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P78424

- PO6F2_HUMAN

UniProt

P78424 - PO6F2_HUMAN

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Protein
POU domain, class 6, transcription factor 2
Gene
POU6F2, RPF1
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Probable transcription factor likely to be involved in early steps in the differentiation of amacrine and ganglion cells. Recognizes and binds to the DNA sequence 5'-ATGCAAAT-3'. Isoform 1 does not bind DNA.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi607 – 66660Homeobox By similarity
Add
BLAST

GO - Molecular functioni

  1. sequence-specific DNA binding Source: InterPro
  2. sequence-specific DNA binding transcription factor activity Source: UniProtKB

GO - Biological processi

  1. central nervous system development Source: ProtInc
  2. ganglion mother cell fate determination Source: ProtInc
  3. regulation of transcription, DNA-templated Source: UniProtKB
  4. transcription from RNA polymerase II promoter Source: ProtInc
  5. visual perception Source: ProtInc
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
POU domain, class 6, transcription factor 2
Alternative name(s):
Retina-derived POU domain factor 1
Short name:
RPF-1
Gene namesi
Name:POU6F2
Synonyms:RPF1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 7

Organism-specific databases

HGNCiHGNC:21694. POU6F2.

Subcellular locationi

Nucleus Inferred

GO - Cellular componenti

  1. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Hereditary susceptibility to Wilms tumor 5 (WT5) [MIM:601583]: Pediatric malignancy of kidney and one of the most common solid cancers in childhood.
Note: The disease is caused by mutations affecting the gene represented in this entry.1 Publication
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti192 – 1921Q → H in WT5. 1 Publication
VAR_022419

Keywords - Diseasei

Disease mutation

Organism-specific databases

MIMi601583. phenotype.
Orphaneti654. Nephroblastoma.
PharmGKBiPA134969420.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 691691POU domain, class 6, transcription factor 2
PRO_0000100762Add
BLAST

Proteomic databases

PaxDbiP78424.
PRIDEiP78424.

PTM databases

PhosphoSiteiP78424.

Expressioni

Tissue specificityi

Expressed only within the CNS, where its expression is restricted to the medical habenulla, to a dispersed population of neurons in the dorsal hypothalamus, and to subsets of ganglion and amacrine cells in the retina.1 Publication

Gene expression databases

ArrayExpressiP78424.
BgeeiP78424.
CleanExiHS_POU6F2.
GenevestigatoriP78424.

Organism-specific databases

HPAiHPA008699.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000395926.

Structurei

3D structure databases

ProteinModelPortaliP78424.
SMRiP78424. Positions 480-664.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini476 – 586111POU-specific
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi167 – 446280Gln-rich
Add
BLAST
Compositional biasi197 – 29397Pro-rich
Add
BLAST
Compositional biasi435 – 46127Ser-rich
Add
BLAST

Sequence similaritiesi

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiNOG241882.
HOVERGENiHBG008230.
InParanoidiP78424.
KOiK09368.
OMAiFEARGNT.
OrthoDBiEOG7353Z3.
PhylomeDBiP78424.
TreeFamiTF350705.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
1.10.260.40. 2 hits.
InterProiIPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR010982. Lambda_DNA-bd_dom.
IPR013847. POU.
IPR000327. POU_specific.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00157. Pou. 2 hits.
[Graphical view]
PRINTSiPR00028. POUDOMAIN.
SMARTiSM00389. HOX. 1 hit.
SM00352. POU. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF47413. SSF47413. 2 hits.
PROSITEiPS50071. HOMEOBOX_2. 1 hit.
PS00035. POU_1. 1 hit.
PS00465. POU_2. 1 hit.
PS51179. POU_3. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: P78424-1) [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

MSALLQDPMI AGQVSKPLLS VRSEMNAELR GEDKAATSDS ELNEPLLAPV    50
ESNDSEDTPS KLFGARGNPA LSDPGTPDQH QASQTHPPFP VGPQPLLTAQ 100
QLASAVAGVM PGGPPALNQP ILIPFNMAGQ LGGQQGLVLT LPTANLTNIQ 150
GLVAAAAAGG IMTLPLQNLQ ATSSLNSQLQ QLQLQLQQQQ QQQQQQPPPS 200
TNQHPQPAPQ APSQSQQQPL QPTPPQQPPP ASQQPPAPTS QLQQAPQPQQ 250
HQPHSHSQNQ NQPSPTQQSS SPPQKPSQSP GHGLPSPLTP PNPLQLVNNP 300
LASQAAAAAA AMSSIASSQA FGNALSSLQG VTGQLVTNAQ GQIIGTIPLM 350
PNPGPSSQAA SGTQGLQVQP ITPQLLTNAQ GQIIATVIGN QILPVINTQG 400
ITLSPIKPGQ QLHQPSQTSV GQAASQGNLL HLAHSQASMS QSPVRQASSS 450
SSSSSSSSAL SVGQLVSNPQ TAAGEVDGVN LEEIREFAKA FKIRRLSLGL 500
TQTQVGQALS ATEGPAYSQS AICRHTILRS HFFLPQEAQE NTIASSLTAK 550
LNPGLLYPAR FEKLDITPKS AQKIKPVLER WMAEAEARHR AGMQNLTEFI 600
GSEPSKKRKR RTSFTPQALE ILNAHFEKNT HPSGQEMTEI AEKLNYDREV 650
VRVWFCNKRQ ALKNTIKRLK QHEPATAVPL EPLTDSLEEN S 691

Note: Major isoform.

Length:691
Mass (Da):73,265
Last modified:April 5, 2011 - v3
Checksum:i3460C858ECBB5535
GO
Isoform 2 (identifier: P78424-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     524-559: Missing.

Show »
Length:655
Mass (Da):69,248
Checksum:iAB9FFB1A958C3978
GO

Sequence cautioni

The sequence AAB49728.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
The sequence AAS07475.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
The sequence AAB49727.1 differs from that shown. Reason: Erroneous gene model prediction.
The sequence EAL23992.1 differs from that shown. Reason: Erroneous gene model prediction.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti192 – 1921Q → H in WT5. 1 Publication
VAR_022419
Natural varianti199 – 1991P → L.
Corresponds to variant rs2074936 [ dbSNP | Ensembl ].
VAR_028410
Natural varianti500 – 5001L → M.
Corresponds to variant rs4992268 [ dbSNP | Ensembl ].
VAR_028411
Natural varianti639 – 6391E → K.
Corresponds to variant rs7804851 [ dbSNP | Ensembl ].
VAR_028412

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei524 – 55936Missing in isoform 2.
VSP_002336Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti196 – 1961Q → QQ in AAB49727. 1 Publication
Sequence conflicti196 – 1961Q → QQ in AAB49728. 1 Publication
Sequence conflicti258 – 2581Q → H in AAB49727. 1 Publication
Sequence conflicti258 – 2581Q → H in AAB49728. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U91934 Genomic DNA. Translation: AAB49727.1. Sequence problems.
U91935 mRNA. Translation: AAB49728.1. Different initiation.
AC005483 Genomic DNA. Translation: AAC83404.2.
AC073345 Genomic DNA. Translation: AAS07475.1. Different initiation.
AC092174 Genomic DNA. Translation: AAP21873.1.
AC011292 Genomic DNA. No translation available.
CH236951 Genomic DNA. Translation: EAL23992.1. Sequence problems.
CCDSiCCDS34620.2. [P78424-1]
CCDS55103.1. [P78424-2]
RefSeqiNP_001159490.1. NM_001166018.1. [P78424-2]
NP_009183.3. NM_007252.3. [P78424-1]
UniGeneiHs.137106.

Genome annotation databases

EnsembliENST00000403058; ENSP00000384004; ENSG00000106536. [P78424-1]
ENST00000518318; ENSP00000430514; ENSG00000106536. [P78424-2]
GeneIDi11281.
KEGGihsa:11281.
UCSCiuc003thb.2. human. [P78424-1]
uc022acb.1. human. [P78424-2]

Polymorphism databases

DMDMi327478564.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U91934 Genomic DNA. Translation: AAB49727.1 . Sequence problems.
U91935 mRNA. Translation: AAB49728.1 . Different initiation.
AC005483 Genomic DNA. Translation: AAC83404.2 .
AC073345 Genomic DNA. Translation: AAS07475.1 . Different initiation.
AC092174 Genomic DNA. Translation: AAP21873.1 .
AC011292 Genomic DNA. No translation available.
CH236951 Genomic DNA. Translation: EAL23992.1 . Sequence problems.
CCDSi CCDS34620.2. [P78424-1 ]
CCDS55103.1. [P78424-2 ]
RefSeqi NP_001159490.1. NM_001166018.1. [P78424-2 ]
NP_009183.3. NM_007252.3. [P78424-1 ]
UniGenei Hs.137106.

3D structure databases

ProteinModelPortali P78424.
SMRi P78424. Positions 480-664.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 9606.ENSP00000395926.

PTM databases

PhosphoSitei P78424.

Polymorphism databases

DMDMi 327478564.

Proteomic databases

PaxDbi P78424.
PRIDEi P78424.

Protocols and materials databases

DNASUi 11281.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000403058 ; ENSP00000384004 ; ENSG00000106536 . [P78424-1 ]
ENST00000518318 ; ENSP00000430514 ; ENSG00000106536 . [P78424-2 ]
GeneIDi 11281.
KEGGi hsa:11281.
UCSCi uc003thb.2. human. [P78424-1 ]
uc022acb.1. human. [P78424-2 ]

Organism-specific databases

CTDi 11281.
GeneCardsi GC07P039012.
HGNCi HGNC:21694. POU6F2.
HPAi HPA008699.
MIMi 601583. phenotype.
609062. gene.
neXtProti NX_P78424.
Orphaneti 654. Nephroblastoma.
PharmGKBi PA134969420.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG241882.
HOVERGENi HBG008230.
InParanoidi P78424.
KOi K09368.
OMAi FEARGNT.
OrthoDBi EOG7353Z3.
PhylomeDBi P78424.
TreeFami TF350705.

Miscellaneous databases

ChiTaRSi POU6F2. human.
GenomeRNAii 11281.
NextBioi 42945.
PROi P78424.
SOURCEi Search...

Gene expression databases

ArrayExpressi P78424.
Bgeei P78424.
CleanExi HS_POU6F2.
Genevestigatori P78424.

Family and domain databases

Gene3Di 1.10.10.60. 1 hit.
1.10.260.40. 2 hits.
InterProi IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR010982. Lambda_DNA-bd_dom.
IPR013847. POU.
IPR000327. POU_specific.
[Graphical view ]
Pfami PF00046. Homeobox. 1 hit.
PF00157. Pou. 2 hits.
[Graphical view ]
PRINTSi PR00028. POUDOMAIN.
SMARTi SM00389. HOX. 1 hit.
SM00352. POU. 1 hit.
[Graphical view ]
SUPFAMi SSF46689. SSF46689. 1 hit.
SSF47413. SSF47413. 2 hits.
PROSITEi PS50071. HOMEOBOX_2. 1 hit.
PS00035. POU_1. 1 hit.
PS00465. POU_2. 1 hit.
PS51179. POU_3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Retina-derived POU-domain factor-1: a complex POU-domain gene implicated in the development of retinal ganglion and amacrine cells."
    Zhou H., Yoshioka T., Nathans J.
    J. Neurosci. 16:2261-2274(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY.
    Tissue: Retina.
  2. "The DNA sequence of human chromosome 7."
    Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L.
    , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
    Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "Human chromosome 7: DNA sequence and biology."
    Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S.
    , Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.
    Science 300:767-772(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "Refinement within single yeast artificial chromosome clones of a minimal region commonly deleted on the short arm of chromosome 7 in Wilms tumours."
    Perotti D., Testi M.A., Mondini P., Pilotti S., Green E.D., Pession A., Sozzi G., Pierotti M.A., Fossati-Bellani F., Radice P.
    Genes Chromosomes Cancer 31:42-47(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT WT5 HIS-192.

Entry informationi

Entry nameiPO6F2_HUMAN
AccessioniPrimary (citable) accession number: P78424
Secondary accession number(s): A4D1W2
, C4AMB9, P78425, Q75ME8, Q86UM6, Q9UDS7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2003
Last sequence update: April 5, 2011
Last modified: July 9, 2014
This is version 133 of the entry and version 3 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 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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