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PRUNE2 prune homolog 2 with BCH domain [ Homo sapiens (human) ]

Gene ID: 158471, updated on 23-Sep-2022

Summary

Official Symbol
PRUNE2provided by HGNC
Official Full Name
prune homolog 2 with BCH domainprovided by HGNC
Primary source
HGNC:HGNC:25209
See related
Ensembl:ENSG00000106772 MIM:610691; AllianceGenome:HGNC:25209
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
BMCC1; BNIPXL; C9orf65; KIAA0367
Summary
The protein encoded by this gene belongs to the B-cell CLL/lymphoma 2 and adenovirus E1B 19 kDa interacting family, whose members play roles in many cellular processes including apotosis, cell transformation, and synaptic function. Several functions for this protein have been demonstrated including suppression of Ras homolog family member A activity, which results in reduced stress fiber formation and suppression of oncogenic cellular transformation. A high molecular weight isoform of this protein has also been shown to colocalize with Adaptor protein complex 2, beta-Adaptin and endodermal markers, suggesting an involvement in post-endocytic trafficking. In prostate cancer cells, this gene acts as a tumor suppressor and its expression is regulated by prostate cancer antigen 3, a non-protein coding gene on the opposite DNA strand in an intron of this gene. Prostate cancer antigen 3 regulates levels of this gene through formation of a double-stranded RNA that undergoes adenosine deaminase actin on RNA-dependent adenosine-to-inosine RNA editing. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]
Expression
Broad expression in prostate (RPKM 10.8), brain (RPKM 9.0) and 20 other tissues See more
Orthologs
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Genomic context

See PRUNE2 in Genome Data Viewer
Location:
9q21.2
Exon count:
26
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (76611376..76906114, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (88767783..89062562, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (79226292..79521030, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376093 Neighboring gene peptidylprolyl isomerase A pseudogene 87 Neighboring gene uncharacterized LOC105376095 Neighboring gene prostate cancer associated 3 Neighboring gene LYPLA2 pseudogene 3 Neighboring gene forkhead box B2

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ50060, FLJ54876, FLJ59118, KIAA0367, A214N16.3, bA214N16.3, DKFZp762K117

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables pyrophosphatase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
protein prune homolog 2
Names
BCH motif-containing molecule at the carboxyl terminal region 1
BNIP2 motif containing molecule at the carboxyl terminal region 1
BNIP2 motif-containing molecule at the C-terminal region 1
olfaxin

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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)

  1. NM_001308047.2NP_001294976.1  protein prune homolog 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains one alternate in-frame exon and lacks two consecutive in-frame exons in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AB002365, AB535152, AL359314, AL390239, BC019095, BC022571, CB146736, FJ808772
    Consensus CDS
    CCDS78407.1
    UniProtKB/Swiss-Prot
    Q8WUY3
    UniProtKB/TrEMBL
    A0A088AWP5, D6RTK6, G8XWS8
    Related
    ENSP00000393843.3, ENST00000443509.6
    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992908
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29203041
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  2. NM_001308048.2NP_001294977.1  protein prune homolog 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site, contains one alternate in-frame exon, and lacks two consecutive in-frame exons in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AB050197, AB535152, AL359314, AL390239, BC019095, BC022571
    UniProtKB/Swiss-Prot
    Q8WUY3
    UniProtKB/TrEMBL
    D6RTK6
    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  3. NM_001308049.2NP_001294978.1  protein prune homolog 2 isoform 4

    See identical proteins and their annotated locations for NP_001294978.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks part of the 5' coding region, contains two alternate 5' exons, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AB050197, AK296269, BC022571
    UniProtKB/Swiss-Prot
    Q8WUY3
    UniProtKB/TrEMBL
    B4DJW7, C9K0Q0
    Conserved Domains (2) summary
    pfam12496
    Location:48164
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:166287
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  4. NM_001308050.2NP_001294979.1  protein prune homolog 2 isoform 5

    See identical proteins and their annotated locations for NP_001294979.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks part of the 5' coding region, contains an alternate 5'-terminal exon, and uses an alternate start codon, compared to variant 1. The encoded isoform (5) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AB050197, AK298805, BC022571
    UniProtKB/Swiss-Prot
    Q8WUY3
    Conserved Domains (2) summary
    pfam12496
    Location:63179
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:181302
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  5. NM_001308051.2NP_001294980.1  protein prune homolog 2 isoform 6

    See identical proteins and their annotated locations for NP_001294980.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks part of the 5' and 3' coding region, contains an alternate 5'-terminal exon, and uses an alternate start codon and an alternate in-frame splice site, compared to variant 1. The encoded isoform (6) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AB050197, AK299857, BC022571, DC342565
    UniProtKB/Swiss-Prot
    Q8WUY3
    UniProtKB/TrEMBL
    B4DSQ3, C9JCJ6
    Conserved Domains (2) summary
    pfam12496
    Location:63180
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:182303
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  6. NM_001330680.2NP_001317609.1  protein prune homolog 2 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL161626, AL359314
    Consensus CDS
    CCDS83375.1
    UniProtKB/TrEMBL
    Q5JUB8
    Related
    ENSP00000365907.2, ENST00000376717.6
  7. NM_015225.3NP_056040.2  protein prune homolog 2 isoform 1

    See identical proteins and their annotated locations for NP_056040.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB050197, AL359314, AL390239, BC019095, BQ008420, DA410068
    Consensus CDS
    CCDS47982.1
    UniProtKB/Swiss-Prot
    Q8N665, Q8WUY3
    Related
    ENSP00000365908.3, ENST00000376718.8
    Conserved Domains (3) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    cd00170
    Location:28993045
    SEC14; Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to ...
    pfam12496
    Location:27992915
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2

RNA

  1. NR_131751.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains one alternate exon and lacks several internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB002365, AB535152, AL359314, AL390239, BC019095, BC022571, FJ808772, FJ808773

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    76611376..76906114 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422884.1XP_047278840.1  protein prune homolog 2 isoform X25

  2. XM_017014349.2XP_016869838.1  protein prune homolog 2 isoform X17

  3. XM_017014352.2XP_016869841.1  protein prune homolog 2 isoform X21

  4. XM_017014346.2XP_016869835.1  protein prune homolog 2 isoform X12

  5. XM_006716986.2XP_006717049.1  protein prune homolog 2 isoform X5

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992915
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29173038
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  6. XM_005251748.2XP_005251805.1  protein prune homolog 2 isoform X8

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992908
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29203041
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  7. XM_006716983.2XP_006717046.1  protein prune homolog 2 isoform X2

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992908
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29203041
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  8. XM_005251754.3XP_005251811.1  protein prune homolog 2 isoform X23

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992916
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29183039
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  9. XM_017014348.2XP_016869837.1  protein prune homolog 2 isoform X16

  10. XM_011518323.3XP_011516625.1  protein prune homolog 2 isoform X9

    UniProtKB/Swiss-Prot
    Q8WUY3
    Related
    ENSP00000397425.1, ENST00000428286.5
    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992916
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29183039
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  11. XM_017014351.2XP_016869840.1  protein prune homolog 2 isoform X19

  12. XM_005251750.2XP_005251807.1  protein prune homolog 2 isoform X10

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992916
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29183039
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  13. XM_006716985.2XP_006717048.1  protein prune homolog 2 isoform X3

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992916
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29183039
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  14. XM_047422883.1XP_047278839.1  protein prune homolog 2 isoform X24

  15. XM_011518327.2XP_011516629.1  protein prune homolog 2 isoform X14

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  16. XM_005251745.2XP_005251802.1  protein prune homolog 2 isoform X6

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  17. XM_005251751.2XP_005251808.1  protein prune homolog 2 isoform X18

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  18. XM_011518328.3XP_011516630.1  protein prune homolog 2 isoform X20

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  19. XM_005251746.2XP_005251803.1  protein prune homolog 2 isoform X7

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  20. XM_011518326.3XP_011516628.1  protein prune homolog 2 isoform X13

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  21. XM_006716982.2XP_006717045.1  protein prune homolog 2 isoform X1

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  22. XM_006716984.3XP_006717047.1  protein prune homolog 2 isoform X4

    Conserved Domains (4) summary
    COG1227
    Location:24278
    PPX1; Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion, Inorganic ion transport and metabolism]
    pfam02833
    Location:221315
    DHHA2; DHHA2 domain
    pfam12496
    Location:27992909
    BNIP2; Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2
    pfam13716
    Location:29213042
    CRAL_TRIO_2; Divergent CRAL/TRIO domain
  23. XM_047422885.1XP_047278841.1  protein prune homolog 2 isoform X26

  24. XM_017014357.3XP_016869846.1  protein prune homolog 2 isoform X29

  25. XM_017014359.3XP_016869848.1  protein prune homolog 2 isoform X30

  26. XM_017014356.3XP_016869845.1  protein prune homolog 2 isoform X28

  27. XM_017014354.3XP_016869843.1  protein prune homolog 2 isoform X27

  28. XM_047422882.1XP_047278838.1  protein prune homolog 2 isoform X24

  29. XM_047422881.1XP_047278837.1  protein prune homolog 2 isoform X20

  30. XM_047422878.1XP_047278834.1  protein prune homolog 2 isoform X11

  31. XM_047422879.1XP_047278835.1  protein prune homolog 2 isoform X13

  32. XM_047422876.1XP_047278832.1  protein prune homolog 2 isoform X4

  33. XM_047422880.1XP_047278836.1  protein prune homolog 2 isoform X15

  34. XM_017014353.3XP_016869842.1  protein prune homolog 2 isoform X22

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    88767783..89062562 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_138818.2: Suppressed sequence

    Description
    NM_138818.2: This RefSeq was permanently suppressed because the CDS was partial.