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Gene: Phf5a (PHD finger protein 5A) Rattus norvegicus

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Symbol:

Phf5a

Name:

PHD finger protein 5A

RGD ID:

621555

Description:

Predicted to enable RNA binding activity and zinc ion binding activity. Involved in positive regulation of DNA-templated transcription. Predicted to be located in nuclear matrix and nuclear speck. Predicted to be part of U12-type spliceosomal complex; U2 snRNP; and U2-type precatalytic spliceosome. Orthologous to human PHF5A (PHD finger protein 5A); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

Ac2-246; Loc192246; PHD finger-like domain protein 5A; PHD finger-like domain-containing protein 5A; SF3b14b; splicing factor 3B-associated 14 kDa protein; transcription factor INI

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PHF5A (PHD finger protein 5A)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Phf5a (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Phf5a (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PHF5A (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PHF5A (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Phf5a (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PHF5A (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PHF5A (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Phf5a (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Phf5a (PHD finger protein 5A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Phf5a (PHD finger protein 5A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	PHF5A (PHD finger protein 5A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	phf5a (PHD finger protein 5A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	RDS3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Phf5a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	phf-5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	phf5a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	phf5a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	115,258,609 - 115,265,174 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	7	115,258,609 - 115,265,174 (-)	Ensembl				GRCr8
mRatBN7.2	7	113,378,469 - 113,385,035 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	113,378,471 - 113,385,460 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	7	115,140,892 - 115,147,461 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	117,364,388 - 117,370,956 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	117,333,828 - 117,340,397 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	123,095,286 - 123,101,851 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	123,095,288 - 123,101,869 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	7	123,070,681 - 123,077,246 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	7	120,216,581 - 120,223,146 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	7	109,697,147 - 109,703,712 (-)	NCBI		Celera
RGSC_v3.1	7	120,250,812 - 120,257,376 (-)	NCBI
Cytogenetic Map	7	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4,6-trinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (EXP)

amiodarone (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

cadmium dichloride (ISO)

chlorpyrifos (ISO)

clobetasol (ISO)

crocidolite asbestos (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

fenthion (ISO)

fipronil (EXP)

flavonoids (EXP)

flutamide (EXP)

folic acid (ISO)

FR900359 (ISO)

gentamycin (EXP)

indometacin (ISO)

ivermectin (ISO)

lead(0) (ISO)

nefazodone (EXP)

nimesulide (EXP)

paracetamol (ISO)

phenol red (ISO)

picoxystrobin (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

rotenone (EXP)

silicon dioxide (ISO)

sodium arsenite (ISO)

tamoxifen (ISO)

tetrachloromethane (ISO)

toluene (EXP)

trichostatin A (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

Triptolide (EXP)

triptonide (ISO)

tungsten (ISO)

tunicamycin (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

DNA-templated transcription (IEA)

mRNA processing (IEA)

mRNA splicing, via spliceosome (IBA,IEA,ISO,ISS)

positive regulation of DNA-templated transcription (IDA)

RNA splicing (IEA)

stem cell differentiation (IEA,ISO)

Cellular Component

nuclear matrix (IEA,ISO)

nuclear speck (IEA,ISO,ISS)

nucleoplasm (IEA,ISO)

nucleus (IC,IEA,ISO)

precatalytic spliceosome (IBA)

spliceosomal complex (IEA)

U12-type spliceosomal complex (IEA,ISO)

U2 snRNP (IBA,IEA,ISO,ISS)

U2-type precatalytic spliceosome (IEA,ISO)

U2-type spliceosomal complex (IEA,ISO)

Molecular Function

DNA binding (IEA)

metal ion binding (IEA)

protein binding (ISO)

RNA binding (IEA,ISO)

zinc ion binding (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

spliceosome pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
4.	Ini, a small nuclear protein that enhances the response of the connexin43 gene to estrogen.	Oltra E, etal., Endocrinology 2003 Jul;144(7):3148-58.
5.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
6.	GOA pipeline	RGD automated data pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12054543	PMID:12234937	PMID:12477932	PMID:15146077	PMID:15489334	PMID:18758164	PMID:22658674	PMID:22681889	PMID:27720643	PMID:27749823	PMID:28541300	PMID:29360106

Genomics

Comparative Map Data

Phf5a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	115,258,609 - 115,265,174 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	7	115,258,609 - 115,265,174 (-)	Ensembl				GRCr8
mRatBN7.2	7	113,378,469 - 113,385,035 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	113,378,471 - 113,385,460 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	7	115,140,892 - 115,147,461 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	117,364,388 - 117,370,956 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	117,333,828 - 117,340,397 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	123,095,286 - 123,101,851 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	123,095,288 - 123,101,869 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	7	123,070,681 - 123,077,246 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	7	120,216,581 - 120,223,146 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	7	109,697,147 - 109,703,712 (-)	NCBI		Celera
RGSC_v3.1	7	120,250,812 - 120,257,376 (-)	NCBI
Cytogenetic Map	7	q34	NCBI

PHF5A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	22	41,459,717 - 41,468,692 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	22	41,459,705 - 41,468,711 (-)	Ensembl			hg38	GRCh38
GRCh37	22	41,855,721 - 41,864,696 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	22	40,185,667 - 40,194,654 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	22	40,180,221 - 40,189,208	NCBI
Celera	22	25,662,105 - 25,671,092 (-)	NCBI		Celera
Cytogenetic Map	22	q13.2	NCBI
HuRef	22	24,821,678 - 24,830,510 (-)	NCBI		HuRef
CHM1_1	22	41,815,604 - 41,824,591 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	22	41,938,569 - 41,947,547 (-)	NCBI		T2T-CHM13v2.0

Phf5a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	81,748,717 - 81,756,093 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	15	81,748,721 - 81,756,112 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	15	81,864,516 - 81,871,892 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	81,864,520 - 81,871,911 (-)	Ensembl			mm10	GRCm38
MGSCv37	15	81,694,946 - 81,702,322 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	15	81,692,572 - 81,699,158 (-)	NCBI		MGSCv36	mm8
Celera	15	83,983,598 - 83,990,971 (-)	NCBI		Celera
Cytogenetic Map	15	E1	NCBI
cM Map	15	38.26	NCBI

Phf5a
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955413	27,018,730 - 27,026,937 (-)	Ensembl
ChiLan1.0	NW_004955413	27,018,730 - 27,026,937 (-)	NCBI	ChiLan1.0	ChiLan1.0

PHF5A
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	23	51,290,050 - 51,299,113 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	22	53,989,315 - 53,998,375 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	22	22,353,811 - 22,362,899 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	22	40,441,275 - 40,450,174 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	22	40,441,275 - 40,450,174 (-)	Ensembl			panPan2	panpan1.1

PHF5A
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	23,798,854 - 23,809,024 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	23,798,969 - 23,808,865 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	23,731,535 - 23,741,497 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	24,543,712 - 24,553,684 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	24,543,361 - 24,554,077 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	24,260,490 - 24,270,455 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	24,581,379 - 24,591,328 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	24,755,822 - 24,765,792 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Phf5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	7,442,447 - 7,451,501 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936492	452,628 - 461,910 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936492	452,628 - 461,915 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PHF5A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	7,071,484 - 7,081,407 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	5	7,071,145 - 7,080,046 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PHF5A
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	19	23,998,277 - 24,008,504 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	19	23,998,127 - 24,008,173 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666045	101,410,244 - 101,420,144 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Phf5a
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624752	7,114,274 - 7,123,706 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624752	7,114,239 - 7,123,706 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Phf5a
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	1	251,602,907 - 251,609,702 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Phf5a
40 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	45
Count of miRNA genes:	42
Interacting mature miRNAs:	43
Transcripts:	ENSRNOT00000005837
Prediction methods:	Miranda, Rnahybrid
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.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1300179	Kidm5	Kidney mass QTL 5	3.51		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	7	92388565	119280177	Rat
1331728	Bp214	Blood pressure QTL 214	2.825		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	82111245	123048330	Rat
1331731	Bp216	Blood pressure QTL 216	2.851		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	104186212	135371468	Rat
70159	Bp61	Blood pressure QTL 61		0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	73618702	118618702	Rat
631687	Hcas1	Hepatocarcinoma susceptibility QTL 1	3.9	0.001	liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	7	93302009	131686183	Rat
61397	Bw17	Body weight QTL 17	6.3		body mass (VT:0001259)	body weight (CMO:0000012)	7	95485047	137014596	Rat
631504	Cm27	Cardiac mass QTL 27	3.45		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	7	46307490	127866166	Rat
634322	Bw12	Body weight QTL 12	0		body mass (VT:0001259)	body weight (CMO:0000012)	7	85043242	130043242	Rat
70173	Niddm19	Non-insulin dependent diabetes mellitus QTL 19	4.33	0.00005	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	7	85497398	130497398	Rat
1549899	Stresp8	Stress response QTL 8	4.37	0.0008	stress-related behavior trait (VT:0010451)	defensive burying duration (CMO:0001961)	7	92362341	137014596	Rat
2317052	Aia17	Adjuvant induced arthritis QTL 17	2.13		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	7	83626689	128626689	Rat
631529	Tls2	T-lymphoma susceptibility QTL 2	0	0.001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	7	82111382	132099989	Rat
731176	Glom5	Glomerulus QTL 5	2.5	0.0035	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	7	98549867	137014596	Rat
7411607	Foco15	Food consumption QTL 15		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	7	77807807	122807807	Rat
631201	Panci1	Pancreas inflammation QTL 1	0	0.001	pancreas integrity trait (VT:0010560)	percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)	7	73557047	118557047	Rat
634336	Anxrr17	Anxiety related response QTL 17	3.66		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	1509236	116977875	Rat
1331768	Kidm10	Kidney mass QTL 10	4.62096		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	7	82111245	123048330	Rat
61357	Bp38	Blood pressure QTL 38	1.6	0.052	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	40540077	123682549	Rat
2313102	Bmd79	Bone mineral density QTL 79	2.3	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	7	96700404	118618702	Rat
2316947	Rf58	Renal function QTL 58	7.8		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	7	49682832	115766396	Rat
1331748	Bp215	Blood pressure QTL 215	4.043		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	110725024	135371468	Rat
10450862	Kidm55	Kidney mass QTL 55	4.9		kidney mass (VT:0002707)	kidney weight (CMO:0000081)	7	72725037	117725037	Rat
61428	Scl3	Serum cholesterol level QTL 3	3.2		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	7	100548246	137014596	Rat
1331746	Kidm9	Kidney mass QTL 9	3.934		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	7	82111245	134948181	Rat
10450856	Livw4	Liver weight QTL 4	3.8		liver mass (VT:0003402)	liver weight (CMO:0000092)	7	72725037	117725037	Rat
7411654	Foco25	Food consumption QTL 25	9.3	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	7	77807807	122807807	Rat
2316955	Stl24	Serum triglyceride level QTL 24	7.1		blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	7	49682832	115766396	Rat
10402855	Bp379	Blood pressure QTL 379		0.21	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	78682549	123682549	Rat
2316952	Pur22	Proteinuria QTL 22	5.2		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	7	49682832	115766396	Rat
631540	Bw9	Body weight QTL 9	4.5		body mass (VT:0001259)	body weight (CMO:0000012)	7	71621154	119349044	Rat
1358891	Bp265	Blood pressure QTL 265	2.21		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	71827901	136544683	Rat

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_138888	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC096601	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF495522	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY321339	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC063807	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC168144	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473950	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223455	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000007	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000005837 ⟹ ENSRNOP00000005837

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	7	115,258,609 - 115,265,174 (-)	Ensembl
mRatBN7.2 Ensembl	7	113,378,471 - 113,385,035 (-)	Ensembl
Rnor_6.0 Ensembl	7	123,095,288 - 123,101,869 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000090984 ⟹ ENSRNOP00000073368

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	7	123,095,810 - 123,101,851 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000113004 ⟹ ENSRNOP00000095542

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	7	113,378,471 - 113,385,460 (-)	Ensembl

RefSeq Acc Id:

NM_138888 ⟹ NP_620243

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	7	115,258,609 - 115,265,174 (-)	NCBI
mRatBN7.2	7	113,378,469 - 113,385,035 (-)	NCBI
Rnor_6.0	7	123,095,286 - 123,101,851 (-)	NCBI
Rnor_5.0	7	123,070,681 - 123,077,246 (-)	NCBI
RGSC_v3.4	7	120,216,581 - 120,223,146 (-)	RGD
Celera	7	109,697,147 - 109,703,712 (-)	RGD

Sequence:

show sequence

ATGGCTAAACATCATCCAGATTTGATTTTCTGCCGCAAGCAGGCTGGTGTAGCTATCGGAAGAC
TGTGTGAAAAATGTGATGGCAAATGTGTGATCTGCGATTCCTACGTGCGTCCCTGTACCCTGGT
TCGCATATGTGATGAGTGTAACTATGGATCCTACCAGGGCCGCTGCGTGATCTGTGGAGGTCCC
GGAGTCTCTGATGCCTACTATTGTAAAGAGTGCACCATTCAGGAGAAGGATAGAGATGGTTGCC
CAAAGATTGTCAATTTGGGGAGCTCTAAGACAGACCTGTTCTATGAGCGCAAAAAATACGGTTT
CAAGAAGAGGTGATGGCTGGGTGGCTCCTTCCTCCCCCATCGAACTGCTGCAGCTTCCAGGAAA
GACGCCTACTACCACCAGCAGAAAGGGAACGGAGTTCAGAGTGTCACCAGAGCAGCCTGCTAGT
GCTAGCGCCCTGGCCCCTGCCACCCCTTCTTTCCCTTCCCCGTGTTGCTGAGATGGAAGCGAGT
TCCCACACAGCAAGCACCCTTGCAGACTGGAGGAGATGTCACTCACTTAGTCTGTAGTTTCCTT
TTGTTTTTAGTTGAAAAGCAAGGCTCTGCTCTCCACATCGATCCTTTCCACTACAAAAGCTTCA
GAGCACGTCAGTATACCGCCTTGACAAAACTGTCATTCAGAAGTGTGCTCTTGCAGCAGCTATG
ATGGGGTTGTCCTGGACCCTCAGGGTGGCCAGGTGCCATCAGAACAGTAATGTGATGTGACATT
TCCCAGGTGGTGCTGGGTTCATTGTTAATTTCCTTCTTATAAATTGGAAGTTTCTGTTATCCTA
ATAAAGTTGTCTGTATTTCTGGAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_620243	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68144	(Get FASTA)	NCBI Sequence Viewer
	AAM14623	(Get FASTA)	NCBI Sequence Viewer
	AAP86271	(Get FASTA)	NCBI Sequence Viewer
	EDM15698	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000095542.1
GenBank Protein	P83871	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_620243 ⟸ NM_138888
- UniProtKB:	P83871 (UniProtKB/Swiss-Prot), B4F759 (UniProtKB/TrEMBL), A0A8L2Q323 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGP GVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR hide sequence

Ensembl Acc Id:

ENSRNOP00000073368 ⟸ ENSRNOT00000090984

Ensembl Acc Id:

ENSRNOP00000005837 ⟸ ENSRNOT00000005837

Ensembl Acc Id:

ENSRNOP00000095542 ⟸ ENSRNOT00000113004

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P83871-F1-model_v2	AlphaFold	P83871	1-110	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13695518

Promoter ID:

EPDNEW_R6042

Type:

multiple initiation site

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:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	7	123,101,880 - 123,101,940	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621555	AgrOrtholog
BioCyc Gene	G2FUF-32660	BioCyc
Ensembl Genes	ENSRNOG00000024170	Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000113004.1	UniProtKB/Swiss-Prot
InterPro	PHF5	UniProtKB/Swiss-Prot
KEGG Report	rno:192246	UniProtKB/Swiss-Prot
NCBI Gene	192246	ENTREZGENE
PANTHER	PTHR13120	UniProtKB/Swiss-Prot
Pfam	PHF5	UniProtKB/Swiss-Prot
PhenoGen	Phf5a	PhenoGen
PIRSF	PHF5	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000024170	RatGTEx
UniProt	A0A8L2Q323	ENTREZGENE, UniProtKB/TrEMBL
	B4F759	ENTREZGENE, UniProtKB/TrEMBL
	P83871	ENTREZGENE, UniProtKB/Swiss-Prot
	Q7TPJ6_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2006-03-30	Phf5a	PHD finger protein 5A		transcription factor INI	Name updated	1299863	APPROVED
2004-09-10	Phf5a	transcription factor INI	Loc192246		Symbol and Name updated	1299863	APPROVED
2002-08-07	Loc192246	transcription factor INI			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains three zinc-finger motifs and a leucine zipper	633219
gene_expression	ubiquitously expressed	633219
gene_expression	ubiquitously expressed	633219
gene_protein	110 amino acids	633219

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)