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Q9D4J7

- PHF6_MOUSE

UniProt

Q9D4J7 - PHF6_MOUSE

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Protein

PHD finger protein 6

Gene

Phf6

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli

Functioni

Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri17 – 5034C2HC-type; pre-PHDAdd
BLAST
Zinc fingeri79 – 13153PHD-type 1; degenerateAdd
BLAST
Zinc fingeri212 – 24736C2HC-type; pre-PHDAdd
BLAST
Zinc fingeri277 – 32953PHD-type 2; degenerateAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. poly(A) RNA binding Source: Ensembl
  3. ribonucleoprotein complex binding Source: Ensembl
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. regulation of transcription, DNA-templated Source: UniProtKB-KW
  2. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 6
Gene namesi
Name:Phf6
Synonyms:Kiaa1823
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome X

Organism-specific databases

MGIiMGI:1918248. Phf6.

Subcellular locationi

Nucleus By similarity. Nucleusnucleolus By similarity
Note: Nuclear, it particularly localizes to the nucleolus.By similarity

GO - Cellular componenti

  1. nucleolus Source: Ensembl
  2. nucleoplasm Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 364363PHD finger protein 6PRO_0000059294Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei138 – 1381PhosphoserineBy similarity
Modified residuei145 – 1451PhosphoserineBy similarity
Modified residuei155 – 1551PhosphoserineBy similarity
Modified residuei199 – 1991PhosphoserineBy similarity
Modified residuei357 – 3571PhosphothreonineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9D4J7.
PaxDbiQ9D4J7.
PRIDEiQ9D4J7.

PTM databases

PhosphoSiteiQ9D4J7.

Expressioni

Tissue specificityi

At 12.5 dpc it is highly expressed in the embryonic central nervous system and at lower levels in other tissues. Very low levels present throughout the adult brain.1 Publication

Developmental stagei

Expression is high in the embryonic and early postnatal stages.1 Publication

Gene expression databases

BgeeiQ9D4J7.
CleanExiMM_PHF6.
ExpressionAtlasiQ9D4J7. baseline and differential.
GenevestigatoriQ9D4J7.

Interactioni

Subunit structurei

Interacts with UBTF. Interacts with the NuRD complex component RBBP4 (via the nucleolar localization motif), the interaction mediates transcriptional repression activity By similarity.By similarity

Protein-protein interaction databases

IntActiQ9D4J7. 1 interaction.
MINTiMINT-4107476.

Structurei

3D structure databases

ProteinModelPortaliQ9D4J7.
SMRiQ9D4J7. Positions 16-131, 208-331.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 131118Extended PHD1 domain (ePHD1)By similarityAdd
BLAST
Regioni208 – 329122Extended PHD2 domain (ePHD2)By similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi13 – 164Nuclear localization signalSequence Analysis
Motifi129 – 1335Nuclear localization signalSequence Analysis
Motifi157 – 16913Nucleolar localization signalSequence AnalysisAdd
BLAST

Domaini

The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.By similarity
The ePHD2 domain folds as an integrated structural module comprizing the C2HC-type zinc finger (pre-PHD) and the atypical PHD-type 2 zinc finger. It mediates non-specific binding to dsDNA, but doesn't bind histones in contrast to many PHD-type zinc fingers By similarity.By similarity

Sequence similaritiesi

Contains 2 C2HC-type zinc fingers.Curated
Contains 2 PHD-type zinc fingers.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri17 – 5034C2HC-type; pre-PHDAdd
BLAST
Zinc fingeri79 – 13153PHD-type 1; degenerateAdd
BLAST
Zinc fingeri212 – 24736C2HC-type; pre-PHDAdd
BLAST
Zinc fingeri277 – 32953PHD-type 2; degenerateAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG282606.
GeneTreeiENSGT00530000063780.
HOGENOMiHOG000026798.
HOVERGENiHBG049389.
InParanoidiQ9D4J7.
OMAiMARGIYK.
OrthoDBiEOG708W01.
TreeFamiTF325426.

Family and domain databases

InterProiIPR001965. Znf_PHD.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9D4J7-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSSSIEQKKG STRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS
60 70 80 90 100
ALVSSHSDNE SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH
110 120 130 140 150
RTYHYHCALH DKAQIREKPS QGIYMVYCRK HKKTAHNSEA DLEESFNEHE
160 170 180 190 200
LEPSSPKTKK KSRKGRPRKT NLKGLPEDSR STSSHGTDEM ESSSYRDRSP
210 220 230 240 250
HRSSPNDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY KCMLFSSGTV
260 270 280 290 300
QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT
310 320 330 340 350
YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGRV
360
AIDQQLTQQQ LNGN
Length:364
Mass (Da):41,139
Last modified:June 1, 2001 - v1
Checksum:iD147BCE8C553F211
GO
Isoform 2 (identifier: Q9D4J7-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     2-80: Missing.

Note: No experimental confirmation available.

Show »
Length:285
Mass (Da):32,414
Checksum:iC42F23F56EDB6702
GO

Sequence cautioni

The sequence BAC29968.1 differs from that shown. Reason: Frameshift at position 284.
The sequence BAC65842.1 differs from that shown. Reason: Erroneous initiation.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei2 – 8079Missing in isoform 2. CuratedVSP_009375Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AK016480 mRNA. Translation: BAB30260.1.
AK028498 mRNA. Translation: BAC25980.1.
AK038320 mRNA. Translation: BAC29968.1. Frameshift.
AK122560 mRNA. Translation: BAC65842.1. Different initiation.
BC043127 mRNA. Translation: AAH43127.1.
BC055330 mRNA. Translation: AAH55330.1.
BC057374 mRNA. Translation: AAH57374.1.
CCDSiCCDS30127.1. [Q9D4J7-1]
RefSeqiNP_001277475.1. NM_001290546.1.
NP_081918.1. NM_027642.2. [Q9D4J7-1]
UniGeneiMm.26870.

Genome annotation databases

EnsembliENSMUST00000078944; ENSMUSP00000077971; ENSMUSG00000025626. [Q9D4J7-1]
ENSMUST00000154864; ENSMUSP00000130358; ENSMUSG00000025626.
GeneIDi70998.
KEGGimmu:70998.
UCSCiuc009teo.1. mouse. [Q9D4J7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AK016480 mRNA. Translation: BAB30260.1 .
AK028498 mRNA. Translation: BAC25980.1 .
AK038320 mRNA. Translation: BAC29968.1 . Frameshift.
AK122560 mRNA. Translation: BAC65842.1 . Different initiation.
BC043127 mRNA. Translation: AAH43127.1 .
BC055330 mRNA. Translation: AAH55330.1 .
BC057374 mRNA. Translation: AAH57374.1 .
CCDSi CCDS30127.1. [Q9D4J7-1 ]
RefSeqi NP_001277475.1. NM_001290546.1.
NP_081918.1. NM_027642.2. [Q9D4J7-1 ]
UniGenei Mm.26870.

3D structure databases

ProteinModelPortali Q9D4J7.
SMRi Q9D4J7. Positions 16-131, 208-331.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q9D4J7. 1 interaction.
MINTi MINT-4107476.

PTM databases

PhosphoSitei Q9D4J7.

Proteomic databases

MaxQBi Q9D4J7.
PaxDbi Q9D4J7.
PRIDEi Q9D4J7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000078944 ; ENSMUSP00000077971 ; ENSMUSG00000025626 . [Q9D4J7-1 ]
ENSMUST00000154864 ; ENSMUSP00000130358 ; ENSMUSG00000025626 .
GeneIDi 70998.
KEGGi mmu:70998.
UCSCi uc009teo.1. mouse. [Q9D4J7-1 ]

Organism-specific databases

CTDi 84295.
MGIi MGI:1918248. Phf6.
Rougei Search...

Phylogenomic databases

eggNOGi NOG282606.
GeneTreei ENSGT00530000063780.
HOGENOMi HOG000026798.
HOVERGENi HBG049389.
InParanoidi Q9D4J7.
OMAi MARGIYK.
OrthoDBi EOG708W01.
TreeFami TF325426.

Miscellaneous databases

NextBioi 332793.
PROi Q9D4J7.
SOURCEi Search...

Gene expression databases

Bgeei Q9D4J7.
CleanExi MM_PHF6.
ExpressionAtlasi Q9D4J7. baseline and differential.
Genevestigatori Q9D4J7.

Family and domain databases

InterProi IPR001965. Znf_PHD.
[Graphical view ]
SMARTi SM00249. PHD. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: C57BL/6J.
    Tissue: Skin, Testis and Thymus.
  2. "Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
    Okazaki N., Kikuno R., Ohara R., Inamoto S., Aizawa H., Yuasa S., Nakajima D., Nagase T., Ohara O., Koga H.
    DNA Res. 10:35-48(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: C57BL/6.
    Tissue: Brain.
  4. Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiPHF6_MOUSE
AccessioniPrimary (citable) accession number: Q9D4J7
Secondary accession number(s): Q80T86, Q8BYT8, Q8C1B5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: June 1, 2001
Last modified: October 29, 2014
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3