboring gene endogenous Bornavirus-like nucleoprotein 3, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

NHGRI GWAS Catalog

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
adult behavior IEA
Inferred from Electronic Annotation
more info
 
aging IEA
Inferred from Electronic Annotation
more info
 
animal organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
cerebral cortex development IEA
Inferred from Electronic Annotation
more info
 
embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
humoral immune response TAS
Traceable Author Statement
more info
PubMed 
lateral ventricle development IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of histone H3-K9 methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of B cell receptor signaling pathway TAS
Traceable Author Statement
more info
 
skeletal muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

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)

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

  1. NG_033894.1 RefSeqGene

    Range
    5001..206205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001280547.1NP_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, OTTHUMP00000227120, ENST00000377852.6, OTTHUMT00000379547
    Conserved Domains (2) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
    pfam12403
    Location:279355
    Pax2_C; Paired-box protein 2 C terminal
  2. NM_001280548.1NP_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, OTTHUMP00000227118, ENST00000377853.6, OTTHUMT00000379545
    Conserved Domains (2) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
    pfam12403
    Location:279341
    Pax2_C; Paired-box protein 2 C terminal
  3. NM_001280549.1NP_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/Swiss-Prot
    Q02548
    UniProtKB/TrEMBL
    E7EQT0
    Related
    ENSP00000429637.1, OTTHUMP00000227121, ENST00000523241.5, OTTHUMT00000379548
    Conserved Domains (1) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
  4. NM_001280550.1NP_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/Swiss-Prot
    Q02548
    UniProtKB/TrEMBL
    E7ERW5
    Related
    ENSP00000429291.1, OTTHUMP00000227122, ENST00000520154.5, OTTHUMT00000379549
    Conserved Domains (1) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
  5. NM_001280551.1NP_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
    C0KTE5, C0KTF5, E7ES87
    Related
    ENSP00000429197.1, OTTHUMP00000227126, ENST00000523145.5, OTTHUMT00000379553
    Conserved Domains (1) summary
    cl21459
    Location:134
    HTH; Helix-turn-helix domains
  6. NM_001280552.1NP_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, OTTHUMP00000227129, ENST00000377847.6, OTTHUMT00000379556
    Conserved Domains (1) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
  7. NM_001280553.1NP_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, OTTHUMP00000227123, ENST00000520281.5, OTTHUMT00000379550
    Conserved Domains (2) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
    pfam12403
    Location:236298
    Pax2_C; Paired-box protein 2 C terminal
  8. NM_001280554.1NP_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, OTTHUMP00000227128, ENST00000414447.5, OTTHUMT00000379555
    Conserved Domains (2) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
    pfam12403
    Location:236346
    Pax2_C; Paired-box protein 2 C terminal
  9. NM_001280555.1NP_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, OTTHUMP00000227124, ENST00000446742.5, OTTHUMT00000379551
    Conserved Domains (2) summary
    pfam12403
    Location:213289
    Pax2_C; Paired-box protein 2 C terminal
    cl21459
    Location:1680
    HTH; Helix-turn-helix domains
  10. NM_001280556.1NP_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/Swiss-Prot
    Q02548
    UniProtKB/TrEMBL
    E7ERK2
    Related
    ENSP00000429359.1, OTTHUMP00000227125, ENST00000522003.5, OTTHUMT00000379552
    Conserved Domains (2) summary
    pfam12403
    Location:171281
    Pax2_C; Paired-box protein 2 C terminal
    cl21459
    Location:134
    HTH; Helix-turn-helix domains
  11. NM_016734.2NP_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
    Q02548
    Related
    ENSP00000350844.4, OTTHUMP00000021378, ENST00000358127.8, OTTHUMT00000052433
    Conserved Domains (2) summary
    smart00351
    Location:16140
    PAX; Paired Box domain
    pfam12403
    Location:279389
    Pax2_C; Paired-box protein 2 C terminal

RNA

  1. NR_103999.1 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
  2. NR_104000.1 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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    36833275..37034479 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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