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Protein

PHD finger protein 6

Gene

Phf6

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 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

GO - Biological processi

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 Componenti: Chromosome X

Organism-specific databases

MGIiMGI:1918248. Phf6.

Subcellular locationi

  • Nucleus By similarity
  • Nucleusnucleolus By similarity
  • Chromosomecentromerekinetochore By similarity

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

GO - Cellular componenti

  • condensed chromosome kinetochore Source: UniProtKB-SubCell
  • nucleolus Source: MGI
  • nucleoplasm Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Kinetochore, 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.
GenevisibleiQ9D4J7. MM.

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.
STRINGi10090.ENSMUSP00000077971.

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.
OMAiCRRTYHY.
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. AlignAdd to basket

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:
     1-80: Missing.

Note: No experimental confirmation available.
Show »
Length:284
Mass (Da):32,283
Checksum:iFE7916AC7DC0C6AB
GO

Sequence cautioni

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 8080Missing in isoform 2. CuratedVSP_009375Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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]
CCDS72380.1. [Q9D4J7-2]
RefSeqiNP_001277475.1. NM_001290546.1. [Q9D4J7-2]
NP_081918.1. NM_027642.2. [Q9D4J7-1]
UniGeneiMm.26870.

Genome annotation databases

EnsembliENSMUST00000078944; ENSMUSP00000077971; ENSMUSG00000025626. [Q9D4J7-1]
ENSMUST00000154864; ENSMUSP00000130358; ENSMUSG00000025626. [Q9D4J7-2]
GeneIDi70998.
KEGGimmu:70998.
UCSCiuc009teo.2. mouse. [Q9D4J7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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]
CCDS72380.1. [Q9D4J7-2]
RefSeqiNP_001277475.1. NM_001290546.1. [Q9D4J7-2]
NP_081918.1. NM_027642.2. [Q9D4J7-1]
UniGeneiMm.26870.

3D structure databases

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

Protein-protein interaction databases

IntActiQ9D4J7. 1 interaction.
MINTiMINT-4107476.
STRINGi10090.ENSMUSP00000077971.

PTM databases

PhosphoSiteiQ9D4J7.

Proteomic databases

MaxQBiQ9D4J7.
PaxDbiQ9D4J7.
PRIDEiQ9D4J7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000078944; ENSMUSP00000077971; ENSMUSG00000025626. [Q9D4J7-1]
ENSMUST00000154864; ENSMUSP00000130358; ENSMUSG00000025626. [Q9D4J7-2]
GeneIDi70998.
KEGGimmu:70998.
UCSCiuc009teo.2. mouse. [Q9D4J7-1]

Organism-specific databases

CTDi84295.
MGIiMGI:1918248. Phf6.
RougeiSearch...

Phylogenomic databases

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

Miscellaneous databases

NextBioi332793.
PROiQ9D4J7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9D4J7.
CleanExiMM_PHF6.
ExpressionAtlasiQ9D4J7. baseline and differential.
GenevisibleiQ9D4J7. MM.

Family and domain databases

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

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: July 22, 2015
This is version 110 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

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 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.