PHF5A (PHD finger protein 5A) - Rat Genome Database

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Gene: PHF5A (PHD finger protein 5A) Homo sapiens
Analyze
Symbol: PHF5A
Name: PHD finger protein 5A
RGD ID: 1348043
HGNC Page HGNC
Description: Enables RNA binding activity and zinc ion binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U12-type spliceosomal complex; U2 snRNP; and U2-type precatalytic spliceosome.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: bK223H9.2; INI; MGC1346; PHD finger-like domain protein 5A; PHD finger-like domain-containing protein 5A; PHD-finger 5a; Rds3; SAP14b; SF3b14b; SF3B7; splicing factor 3B associated 14 kDa protein; splicing factor 3b, subunit 7; splicing factor 3B-associated 14 kDa protein
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC100289442   PHF5CP   PHF5DP   PHF5EP   PHF5FP   PHF5GP   PHF5HP  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2241,459,717 - 41,468,692 (-)EnsemblGRCh38hg38GRCh38
GRCh382241,459,717 - 41,468,692 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372241,855,721 - 41,864,696 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,185,667 - 40,194,654 (-)NCBINCBI36hg18NCBI36
Build 342240,180,221 - 40,189,208NCBI
Celera2225,662,105 - 25,671,092 (-)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2224,821,678 - 24,830,510 (-)NCBIHuRef
CHM1_12241,815,604 - 41,824,591 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function
DNA binding  (IEA)
protein binding  (IPI,ISO)
RNA binding  (HDA,IDA)
zinc ion binding  (IDA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Pipeline to import KEGG annotations from KEGG into RGD
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10591208   PMID:12054543   PMID:12226669   PMID:12234937   PMID:12477932   PMID:15146077   PMID:15461802   PMID:15489334   PMID:17332742   PMID:18076038   PMID:19394292   PMID:20360068  
PMID:21873635   PMID:21988832   PMID:22365833   PMID:22658674   PMID:22681889   PMID:22939629   PMID:23602568   PMID:23651857   PMID:24457600   PMID:24705354   PMID:24981860   PMID:25963833  
PMID:26244496   PMID:26344197   PMID:26496610   PMID:26527279   PMID:27634302   PMID:27684187   PMID:27720643   PMID:28077445   PMID:28330616   PMID:28541300   PMID:28561026   PMID:29128334  
PMID:29298432   PMID:29360106   PMID:29566713   PMID:29700004   PMID:29802200   PMID:29845934   PMID:30033366   PMID:30404004   PMID:30463901   PMID:30766880   PMID:30804502   PMID:30890647  
PMID:30932358   PMID:30948266   PMID:31054974   PMID:31076518   PMID:31091453   PMID:31182584   PMID:31753913   PMID:31980649   PMID:32129710   PMID:32228507   PMID:32416067   PMID:32694731  
PMID:32780723   PMID:32807901   PMID:32814053   PMID:33226137   PMID:33277362  


Genomics

Comparative Map Data
PHF5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2241,459,717 - 41,468,692 (-)EnsemblGRCh38hg38GRCh38
GRCh382241,459,717 - 41,468,692 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372241,855,721 - 41,864,696 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,185,667 - 40,194,654 (-)NCBINCBI36hg18NCBI36
Build 342240,180,221 - 40,189,208NCBI
Celera2225,662,105 - 25,671,092 (-)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2224,821,678 - 24,830,510 (-)NCBIHuRef
CHM1_12241,815,604 - 41,824,591 (-)NCBICHM1_1
Phf5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391581,748,717 - 81,756,093 (-)NCBIGRCm39mm39
GRCm39 Ensembl1581,748,721 - 81,756,112 (-)Ensembl
GRCm381581,864,516 - 81,871,892 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1581,864,520 - 81,871,911 (-)EnsemblGRCm38mm10GRCm38
MGSCv371581,694,946 - 81,702,322 (-)NCBIGRCm37mm9NCBIm37
MGSCv361581,692,572 - 81,699,158 (-)NCBImm8
Celera1583,983,598 - 83,990,971 (-)NCBICelera
Cytogenetic Map15E1NCBI
Phf5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,378,469 - 113,385,035 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,378,471 - 113,385,460 (-)Ensembl
Rnor_6.07123,095,286 - 123,101,851 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,095,288 - 123,101,869 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,070,681 - 123,077,246 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,216,581 - 120,223,146 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,250,812 - 120,257,376 (-)NCBI
Celera7109,697,147 - 109,703,712 (-)NCBICelera
Cytogenetic Map7q34NCBI
Phf5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541327,018,730 - 27,026,937 (-)NCBIChiLan1.0ChiLan1.0
PHF5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12240,441,275 - 40,450,174 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2240,441,275 - 40,450,174 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02222,353,811 - 22,362,899 (-)NCBIMhudiblu_PPA_v0panPan3
PHF5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11023,798,854 - 23,809,024 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1023,798,969 - 23,808,865 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1023,731,535 - 23,741,497 (+)NCBI
ROS_Cfam_1.01024,543,712 - 24,553,684 (+)NCBI
UMICH_Zoey_3.11024,260,490 - 24,270,455 (+)NCBI
UNSW_CanFamBas_1.01024,581,379 - 24,591,328 (+)NCBI
UU_Cfam_GSD_1.01024,755,822 - 24,765,792 (+)NCBI
Phf5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049457,442,447 - 7,451,501 (+)NCBI
SpeTri2.0NW_004936492452,628 - 461,915 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHF5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl57,071,271 - 7,082,696 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.157,071,145 - 7,080,046 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PHF5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11923,998,277 - 24,008,504 (-)NCBI
ChlSab1.1 Ensembl1923,998,127 - 24,008,173 (-)Ensembl
Vero_WHO_p1.0NW_023666045101,410,244 - 101,420,144 (+)NCBI
Phf5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247527,114,239 - 7,123,706 (+)NCBI

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:882
Count of miRNA genes:565
Interacting mature miRNAs:625
Transcripts:ENST00000216252, ENST00000459687, ENST00000491254
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 adipose tissue appendage entire extraembryonic component
High
Medium 2431 2412 1684 586 1616 428 4351 2010 3395 404 1448 1607 171 1204 2784 4
Low 1 572 39 36 332 36 4 183 313 14 1 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000216252   ⟹   ENSP00000216252
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2241,459,717 - 41,468,692 (-)Ensembl
RefSeq Acc Id: ENST00000459687
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2241,460,303 - 41,468,625 (-)Ensembl
RefSeq Acc Id: ENST00000491254
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2241,460,432 - 41,468,499 (-)Ensembl
RefSeq Acc Id: NM_032758   ⟹   NP_116147
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382241,459,717 - 41,468,692 (-)NCBI
GRCh372241,855,721 - 41,864,708 (-)RGD
Build 362240,185,667 - 40,194,654 (-)NCBI Archive
Celera2225,662,105 - 25,671,092 (-)RGD
HuRef2224,821,678 - 24,830,510 (-)RGD
CHM1_12241,815,604 - 41,824,591 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_116147   ⟸   NM_032758
- UniProtKB: Q7RTV0 (UniProtKB/Swiss-Prot),   A0A024R1U2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000216252   ⟸   ENST00000216252

Promoters
RGD ID:6799654
Promoter ID:HG_KWN:42986
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:NM_001098,   OTTHUMT00000259153,   OTTHUMT00000320686,   OTTHUMT00000320687,   OTTHUMT00000320688,   UC003BAD.1
Position:
Human AssemblyChrPosition (strand)Source
Build 362240,193,851 - 40,195,152 (+)MPROMDB
RGD ID:13604258
Promoter ID:EPDNEW_H28313
Type:initiation region
Name:PHF5A_1
Description:PHD finger protein 5A
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
GRCh382241,468,678 - 41,468,738EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 22q12.3-13.33(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 22q13.1-13.33(chr22:40202014-50735806)x3 copy number gain See cases [RCV000134513] Chr22:40202014..50735806 [GRCh38]
Chr22:40598018..51174234 [GRCh37]
Chr22:38927964..49521100 [NCBI36]
Chr22:22q13.1-13.33
pathogenic
GRCh38/hg38 22q13.2(chr22:41277822-42414957)x3 copy number gain See cases [RCV000136785] Chr22:41277822..42414957 [GRCh38]
Chr22:41673826..42810963 [GRCh37]
Chr22:40003772..41140907 [NCBI36]
Chr22:22q13.2
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 22q13.1-13.33(chr22:40425714-51220961)x3 copy number gain See cases [RCV000240459] Chr22:40425714..51220961 [GRCh37]
Chr22:22q13.1-13.33
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 22q13.2(chr22:41835094-42756616)x3 copy number gain See cases [RCV000511241] Chr22:41835094..42756616 [GRCh37]
Chr22:22q13.2
uncertain significance
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 22q11.1-13.33(chr22:16888900-51197838)x3 copy number gain See cases [RCV000512333] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
NC_000022.11:g.(?_41301335)_(42070317_?)del deletion Common variable immunodeficiency 4 [RCV000648330] Chr22:41301335..42070317 [GRCh38]
Chr22:41697339..42466321 [GRCh37]
Chr22:22q13.2
uncertain significance
GRCh37/hg19 22q13.2(chr22:41849322-42756616)x3 copy number gain not provided [RCV000684486] Chr22:41849322..42756616 [GRCh37]
Chr22:22q13.2
likely 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 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 22q13.2(chr22:41742988-41946225)x3 copy number gain not provided [RCV000848205] Chr22:41742988..41946225 [GRCh37]
Chr22:22q13.2
uncertain significance
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 22q13.1-13.33(chr22:40502364-51197838)x3 copy number gain not provided [RCV001007502] Chr22:40502364..51197838 [GRCh37]
Chr22:22q13.1-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:41853620-42385978)x1 copy number loss not provided [RCV001258783] Chr22:41853620..42385978 [GRCh37]
Chr22:22q13.2
uncertain significance
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
NC_000022.10:g.(?_41697339)_(42466321_?)del deletion Common variable immunodeficiency 4 [RCV001305750] Chr22:41697339..42466321 [GRCh37]
Chr22:22q13.2
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:18000 AgrOrtholog
COSMIC PHF5A COSMIC
Ensembl Genes ENSG00000100410 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000216252 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000216252 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000100410 GTEx
HGNC ID HGNC:18000 ENTREZGENE
Human Proteome Map PHF5A Human Proteome Map
InterPro PHF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:84844 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 84844 ENTREZGENE
OMIM 617846 OMIM
PANTHER PTHR13120 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PHF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134876104 PharmGKB
PIRSF PHF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A024R1U2 ENTREZGENE, UniProtKB/TrEMBL
  PHF5A_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9UH06 UniProtKB/Swiss-Prot