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Q9D4J7 (PHF6_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 101. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
PHD finger protein 6
Gene names
Name:Phf6
Synonyms:Kiaa1823
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length364 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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

Subunit structure

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

Subcellular location

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

Tissue specificity

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. Ref.4

Developmental stage

Expression is high in the embryonic and early postnatal stages. Ref.4

Domain

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.

Sequence similarities

Contains 2 C2HC-type zinc fingers.

Contains 2 PHD-type zinc fingers.

Sequence caution

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

The sequence BAC65842.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processregulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleolus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9D4J7-1)

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.
Isoform 2 (identifier: Q9D4J7-2)

The sequence of this isoform differs from the canonical sequence as follows:
     2-80: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 364363PHD finger protein 6
PRO_0000059294

Regions

Zinc finger17 – 5034C2HC-type; pre-PHD
Zinc finger79 – 13153PHD-type 1; degenerate
Zinc finger212 – 24736C2HC-type; pre-PHD
Zinc finger277 – 32953PHD-type 2; degenerate
Region14 – 131118Extended PHD1 domain (ePHD1) By similarity
Region208 – 329122Extended PHD2 domain (ePHD2) By similarity
Motif13 – 164Nuclear localization signal Potential
Motif129 – 1335Nuclear localization signal Potential
Motif157 – 16913Nucleolar localization signal Potential

Amino acid modifications

Modified residue21N-acetylserine By similarity
Modified residue1381Phosphoserine By similarity
Modified residue1451Phosphoserine By similarity
Modified residue1551Phosphoserine By similarity
Modified residue1991Phosphoserine By similarity
Modified residue3571Phosphothreonine By similarity

Natural variations

Alternative sequence2 – 8079Missing in isoform 2.
VSP_009375

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 1, 2001. Version 1.
Checksum: D147BCE8C553F211

FASTA36441,139
        10         20         30         40         50         60 
MSSSIEQKKG STRQRKCGFC KSNRDKECGQ LLISENQKVA AHHKCMLFSS ALVSSHSDNE 

        70         80         90        100        110        120 
SLGGFSIEDV QKEIKRGTKL MCSLCHCPGA TIGCDVKTCH RTYHYHCALH DKAQIREKPS 

       130        140        150        160        170        180 
QGIYMVYCRK HKKTAHNSEA DLEESFNEHE LEPSSPKTKK KSRKGRPRKT NLKGLPEDSR 

       190        200        210        220        230        240 
STSSHGTDEM ESSSYRDRSP HRSSPNDTRP KCGFCHVGEE ENEARGKLHI FNAKKAAAHY 

       250        260        270        280        290        300 
KCMLFSSGTV QLTTTSRAEF GDFDIKTVLQ EIKRGKRMKC TLCSQPGATI GCEIKACVKT 

       310        320        330        340        350        360 
YHYHCGVQDK AKYIENMSRG IYKLYCKNHS GNDERDEEDE ERESKSRGRV AIDQQLTQQQ 


LNGN 

« Hide

Isoform 2 [UniParc].

Checksum: C42F23F56EDB6702
Show »

FASTA28532,414

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"Mutations in PHF6 are associated with Boerjeson-Forssman-Lehmann syndrome."
Lower K.M., Turner G., Kerr B.A., Mathews K.D., Shaw M.A., Gedeon A.K., Schelley S., Hoyme H.E., White S.M., Delatycki M.B., Lampe A.K., Clayton-Smith J., Stewart H., van Ravenswaay C.M.A., de Vries B.B.A., Cox B., Grompe M., Ross S. expand/collapse author list , Thomas P., Mulley J.C., Gecz J.
Nat. Genet. 32:661-665(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS30127.1. [Q9D4J7-1]
RefSeqNP_001277475.1. NM_001290546.1.
NP_081918.1. NM_027642.2. [Q9D4J7-1]
UniGeneMm.26870.

3D structure databases

ProteinModelPortalQ9D4J7.
SMRQ9D4J7. Positions 16-131, 208-331.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9D4J7. 1 interaction.
MINTMINT-4107476.

PTM databases

PhosphoSiteQ9D4J7.

Proteomic databases

PaxDbQ9D4J7.
PRIDEQ9D4J7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000078944; ENSMUSP00000077971; ENSMUSG00000025626. [Q9D4J7-1]
ENSMUST00000154864; ENSMUSP00000130358; ENSMUSG00000025626.
GeneID70998.
KEGGmmu:70998.
UCSCuc009teo.1. mouse. [Q9D4J7-1]

Organism-specific databases

CTD84295.
MGIMGI:1918248. Phf6.
RougeSearch...

Phylogenomic databases

eggNOGNOG282606.
GeneTreeENSGT00530000063780.
HOGENOMHOG000026798.
HOVERGENHBG049389.
OMAMARGIYK.
OrthoDBEOG708W01.
TreeFamTF325426.

Gene expression databases

ArrayExpressQ9D4J7.
BgeeQ9D4J7.
CleanExMM_PHF6.
GenevestigatorQ9D4J7.

Family and domain databases

InterProIPR001965. Znf_PHD.
[Graphical view]
SMARTSM00249. PHD. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

NextBio332793.
PROQ9D4J7.
SOURCESearch...

Entry information

Entry namePHF6_MOUSE
AccessionPrimary (citable) accession number: Q9D4J7
Secondary accession number(s): Q80T86, Q8BYT8, Q8C1B5
Entry history
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: June 1, 2001
Last modified: July 9, 2014
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot