Phf13 (PHD finger protein 13) - Rat Genome Database

Name: Phf13
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Phf13 (PHD finger protein 13) Rattus norvegicus

Analyze

Symbol:

Phf13

Name:

PHD finger protein 13

RGD ID:

1308145

Description:

Predicted to enable chromatin binding activity; chromatin-protein adaptor activity; and methylated histone binding activity. Predicted to be involved in mitotic chromosome condensation and regulation of DNA repair. Predicted to be active in nucleus. Orthologous to human PHF13 (PHD finger protein 13); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; endosulfan.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC313742

RGD Orthologs

Alliance Genes

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):	PHF13 (PHD finger protein 13)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Phf13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Phf13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PHF13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PHF13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Phf13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PHF13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PHF13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Phf13 (PHD finger protein 13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PHF13 (PHD finger protein 13)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Mus musculus (house mouse):	Phf13 (PHD finger protein 13)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	phf13 (PHD finger protein 13)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	phf13	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	167,777,303 - 167,784,077 (-)	NCBI		GRCr8
mRatBN7.2	5	162,494,574 - 162,501,350 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	162,494,573 - 162,501,350 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	165,197,659 - 165,204,444 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	167,018,507 - 167,025,304 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	166,980,706 - 166,987,503 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	169,161,412 - 169,167,831 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	169,161,412 - 169,167,831 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	172,719,997 - 172,726,441 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	169,215,834 - 169,222,883 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	169,226,020 - 169,234,653 (-)	NCBI
Celera	5	160,727,367 - 160,734,068 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

chromosome 1p36 deletion syndrome (ISO)

genetic disease (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

2-methylcholine (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (ISO)

antirheumatic drug (ISO)

atrazine (ISO)

benzene (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

caffeine (ISO)

chlordecone (ISO)

chlorpyrifos (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dibutyl phthalate (ISO)

dorsomorphin (ISO)

endosulfan (EXP)

ethanol (ISO)

folic acid (ISO)

formaldehyde (ISO)

FR900359 (ISO)

inulin (ISO)

ketamine (EXP)

methamphetamine (EXP)

methyl methanesulfonate (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

SB 431542 (ISO)

Soman (EXP)

thioacetamide (EXP)

trichostatin A (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chromatin organization (IEA)

chromosome segregation (ISO)

mitotic cell cycle (ISO)

mitotic chromosome condensation (IBA,ISO)

regulation of DNA repair (ISO)

Cellular Component

nucleus (IBA,ISO)

Molecular Function

chromatin binding (IBA,ISO)

chromatin-protein adaptor activity (ISO)

metal ion binding (IEA)

methylated histone binding (ISO)

protein binding (ISO)

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.	GOA pipeline	RGD automated data pipeline
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:19638409

Genomics

Comparative Map Data

Phf13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	167,777,303 - 167,784,077 (-)	NCBI		GRCr8
mRatBN7.2	5	162,494,574 - 162,501,350 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	162,494,573 - 162,501,350 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	165,197,659 - 165,204,444 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	167,018,507 - 167,025,304 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	166,980,706 - 166,987,503 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	169,161,412 - 169,167,831 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	169,161,412 - 169,167,831 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	172,719,997 - 172,726,441 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	169,215,834 - 169,222,883 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	169,226,020 - 169,234,653 (-)	NCBI
Celera	5	160,727,367 - 160,734,068 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

PHF13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	6,613,731 - 6,624,030 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	6,613,731 - 6,624,030 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	6,673,791 - 6,684,090 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	6,596,332 - 6,606,643 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	6,608,010 - 6,618,322	NCBI
Celera	1	5,787,615 - 5,797,954 (+)	NCBI		Celera
Cytogenetic Map	1	p36.31	NCBI
HuRef	1	5,821,676 - 5,831,583 (+)	NCBI		HuRef
CHM1_1	1	6,662,474 - 6,672,816 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	6,139,395 - 6,149,694 (+)	NCBI		T2T-CHM13v2.0

Phf13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	152,074,088 - 152,080,636 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	152,074,090 - 152,080,715 (-)	Ensembl		GRCm39 Ensembl
GRCm38	4	151,989,631 - 151,996,179 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	151,989,633 - 151,996,258 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	151,363,740 - 151,370,288 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	150,833,433 - 150,836,362 (-)	NCBI		MGSCv36	mm8
Celera	4	154,274,605 - 154,281,210 (-)	NCBI		Celera
Cytogenetic Map	4	E2	NCBI
cM Map	4	82.81	NCBI

Phf13
(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_004955486	6,017,748 - 6,025,614 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955486	6,018,614 - 6,025,473 (-)	NCBI	ChiLan1.0	ChiLan1.0

PHF13
(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	1	221,601,412 - 221,613,628 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	220,243,605 - 220,254,236 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	5,377,740 - 5,388,024 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	6,631,620 - 6,639,972 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	6,631,621 - 6,639,972 (+)	Ensembl	panpan1.1		panPan2

PHF13
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	60,434,218 - 60,441,930 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	5	60,433,328 - 60,439,672 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	60,443,828 - 60,451,377 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	5	60,650,231 - 60,657,779 (+)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	5	60,649,517 - 60,657,077 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	5	60,515,731 - 60,523,286 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	5	60,918,173 - 60,925,716 (+)	NCBI		UU_Cfam_GSD_1.0

Phf13
(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_024405058	30,881,413 - 30,886,984 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936623	1,366,401 - 1,372,222 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936623	1,364,422 - 1,372,226 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PHF13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	67,445,978 - 67,454,189 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	67,445,960 - 67,452,144 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	62,388,142 - 62,394,203 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PHF13
(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	20	125,122,118 - 125,133,013 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	125,121,886 - 125,132,966 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666054	29,165,887 - 29,177,029 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Phf13
(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_004624818	4,913,287 - 4,921,118 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624818	4,913,209 - 4,921,093 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Phf13
17 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	833
Count of miRNA genes:	324
Interacting mature miRNAs:	423
Transcripts:	ENSRNOT00000012407
Prediction methods:	Microtar, Miranda
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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	82394392	166664054	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	121846814	166846814	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	124965598	166875058	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	126424772	166875058	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	127798274	166875058	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	127798274	166875058	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	128506074	166875058	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	128506074	166875058	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	128924607	166875058	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	130130159	166875058	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	131345754	166875058	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132717196	165560427	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	135927956	166875058	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	135929696	166875058	Rat
1331721	Bp210	Blood pressure QTL 210	3.413		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	143069996	166846814	Rat
1354631	Swd2	Spike wave discharge measurement QTL 2	3.64	0.0002	brain electrophysiology trait (VT:0010557)	brain total spike-and-wave discharge duration (CMO:0001740)	5	151113452	164465185	Rat
631272	Lanf1	Left ventricular atrial natriuretic factor QTL 1	12		heart left ventricle natriuretic peptide A amount (VT:0010596)	heart left ventricle natriuretic peptide A level (CMO:0002165)	5	151113452	166875058	Rat
1549904	Neuinf1	Neuroinflammation QTL 1	3	0	nervous system integrity trait (VT:0010566)	blood T lymphocyte count (CMO:0000110)	5	154828214	166875058	Rat

Markers in Region

RH143852

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	162,501,020 - 162,501,241 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	169,167,502 - 169,167,722	NCBI	Rnor6.0
Rnor_5.0	5	172,726,112 - 172,726,332	UniSTS	Rnor5.0
RGSC_v3.4	5	169,222,554 - 169,222,774	UniSTS	RGSC3.4
Celera	5	160,733,739 - 160,733,959	UniSTS
RH 3.4 Map	5	1143.3	UniSTS
Cytogenetic Map	5	q36	UniSTS

UniSTS:496742

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	162,496,500 - 162,496,595 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	169,163,339 - 169,163,433	NCBI	Rnor6.0
Rnor_5.0	5	172,721,924 - 172,722,018	UniSTS	Rnor5.0
RGSC_v3.4	5	169,217,761 - 169,217,855	UniSTS	RGSC3.4
Celera	5	160,729,294 - 160,729,388	UniSTS
Cytogenetic Map	5	q36	UniSTS

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	appendage
High
Medium		20	6	6		6			56	20	38	1
Low	3	23	51	35	19	35	8	11	18	15	3	10	8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107995	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC083880	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000012407 ⟹ ENSRNOP00000012407

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	162,494,574 - 162,501,350 (-)	Ensembl
Rnor_6.0 Ensembl	5	169,161,412 - 169,167,831 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000118274 ⟹ ENSRNOP00000079267

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	162,494,573 - 162,500,165 (-)	Ensembl

RefSeq Acc Id:

NM_001107995 ⟹ NP_001101465

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	167,777,303 - 167,784,077 (-)	NCBI
mRatBN7.2	5	162,494,574 - 162,501,350 (-)	NCBI
Rnor_6.0	5	169,161,412 - 169,167,831 (-)	NCBI
Rnor_5.0	5	172,719,997 - 172,726,441 (-)	NCBI
RGSC_v3.4	5	169,215,834 - 169,222,883 (-)	RGD
Celera	5	160,727,367 - 160,734,068 (-)	RGD

Sequence:

show sequence

CGGGGAGCCGGTCGGGTTCCCGCTCGCTGTCGCCGCCGCCGCCCCCCACAGTGCCTCTCCCGCC
TCTCCACAGCGCCGGTCGTGGGAGCTGCATCCTCCACTCAGTTCTCTGAGGAGACTCCAGTTCG
GGATCAGCGAACCTACGACGCGACACACCGACACCCCCCGTCAAATCCAGCCTGGGCGACCCCT
CCCCGGCCGGGTCCGCCCTCGCCCTGCTCGGTGCCGGAGTCCCCCGGCCCTGAGCGTCCCGTGG
GCCCGCTCCCGCACTCTAGCCTCGGCACTCCCACAGCCGCCGCCCCCCACCCGGAACATGGACT
CCGACTCCTGCGCCGCCGCCTTCCACCCCGAGGAGTACTCCCCCACTTGTAAGAGGCGCCGGAC
TGTGGAAGACTTCAACAAGTTCTGCACCTTCGTGCTGGCCTATGCAGGCTACATCCCCTATCCG
AAGGAGGAGCTCCCCCTGAGGAGCAGCCCCAGTCCTGCCAACAGCACTGCAGGGACCATCGACA
GTGATGGCTGGGACACTGGTTTCTCTGACATTACATCTTCAGTGCCCGACCGATGCTTCAGCCA
CCTGCAGCCTTCCCTCTTGCAGAGAGCTAAGCCCAGTGACTTCCTGCTGGACAGGAAGAAAACG
GACAAGCTGAAGAAGAAGAGGAGGAGGAAGCGCAGGGACAGCGACGTGCCTGGGAAGGAGGAGT
ACAGGGGGAGCCTGCTGAAGCTGGAAGCTGCTGACCCGTATGTGGAGGCCCCCTCAAGTCCCAC
CATGCAGGATATTCCCCAGGCCTCTGCTGACCCCTGCTCGGGCTGGGACTCTGACACTCCTTCA
AGTGGTTCTTGTGCTACTGTGTCACCTGATCAGGTCACAGAAATAAAAACTGAAGGGAAACGGA
CTATTGTCCGCCAGGGAAAGCAGGTGGTGTTCCGAGACGAAGACAGCACTGGTAATGATGAAGA
CATCATGGTGGACTCAGATGATGATTCCTGGGATCTTGTCACCTGTTTCTGCATGAAGCCCTTC
GCTGGTCGCCCCATGATCGAGTGTAACGAATGCCACACCTGGATCCACCTGTCTTGTGCGAAGA
TCCGCAAGTCCAATGTTCCGGAAGTGTTTGTCTGCCAAAAGTGCCGGGACTCCAAGTTTGATAT
CCGTCGCTCCAACCGGTCCCGAATGGGCTCCCGGAAGCTGTTTCTGGACTGATCTGGGGCTGTC
AAGGAGATAGGCGGGACTGGAAGGGCCTGGGCTCTGGCCTCCCTTAGTTGAGCACAGAACTCGC
AGCTCTGGTGTGGGCAGACCCTGCCACTCAGGTGCCTAAGCAAAGGACGAGCCGTCCAGATAGA
ACTGTACATAGCTAGTGAGCAGGTAAAAGGGTCAGCGCTGCTGCTCCAGCTGTGTTCTCTGCGT
TGGTGGCAGACTGAGCACCAGATCTGCTTCTGCTAACAGTGAGTGTGCACAGTCATTGTTAGTC
AGTTCCCGCCAGCCATCGGGCGGTGCTGGCTGTCAGTCCCGTGTCCTGTGTGCTGGGGAGGTGT
TGTGTTTATTCTCAGTGTTGCTCTTTTATCCCAAGTGTCTATGCAGCCGTCCAGGTTGCCCGCC
CCTTTGTGGTCTCACTTCCCTGCCTCAGTTGTACTTTCTGAGACAGGGAGCTGTTTCCTGAGAG
GTCCGGTGTCCCCAAGAGGAGCCCTGGGTGGGGGGTGAGTGGTGGTTCTTTGGTTTTTCACTGT
TTAAAGGGACAGTGTGTAGCCATTTTTCCACAGAGCGAGGGTGGGGGTGGAGGTGTTCTGTGTT
CATAACTCAGTTTCTTGTTTTGCACGATGTAAAAAACAAAAACCATTTTTTTTCCACACGACAC
AGCCCAAAGTGTTAGCCACTGTCCTACTGGGTGCCCGTCTCTGCTGGTGGTGGTCGGTGACCAG
GGTGCCCAGCACTGTGCGGTGGGAGCACATGTTTCCTCCTTAAGCTGCTCCAGTGGCAGTCCAC
AGAAGACACTGTCTTTGGGACCTGTGTGTGGTTCTTCAGATAATGGGTGACGAGTCAGGGCACT
CTGCCTTGCATACAGGCTGACCTGTTGGGTTCCTGGGGTGCTGCAGCAGGGGTCTGAGTTAGTT
GCTGTAACATCAGCTTGCAGGGCTTCAAAGGTGTGAACCAGAGTCCTGATCTGGGTGAGGGCTG
GCTCAGCTCCTGGACACTGGTGACCTGTCCTGGGGCAGGGGAGGAAGGAGAGGACGATGTGGGC
TCTCGCCCCGGCGTTTCCAATGCTTGTTCTTTCTCAGCAGTGTTTGGCAGAGCCATGGGTGTGT
TTCATACCCATCTATCACATGTGTTCTGTGTTAGACATGAGACAGCAGAGCGGCCAAGTGTGTC
ACCTTTCTTCCCCTTCCTGGAACACCTGCAGGGTCACCAGGCATCTTAAGCACCAAAGGAGCTC
AGACTGTAGACTGTAATTTGGCTAATTGGAGCCTTTTTTTTTTTTCCTTTCTTGTCTTAGCATC
TTTCCCAGTTTAAGTAACTTTTTCATGTTAAAGTACAGAGAAGTACTGCTGAGCTGTTGGTTGT
GCAGACTTCAAGAGAGCTTTGCTAAGGAGAAGGAGCTATGACAGAAGCAGTCTTGTCCCTAGGC
TATTGTGTGGCTCTGACTGGGGCAAACACCCAGGACAAGTCAGGAATTTGCCAAAGACCTGCCC
CGTGACAGTTCTTGTCCAGTGTCTTCACCCTGAGAATAACCAAAGTTCCAGTAGGTTTTTAAGT
GCATTTAAGATGTGTGTGGTTTTGTTGTGGAGCGGCGGGGCTGCCATTCTTACATCCATGTGCT
CAGAGATTACTCAATGCCTCTGGAATACATTGGACATCTCAGTTTCTGTTTGCTTGCTTTGTTT
TTAAGGGGATCTTTCCCTGTGGGTGGTGTCCGAAGTCAGACACCTTGGTTTGGGGGTAGGTGAG
CTGGGCAGCTGCAATCAGCTTGTTTATGCAAACTGGGCTCGACCCTCTAGGGGCTCCTGGTTGA
TGGCTGATGGCGGGAGGGAAAGGTGTCATCCCCAAGCAGACCCTTCCCGTTGGCTTCGGCCAGG
CCAGACACAGCATCGTTTACATGTTCTGTGTAATTATAATGTTTATGTGTATAAAGCAAGCTGT
TTCTGTGAAACTGTATATTTTGTAAATAAAGATATTGCTACTTT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001101465	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL81210	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000012407
	ENSRNOP00000012407.4
	ENSRNOP00000079267.1

RefSeq Acc Id:

NP_001101465 ⟸ NM_001107995

- UniProtKB:

D3ZG56 (UniProtKB/TrEMBL), A6IUF9 (UniProtKB/TrEMBL), A0A8I5ZN36 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDSDSCAAAFHPEEYSPTCKRRRTVEDFNKFCTFVLAYAGYIPYPKEELPLRSSPSPANSTAGT
IDSDGWDTGFSDITSSVPDRCFSHLQPSLLQRAKPSDFLLDRKKTDKLKKKRRRKRRDSDVPGK
EEYRGSLLKLEAADPYVEAPSSPTMQDIPQASADPCSGWDSDTPSSGSCATVSPDQVTEIKTEG
KRTIVRQGKQVVFRDEDSTGNDEDIMVDSDDDSWDLVTCFCMKPFAGRPMIECNECHTWIHLSC
AKIRKSNVPEVFVCQKCRDSKFDIRRSNRSRMGSRKLFLD

hide sequence

RefSeq Acc Id:

ENSRNOP00000012407 ⟸ ENSRNOT00000012407

RefSeq Acc Id:

ENSRNOP00000079267 ⟸ ENSRNOT00000118274

Protein Domains

Zinc finger PHD-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZG56-F1-model_v2	AlphaFold	D3ZG56	1-296	view protein structure

Transcriptome

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

Promoters

RGD ID:

13694294

Promoter ID:

EPDNEW_R4817

Type:

multiple initiation site

Name:

Phf13_1

Description:

PHD finger protein 13

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	5	169,167,847 - 169,167,907	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308145	AgrOrtholog
BioCyc Gene	G2FUF-39030	BioCyc
Ensembl Genes	ENSRNOG00000009046	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000012407	ENTREZGENE
	ENSRNOT00000012407.6	UniProtKB/TrEMBL
	ENSRNOT00000118274.1	UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.10	UniProtKB/TrEMBL
InterPro	PHD_PHF13	UniProtKB/TrEMBL
	Znf_FYVE_PHD	UniProtKB/TrEMBL
	Znf_PHD	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
KEGG Report	rno:313742	UniProtKB/TrEMBL
NCBI Gene	313742	ENTREZGENE
PANTHER	PHD FINGER PROTEIN 13	UniProtKB/TrEMBL
	UNCHARACTERIZED	UniProtKB/TrEMBL
Pfam	PHD_5	UniProtKB/TrEMBL
PhenoGen	Phf13	PhenoGen
RatGTEx	ENSRNOG00000009046	RatGTEx
SMART	PHD	UniProtKB/TrEMBL
Superfamily-SCOP	FYVE_PHD_ZnF	UniProtKB/TrEMBL
UniProt	A0A8I5ZN36	ENTREZGENE, UniProtKB/TrEMBL
	A6IUF9	ENTREZGENE, UniProtKB/TrEMBL
	D3ZG56	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Phf13	PHD finger protein 13	Phf13_predicted	PHD finger protein 13 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Phf13_predicted	PHD finger protein 13 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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)

Send us a Message

Imported Disease Annotations - ClinVar