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Q9D4J7

- PHF6_MOUSE

UniProt

Q9D4J7 - PHF6_MOUSE

Protein

PHD finger protein 6

Gene

Phf6

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 102 (01 Oct 2014)
      Sequence version 1 (01 Jun 2001)
      Previous versions | rss
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    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. zinc ion binding Source: InterPro

    GO - Biological processi

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

    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: UniProtKB-SubCell

    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

    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

    ArrayExpressiQ9D4J7.
    BgeeiQ9D4J7.
    CleanExiMM_PHF6.
    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.
    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

    MSSSIEQKKG STRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS    50
    ALVSSHSDNE SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH 100
    RTYHYHCALH DKAQIREKPS QGIYMVYCRK HKKTAHNSEA DLEESFNEHE 150
    LEPSSPKTKK KSRKGRPRKT NLKGLPEDSR STSSHGTDEM ESSSYRDRSP 200
    HRSSPNDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY KCMLFSSGTV 250
    QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT 300
    YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGRV 350
    AIDQQLTQQQ LNGN 364
    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

    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.
    OMAi MARGIYK.
    OrthoDBi EOG708W01.
    TreeFami TF325426.

    Miscellaneous databases

    NextBioi 332793.
    PROi Q9D4J7.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9D4J7.
    Bgeei Q9D4J7.
    CleanExi MM_PHF6.
    Genevestigatori Q9D4J7.

    Family and domain databases

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

    Publicationsi

    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 1, 2014
    This is version 102 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