PITHD1 (PITH domain containing 1) - Rat Genome Database

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Gene: PITHD1 (PITH domain containing 1) Homo sapiens
Analyze
Symbol: PITHD1
Name: PITH domain containing 1
RGD ID: 1603974
HGNC Page HGNC:25022
Description: Involved in positive regulation of DNA-templated transcription and positive regulation of megakaryocyte differentiation. Located in cytoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C1orf128; chromosome 1 open reading frame 128; HT014; PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1; PITH domain-containing protein 1; RP5-886K2.4; TXNL1 C-terminal like; TXNL1CL
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
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
GRCh38123,778,418 - 23,788,232 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl123,778,418 - 23,788,232 (+)EnsemblGRCh38hg38GRCh38
GRCh37124,104,908 - 24,114,722 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36123,977,470 - 23,987,309 (+)NCBINCBI36hg18NCBI36
Celera122,434,441 - 22,444,284 (+)NCBI
Cytogenetic Map1p36.11NCBI
HuRef122,356,450 - 22,366,299 (+)NCBIHuRef
CHM1_1124,217,668 - 24,227,511 (+)NCBICHM1_1
T2T-CHM13v2.0123,613,387 - 23,623,208 (+)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA,IEA)
nucleus  (HDA,IBA)
sperm cytoplasmic droplet  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:16169070   PMID:16236267   PMID:16344560   PMID:19322201   PMID:21630459   PMID:21873635   PMID:24981860   PMID:25134913   PMID:26186194   PMID:26344197  
PMID:26972000   PMID:27432908   PMID:28514442   PMID:29791485   PMID:31091453   PMID:31533654   PMID:31915251   PMID:31950832   PMID:32989298   PMID:33961781   PMID:34115363   PMID:34315543  
PMID:34728620  


Genomics

Comparative Map Data
PITHD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38123,778,418 - 23,788,232 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl123,778,418 - 23,788,232 (+)EnsemblGRCh38hg38GRCh38
GRCh37124,104,908 - 24,114,722 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36123,977,470 - 23,987,309 (+)NCBINCBI36hg18NCBI36
Celera122,434,441 - 22,444,284 (+)NCBI
Cytogenetic Map1p36.11NCBI
HuRef122,356,450 - 22,366,299 (+)NCBIHuRef
CHM1_1124,217,668 - 24,227,511 (+)NCBICHM1_1
T2T-CHM13v2.0123,613,387 - 23,623,208 (+)NCBI
Pithd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394135,702,913 - 135,714,555 (-)NCBIGRCm39mm39
GRCm39 Ensembl4135,702,771 - 135,714,575 (-)Ensembl
GRCm384135,975,602 - 135,987,244 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4135,975,460 - 135,987,264 (-)EnsemblGRCm38mm10GRCm38
MGSCv374135,531,517 - 135,543,159 (-)NCBIGRCm37mm9NCBIm37
MGSCv364135,247,681 - 135,259,321 (-)NCBImm8
Celera4134,176,727 - 134,188,088 (-)NCBICelera
Cytogenetic Map4D3NCBI
Pithd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25148,205,995 - 148,216,511 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5148,205,998 - 148,217,080 (-)Ensembl
Rnor_6.05154,322,562 - 154,333,080 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5154,322,551 - 154,332,940 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05158,087,413 - 158,097,947 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45154,758,057 - 154,768,487 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15154,768,000 - 154,778,565 (-)NCBI
Celera5146,612,852 - 146,623,219 (-)NCBICelera
Cytogenetic Map5q36NCBI
Pithd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554523,696,632 - 3,708,166 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554523,696,632 - 3,708,166 (+)NCBIChiLan1.0ChiLan1.0
PITHD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1123,954,980 - 23,964,085 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl123,954,980 - 23,964,085 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0122,970,081 - 22,979,841 (+)NCBIMhudiblu_PPA_v0panPan3
PITHD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1275,714,592 - 75,721,301 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl275,708,988 - 75,721,286 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha272,284,653 - 72,291,039 (-)NCBI
ROS_Cfam_1.0276,273,853 - 76,280,239 (-)NCBI
ROS_Cfam_1.0 Ensembl276,273,855 - 76,280,247 (-)Ensembl
UMICH_Zoey_3.1273,096,203 - 73,102,588 (-)NCBI
UNSW_CanFamBas_1.0274,102,852 - 74,109,279 (-)NCBI
UU_Cfam_GSD_1.0275,108,452 - 75,114,840 (-)NCBI
Pithd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505843,108,834 - 43,118,284 (+)NCBI
SpeTri2.0NW_0049364748,933,598 - 8,943,066 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PITHD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl681,591,018 - 81,598,868 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1681,590,868 - 81,598,874 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2675,427,987 - 75,435,969 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PITHD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120108,896,650 - 108,906,409 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20108,897,503 - 108,906,289 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660337,428,645 - 7,438,407 (+)NCBIVero_WHO_p1.0
Pithd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247648,325,683 - 8,337,185 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247648,325,680 - 8,337,185 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
G44729  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37124,114,031 - 24,114,190UniSTSGRCh37
Build 36123,986,618 - 23,986,777RGDNCBI36
Celera122,443,593 - 22,443,752RGD
Cytogenetic Map1p36.11UniSTS
HuRef122,365,608 - 22,365,767UniSTS
SHGC-74385  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37124,114,513 - 24,114,639UniSTSGRCh37
Build 36123,987,100 - 23,987,226RGDNCBI36
Celera122,444,075 - 22,444,201RGD
Cytogenetic Map1p36.11UniSTS
HuRef122,366,090 - 22,366,216UniSTS
TNG Radiation Hybrid Map110234.0UniSTS
GeneMap99-GB4 RH Map182.39UniSTS
NCBI RH Map1124.2UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:887
Count of miRNA genes:414
Interacting mature miRNAs:460
Transcripts:ENST00000246151, ENST00000374524, ENST00000415372
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 2439 2841 1723 621 1923 462 4357 2089 3713 418 1460 1613 175 1 1204 2788 6 2
Low 150 3 3 28 3 108 21 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000246151   ⟹   ENSP00000246151
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl123,778,418 - 23,788,232 (+)Ensembl
RefSeq Acc Id: ENST00000374524   ⟹   ENSP00000363648
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl123,785,192 - 23,788,232 (+)Ensembl
RefSeq Acc Id: ENST00000415372   ⟹   ENSP00000405957
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl123,779,357 - 23,786,378 (+)Ensembl
RefSeq Acc Id: NM_020362   ⟹   NP_065095
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38123,778,418 - 23,788,232 (+)NCBI
GRCh37124,104,876 - 24,114,722 (+)RGD
Build 36123,977,470 - 23,987,309 (+)NCBI Archive
Celera122,434,441 - 22,444,284 (+)RGD
HuRef122,356,450 - 22,366,299 (+)RGD
CHM1_1124,217,668 - 24,227,511 (+)NCBI
T2T-CHM13v2.0123,613,387 - 23,623,208 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011541804   ⟹   XP_011540106
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38123,778,418 - 23,788,232 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_065095   ⟸   NM_020362
- UniProtKB: Q9GZP4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011540106   ⟸   XM_011541804
- Peptide Label: isoform X1
- UniProtKB: B4DKP7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000363648   ⟸   ENST00000374524
RefSeq Acc Id: ENSP00000405957   ⟸   ENST00000415372
RefSeq Acc Id: ENSP00000246151   ⟸   ENST00000246151
Protein Domains
PITH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9GZP4-F1-model_v2 AlphaFold Q9GZP4 1-211 view protein structure

Promoters
RGD ID:6854484
Promoter ID:EPDNEW_H407
Type:initiation region
Name:PITHD1_1
Description:PITH domain containing 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38123,778,418 - 23,778,478EPDNEW
RGD ID:6784747
Promoter ID:HG_KWN:1333
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:OTTHUMT00000008241,   OTTHUMT00000008243
Position:
Human AssemblyChrPosition (strand)Source
Build 36123,977,171 - 23,977,671 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_007260.2(LYPLA2):c.74C>T (p.Ala25Val) single nucleotide variant Malignant melanoma [RCV000064612] Chr1:23792756 [GRCh38]
Chr1:24119246 [GRCh37]
Chr1:23991833 [NCBI36]
Chr1:1p36.11
not provided
NM_007260.2(LYPLA2):c.75C>T (p.Ala25=) single nucleotide variant Malignant melanoma [RCV000064613] Chr1:23792757 [GRCh38]
Chr1:24119247 [GRCh37]
Chr1:23991834 [NCBI36]
Chr1:1p36.11
not provided
Single allele complex Ductal breast carcinoma [RCV000207058] Chr1:909238..24706269 [GRCh37]
Chr1:1p36.33-36.11
uncertain significance
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12
likely benign
chr1:17555508-24706269 complex variant complex Ductal breast carcinoma [RCV000207266] Chr1:17555508..24706269 [GRCh37]
Chr1:1p36.13-36.11
uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.22-21.1(chr1:103343285-103455144)x3 copy number gain Global developmental delay [RCV000787285] Chr1:103343285..103455144 [GRCh37]
Chr1:1p36.22-21.1
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:25022 AgrOrtholog
COSMIC PITHD1 COSMIC
Ensembl Genes ENSG00000057757 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000246151 ENTREZGENE
  ENSP00000246151.4 UniProtKB/Swiss-Prot
  ENSP00000363648 ENTREZGENE
  ENSP00000363648.1 UniProtKB/TrEMBL
  ENSP00000405957.1 UniProtKB/TrEMBL
Ensembl Transcript ENST00000246151 ENTREZGENE
  ENST00000246151.9 UniProtKB/Swiss-Prot
  ENST00000374524 ENTREZGENE
  ENST00000374524.1 UniProtKB/TrEMBL
  ENST00000415372.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.470 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000057757 GTEx
HGNC ID HGNC:25022 ENTREZGENE
Human Proteome Map PITHD1 Human Proteome Map
InterPro Galactose-bd-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PITH1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PITH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PITH_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:57095 UniProtKB/Swiss-Prot
NCBI Gene 57095 ENTREZGENE
OMIM 618784 OMIM
PANTHER PTHR12175 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PITH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142672446 PharmGKB
PROSITE PITH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B4DKP7 ENTREZGENE, UniProtKB/TrEMBL
  PITH1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  X6R8S9_HUMAN UniProtKB/TrEMBL
  X6RHB9_HUMAN UniProtKB/TrEMBL
UniProt Secondary B2R7J4 UniProtKB/Swiss-Prot
  Q5QPN6 UniProtKB/Swiss-Prot
  Q5QPN7 UniProtKB/Swiss-Prot
  Q9NRI8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-12 PITHD1  PITH domain containing 1    PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1  Symbol and/or name change 5135510 APPROVED
2011-07-27 PITHD1  PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1  C1orf128  chromosome 1 open reading frame 128  Symbol and/or name change 5135510 APPROVED