PDXP (pyridoxal phosphatase) - Rat Genome Database

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Gene: PDXP (pyridoxal phosphatase) Homo sapiens
Analyze
Symbol: PDXP
Name: pyridoxal phosphatase
RGD ID: 1351799
HGNC Page HGNC
Description: Enables heat shock protein binding activity; phosphoprotein phosphatase activity; and pyridoxal phosphatase activity. Involved in several processes, including positive regulation of actin filament depolymerization; pyridoxal phosphate catabolic process; and regulation of cell cycle process. Acts upstream of or within actin rod assembly and cellular response to ATP. Located in cytosol. Colocalizes with several cellular components, including cleavage furrow; midbody; and ruffle membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: chronophin; CIN; dJ37E16.5; FLJ32703; PLP; PLP phosphatase; pyridoxal (pyridoxine, vitamin B6) phosphatase; pyridoxal phosphate phosphatase; testicular secretory protein Li 36
RGD Orthologs
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2237,658,723 - 37,666,932 (+)EnsemblGRCh38hg38GRCh38
GRCh382237,658,723 - 37,666,932 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372238,054,730 - 38,062,939 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362236,384,683 - 36,392,885 (+)NCBINCBI36hg18NCBI36
Build 342236,379,237 - 36,387,439NCBI
Celera2221,856,602 - 21,864,785 (+)NCBI
Cytogenetic Map22q13.1NCBI
HuRef2221,021,805 - 21,030,000 (+)NCBIHuRef
CHM1_12238,013,473 - 38,021,654 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8132548   PMID:10591208   PMID:14522954   PMID:14702039   PMID:15489334   PMID:15580268   PMID:16336786   PMID:17500066   PMID:18029348   PMID:18510874   PMID:19000834   PMID:21873635  
PMID:21897333   PMID:22658674   PMID:22939629   PMID:23223568   PMID:23376485   PMID:25640309   PMID:25921289   PMID:26324884   PMID:29459360   PMID:29540532   PMID:29724193   PMID:29791485  
PMID:29955894   PMID:31073040   PMID:31091453   PMID:31985874  


Genomics

Comparative Map Data
PDXP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2237,658,723 - 37,666,932 (+)EnsemblGRCh38hg38GRCh38
GRCh382237,658,723 - 37,666,932 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372238,054,730 - 38,062,939 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362236,384,683 - 36,392,885 (+)NCBINCBI36hg18NCBI36
Build 342236,379,237 - 36,387,439NCBI
Celera2221,856,602 - 21,864,785 (+)NCBI
Cytogenetic Map22q13.1NCBI
HuRef2221,021,805 - 21,030,000 (+)NCBIHuRef
CHM1_12238,013,473 - 38,021,654 (+)NCBICHM1_1
Pdxp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391578,796,342 - 78,803,717 (+)NCBIGRCm39mm39
GRCm39 Ensembl1578,798,119 - 78,803,717 (+)Ensembl
GRCm381578,912,160 - 78,919,517 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1578,913,919 - 78,919,517 (+)EnsemblGRCm38mm10GRCm38
MGSCv371578,744,349 - 78,749,947 (+)NCBIGRCm37mm9NCBIm37
MGSCv361578,741,174 - 78,746,772 (+)NCBImm8
MGSCv361579,638,039 - 79,643,637 (+)NCBImm8
Celera8110,672,269 - 110,684,203 (-)NCBICelera
Cytogenetic Map15E1NCBI
Pdxp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27110,472,515 - 110,477,963 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7110,472,515 - 110,477,963 (+)Ensembl
Rnor_6.07120,140,460 - 120,145,908 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7120,140,460 - 120,145,908 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07120,132,151 - 120,137,599 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47116,880,751 - 116,886,199 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7106,806,678 - 106,812,126 (+)NCBICelera
Cytogenetic Map7q34NCBI
Pdxp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541324,055,900 - 24,063,902 (+)NCBIChiLan1.0ChiLan1.0
PDXP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11026,945,751 - 26,952,234 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1026,946,838 - 26,952,217 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1026,900,405 - 26,906,862 (-)NCBI
ROS_Cfam_1.01027,737,639 - 27,744,136 (-)NCBI
UMICH_Zoey_3.11027,459,875 - 27,466,333 (-)NCBI
UNSW_CanFamBas_1.01027,768,698 - 27,775,155 (-)NCBI
UU_Cfam_GSD_1.01027,945,988 - 27,952,450 (-)NCBI
LOC101971587
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494510,410,176 - 10,416,350 (-)NCBI
SpeTri2.0NW_0049364923,420,590 - 3,426,764 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDXP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl510,162,642 - 10,169,512 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1510,162,642 - 10,169,726 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.257,735,323 - 7,737,336 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pdxp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475210,244,424 - 10,251,072 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH67  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372238,062,709 - 38,062,908UniSTSGRCh37
Build 362236,392,655 - 36,392,854RGDNCBI36
Celera2221,864,555 - 21,864,754RGD
Cytogenetic Map22q12.3UniSTS
HuRef2221,029,770 - 21,029,969UniSTS
WI-19614  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372238,062,557 - 38,062,807UniSTSGRCh37
Build 362236,392,503 - 36,392,753RGDNCBI36
Celera2221,864,403 - 21,864,653RGD
Cytogenetic Map22q12.3UniSTS
HuRef2221,029,618 - 21,029,868UniSTS
GeneMap99-GB4 RH Map22118.29UniSTS
Whitehead-RH Map22120.7UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1164
Count of miRNA genes:407
Interacting mature miRNAs:445
Transcripts:ENST00000215904, ENST00000403251
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 31 21 10 123 10 125 35 1256 6 35 73 3
Low 2318 2157 1544 558 1302 420 3165 1900 2425 270 1286 1305 150 1 898 2192 4 2
Below cutoff 90 815 153 51 486 31 1044 255 53 117 132 230 21 304 586 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000215904   ⟹   ENSP00000215904
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2237,658,723 - 37,666,932 (+)Ensembl
RefSeq Acc Id: ENST00000403251   ⟹   ENSP00000385336
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2237,664,911 - 37,666,932 (+)Ensembl
RefSeq Acc Id: NM_020315   ⟹   NP_064711
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382237,658,723 - 37,666,932 (+)NCBI
GRCh372238,054,737 - 38,062,939 (+)RGD
Build 362236,384,683 - 36,392,885 (+)NCBI Archive
Celera2221,856,602 - 21,864,785 (+)RGD
HuRef2221,021,805 - 21,030,000 (+)RGD
CHM1_12238,013,473 - 38,021,654 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_064711   ⟸   NM_020315
- UniProtKB: Q96GD0 (UniProtKB/Swiss-Prot),   A0A024R1I3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000215904   ⟸   ENST00000215904
RefSeq Acc Id: ENSP00000385336   ⟸   ENST00000403251

Promoters
RGD ID:6800499
Promoter ID:HG_KWN:42724
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000104105,   OTTHUMT00000319489
Position:
Human AssemblyChrPosition (strand)Source
Build 362236,383,716 - 36,385,717 (-)MPROMDB
RGD ID:13603988
Promoter ID:EPDNEW_H28178
Type:initiation region
Name:PDXP_1
Description:pyridoxal phosphatase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28179  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382237,658,723 - 37,658,783EPDNEW
RGD ID:13603990
Promoter ID:EPDNEW_H28179
Type:initiation region
Name:PDXP_2
Description:pyridoxal phosphatase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28178  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382237,659,205 - 37,659,265EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q12.3-13.1(chr22:35333993-38900177)x1 copy number loss See cases [RCV000051364] Chr22:35333993..38900177 [GRCh38]
Chr22:35729986..39296182 [GRCh37]
Chr22:34059986..37626128 [NCBI36]
Chr22:22q12.3-13.1
pathogenic
GRCh38/hg38 22q12.3-13.1(chr22:36552376-37669915)x1 copy number loss See cases [RCV000051365] Chr22:36552376..37669915 [GRCh38]
Chr22:36948423..38065922 [GRCh37]
Chr22:35278369..36395868 [NCBI36]
Chr22:22q12.3-13.1
pathogenic
GRCh38/hg38 22q12.3-13.1(chr22:36859030-39236985)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051366]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051366]|See cases [RCV000051366] Chr22:36859030..39236985 [GRCh38]
Chr22:37255072..39632990 [GRCh37]
Chr22:35585018..37962936 [NCBI36]
Chr22:22q12.3-13.1
pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3 copy number gain See cases [RCV000051682] Chr22:33768441..50739977 [GRCh38]
Chr22:34164428..51178405 [GRCh37]
Chr22:32494428..49525271 [NCBI36]
Chr22:22q12.3-13.33
pathogenic
GRCh38/hg38 22q12.3-13.1(chr22:36068124-38002382)x3 copy number gain See cases [RCV000051683] Chr22:36068124..38002382 [GRCh38]
Chr22:36464172..38398389 [GRCh37]
Chr22:34794118..36728335 [NCBI36]
Chr22:22q12.3-13.1
pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:37061769-50738932)x3 copy number gain See cases [RCV000051684] Chr22:37061769..50738932 [GRCh38]
Chr22:37457809..51177360 [GRCh37]
Chr22:35787755..49524226 [NCBI36]
Chr22:22q12.3-13.33
pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
GRCh38/hg38 22q13.1(chr22:37447222-39103680)x1 copy number loss See cases [RCV000141783] Chr22:37447222..39103680 [GRCh38]
Chr22:37843259..39499685 [GRCh37]
Chr22:36173205..37829631 [NCBI36]
Chr22:22q13.1
pathogenic
GRCh38/hg38 22q13.1(chr22:37537317-37803357)x3 copy number gain See cases [RCV000142655] Chr22:37537317..37803357 [GRCh38]
Chr22:37933324..38199364 [GRCh37]
Chr22:36263270..36529310 [NCBI36]
Chr22:22q13.1
uncertain significance
GRCh37/hg19 22q12.3-13.1(chr22:37090025-39601950)x3 copy number gain See cases [RCV000446037] Chr22:37090025..39601950 [GRCh37]
Chr22:22q12.3-13.1
uncertain significance
GRCh37/hg19 22q12.3-13.1(chr22:35680095-38098981)x1 copy number loss See cases [RCV000207444] Chr22:35680095..38098981 [GRCh37]
Chr22:22q12.3-13.1
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237518)x3 copy number gain See cases [RCV000240091] Chr22:16054691..51237518 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q12.3-13.33(chr22:35728929-51220961)x3 copy number gain See cases [RCV000240469] Chr22:35728929..51220961 [GRCh37]
Chr22:22q12.3-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51220902)x3 copy number gain See cases [RCV000446956] Chr22:16054691..51220902 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237463)x3 copy number gain See cases [RCV000448847] Chr22:16054691..51237463 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.1(chr22:37866631-39054815)x1 copy number loss See cases [RCV000511673] Chr22:37866631..39054815 [GRCh37]
Chr22:22q13.1
pathogenic
GRCh37/hg19 22q12.3-13.1(chr22:36877226-38548989)x1 copy number loss See cases [RCV000512008] Chr22:36877226..38548989 [GRCh37]
Chr22:22q12.3-13.1
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838) copy number gain See cases [RCV000510873] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q12.3-13.1(chr22:35674826-39466442)x3 copy number gain See cases [RCV000512385] Chr22:35674826..39466442 [GRCh37]
Chr22:22q12.3-13.1
likely pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838)x3 copy number gain See cases [RCV000512333] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054667-51243435)x3 copy number gain not provided [RCV000741689] Chr22:16054667..51243435 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.1(chr22:38054262-38079239)x0 copy number loss not provided [RCV000741958] Chr22:38054262..38079239 [GRCh37]
Chr22:22q13.1
benign
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51195728)x3 copy number gain not provided [RCV000741691] Chr22:16114244..51195728 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51211392)x3 copy number gain not provided [RCV000741692] Chr22:16114244..51211392 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q12.2-13.33(chr22:30654764-51197838)x3 copy number gain not provided [RCV001007181] Chr22:30654764..51197838 [GRCh37]
Chr22:22q12.2-13.33
pathogenic
GRCh37/hg19 22q13.1(chr22:38002218-38973070)x1 copy number loss not provided [RCV001007501] Chr22:38002218..38973070 [GRCh37]
Chr22:22q13.1
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888899-51197838)x3 copy number gain not provided [RCV000846344] Chr22:16888899..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16197005-51224252)x3 copy number gain See cases [RCV001263056] Chr22:16197005..51224252 [GRCh37]
Chr22:22q11.1-13.33
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:30259 AgrOrtholog
COSMIC PDXP COSMIC
Ensembl Genes ENSG00000241360 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000215904 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000385336 UniProtKB/TrEMBL
Ensembl Transcript ENST00000215904 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000403251 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1000 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000241360 GTEx
HGNC ID HGNC:30259 ENTREZGENE
Human Proteome Map PDXP Human Proteome Map
InterPro HAD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HAD-SF_hydro_IIA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HAD_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PGP_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:57026 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 57026 ENTREZGENE
OMIM 609246 OMIM
Pfam Hydrolase_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134882132 PharmGKB
PIRSF PGP-type_phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56784 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs HAD-SF-IIA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PGP_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A024R1I3 ENTREZGENE, UniProtKB/TrEMBL
  B1AHD3_HUMAN UniProtKB/TrEMBL
  PLPP_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9UGY2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-26 PDXP  pyridoxal phosphatase    pyridoxal (pyridoxine, vitamin B6) phosphatase  Symbol and/or name change 5135510 APPROVED
2011-09-01 PDXP  pyridoxal (pyridoxine, vitamin B6) phosphatase  PDXP  pyridoxal (pyridoxine, vitamin B6) phosphatase  Symbol and/or name change 5135510 APPROVED