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    PAX5 paired box 5 [ Homo sapiens (human) ]

    Gene ID: 5079, updated on 5-Nov-2017
    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]
    Orthologs
    Location:
    9p13.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (36833274..37035949, 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 microRNA 4476 Neighboring gene uncharacterized LOC105376032 Neighboring gene uncharacterized LOC105376031 Neighboring gene ribosomal protein L32 pseudogene 21 Neighboring gene endogenous Bornavirus-like nucleoprotein 3, pseudogene

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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
    Products Interactant Other Gene Complex Source Pubs Description

    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 from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription from RNA polymerase II promoter 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 from RNA polymerase II promoter 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
     
    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

    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 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      36833274..37035949 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517896.2XP_011516198.1  paired box protein Pax-5 isoform X1

      See identical proteins and their annotated locations for XP_011516198.1

      Conserved Domains (2) summary
      smart00351
      Location:16140
      PAX; Paired Box domain
      pfam12403
      Location:298408
      Pax2_C; Paired-box protein 2 C terminal
    2. XM_011517897.2XP_011516199.1  paired box protein Pax-5 isoform X2

      Conserved Domains (2) summary
      smart00351
      Location:15139
      PAX; Paired Box domain
      pfam12403
      Location:297407
      Pax2_C; Paired-box protein 2 C terminal
    3. XM_005251481.4XP_005251538.1  paired box protein Pax-5 isoform X3

      See identical proteins and their annotated locations for XP_005251538.1

      Conserved Domains (2) summary
      smart00351
      Location:15139
      PAX; Paired Box domain
      pfam12403
      Location:278388
      Pax2_C; Paired-box protein 2 C terminal

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      36834374..37035683 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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