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Protein

PR domain zinc finger protein 13

Gene

PRDM13

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

May be involved in transcriptional regulation.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri137 – 15923C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri573 – 59523C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri601 – 62323C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri630 – 65324C2H2-type 4PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, S-adenosyl-L-methionine, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain zinc finger protein 13 (EC:2.1.1.-)
Alternative name(s):
PR domain-containing protein 13
Gene namesi
Name:PRDM13
Synonyms:PFM10
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:13998. PRDM13.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33711.

Polymorphism and mutation databases

BioMutaiPRDM13.
DMDMi317373271.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 707707PR domain zinc finger protein 13PRO_0000047770Add
BLAST

Proteomic databases

PaxDbiQ9H4Q3.
PRIDEiQ9H4Q3.

PTM databases

iPTMnetiQ9H4Q3.
PhosphoSiteiQ9H4Q3.

Expressioni

Gene expression databases

BgeeiQ9H4Q3.
CleanExiHS_PRDM13.
ExpressionAtlasiQ9H4Q3. baseline and differential.
GenevisibleiQ9H4Q3. HS.

Interactioni

Protein-protein interaction databases

BioGridi121879. 1 interaction.
STRINGi9606.ENSP00000358217.

Structurei

3D structure databases

ProteinModelPortaliQ9H4Q3.
SMRiQ9H4Q3. Positions 8-162, 562-657.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 112112SETPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi301 – 3077Poly-Ala
Compositional biasi352 – 36312Poly-HisAdd
BLAST
Compositional biasi372 – 3787Poly-Pro
Compositional biasi554 – 56512Poly-GlyAdd
BLAST

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 4 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri137 – 15923C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri573 – 59523C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri601 – 62323C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri630 – 65324C2H2-type 4PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00840000129938.
HOGENOMiHOG000049198.
HOVERGENiHBG053667.
InParanoidiQ9H4Q3.
OMAiASAFKHV.
OrthoDBiEOG7ZWD3Q.
PhylomeDBiQ9H4Q3.
TreeFamiTF106398.

Family and domain databases

Gene3Di3.30.160.60. 2 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9H4Q3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHGAARAPAT SVSADCCIPA GLRLGPVPGT FKLGKYLSDR REPGPKKKVR
60 70 80 90 100
MVRGELVDES GGSPLEWIGL IRAARNSQEQ TLEAIADLPG GQIFYRALRD
110 120 130 140 150
VQPGEELTVW YSNSLAQWFD IPTTATPTHD EKGEERYICW YCWRTFRYPN
160 170 180 190 200
SLKAHLRFHC VFSGGGGGAF LHHEHAARQG AVPAADGLGL SPKPPAPDFA
210 220 230 240 250
APSQAGTLRP HPLGPPPVQA CGAREGIKRE ASSAPSATSP TPGKWGQPKK
260 270 280 290 300
GKEQLDRALD MSGAARGQGH FLGIVGGSSA GVGSLAFYPG VRSAFKPAGL
310 320 330 340 350
ARAAAAAHGD PYREESSSKQ GAGLALGRLL GGGRACGRPG SGENSAAGGA
360 370 380 390 400
GHHHHHHAHH HHHPKCLLAG DPPPPPPPGL PCSGALRGFP LLSVPPEEAS
410 420 430 440 450
AFKHVERAPP AAAALPGARY AQLPPAPGLP LERCALPPLD PGGLKAYPGG
460 470 480 490 500
ECSHLPAVMP AFTVYNGELL YGSPATTAYY PLKLHFGGLL KYPESISYFS
510 520 530 540 550
GPAAAALSPA ELGSLASIDR EIAMHNQQLS EMAAGKGRGR LDSGTLPPAV
560 570 580 590 600
AAAGGTGGGG SGGSGAGKPK TGHLCLYCGK LYSRKYGLKI HMRTHTGYKP
610 620 630 640 650
LKCKVCLRPF GDPSNLNKHI RLHAEGNTPY RCEFCGKVLV RRRDLERHVK
660 670 680 690 700
SRHPGQSLLA KAGDGPGAEP GYPPEPGDPK SDDSDVDVCF TDDQSDPEVG

GGGERDL
Length:707
Mass (Da):73,981
Last modified:January 11, 2011 - v2
Checksum:i5A334E26E6674B13
GO

Sequence cautioni

The sequence AAG13448.1 differs from that shown.Non-canonical splice intron-exon junction.Curated
The sequence CAI19763.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAI22063.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY004253 mRNA. Translation: AAG13448.1. Sequence problems.
AL035087, AL137784 Genomic DNA. Translation: CAI22063.1. Sequence problems.
AL137784, AL035087 Genomic DNA. Translation: CAI19763.1. Sequence problems.
AL137784, AL035087 Genomic DNA. Translation: CAI19764.1.
AL035087, AL137784 Genomic DNA. Translation: CAI22064.1.
CH471051 Genomic DNA. Translation: EAW48462.1.
CCDSiCCDS43487.1.
RefSeqiNP_067633.2. NM_021620.3.
UniGeneiHs.287386.

Genome annotation databases

EnsembliENST00000369215; ENSP00000358217; ENSG00000112238.
GeneIDi59336.
KEGGihsa:59336.
UCSCiuc003pqg.2. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY004253 mRNA. Translation: AAG13448.1. Sequence problems.
AL035087, AL137784 Genomic DNA. Translation: CAI22063.1. Sequence problems.
AL137784, AL035087 Genomic DNA. Translation: CAI19763.1. Sequence problems.
AL137784, AL035087 Genomic DNA. Translation: CAI19764.1.
AL035087, AL137784 Genomic DNA. Translation: CAI22064.1.
CH471051 Genomic DNA. Translation: EAW48462.1.
CCDSiCCDS43487.1.
RefSeqiNP_067633.2. NM_021620.3.
UniGeneiHs.287386.

3D structure databases

ProteinModelPortaliQ9H4Q3.
SMRiQ9H4Q3. Positions 8-162, 562-657.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121879. 1 interaction.
STRINGi9606.ENSP00000358217.

PTM databases

iPTMnetiQ9H4Q3.
PhosphoSiteiQ9H4Q3.

Polymorphism and mutation databases

BioMutaiPRDM13.
DMDMi317373271.

Proteomic databases

PaxDbiQ9H4Q3.
PRIDEiQ9H4Q3.

Protocols and materials databases

DNASUi59336.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369215; ENSP00000358217; ENSG00000112238.
GeneIDi59336.
KEGGihsa:59336.
UCSCiuc003pqg.2. human.

Organism-specific databases

CTDi59336.
GeneCardsiPRDM13.
HGNCiHGNC:13998. PRDM13.
neXtProtiNX_Q9H4Q3.
PharmGKBiPA33711.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00840000129938.
HOGENOMiHOG000049198.
HOVERGENiHBG053667.
InParanoidiQ9H4Q3.
OMAiASAFKHV.
OrthoDBiEOG7ZWD3Q.
PhylomeDBiQ9H4Q3.
TreeFamiTF106398.

Miscellaneous databases

GenomeRNAii59336.
NextBioi65206.
PROiQ9H4Q3.

Gene expression databases

BgeeiQ9H4Q3.
CleanExiHS_PRDM13.
ExpressionAtlasiQ9H4Q3. baseline and differential.
GenevisibleiQ9H4Q3. HS.

Family and domain databases

Gene3Di3.30.160.60. 2 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A family of novel PR-domain (PRDM) genes as candidate tumor suppressors."
    Yang X.-H., Huang S.
    Submitted (JUL-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiPRD13_HUMAN
AccessioniPrimary (citable) accession number: Q9H4Q3
Secondary accession number(s): Q5TGC1, Q5TGC2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: January 11, 2011
Last modified: May 11, 2016
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.