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Protein

Forkhead box protein D1

Gene

Foxd1

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

Functioni

Transcription factor required for formation of positional identity in the developing retina, regionalization of the optic chiasm and morphogenesis of the kidney. Can neuralize ectodermal cells directly.3 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi130 – 22495Fork-headPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: MGI
  • DNA binding, bending Source: MGI
  • RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: NTNU_SB
  • sequence-specific DNA binding Source: MGI
  • transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding Source: NTNU_SB

GO - Biological processi

  • axon guidance Source: MGI
  • branching involved in ureteric bud morphogenesis Source: MGI
  • dichotomous subdivision of terminal units involved in ureteric bud branching Source: UniProtKB
  • kidney development Source: MGI
  • luteinizing hormone secretion Source: CACAO
  • metanephric capsule development Source: UniProtKB
  • metanephric capsule specification Source: UniProtKB
  • metanephric nephron development Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • nephrogenic mesenchyme development Source: UniProtKB
  • pattern specification involved in metanephros development Source: UniProtKB
  • positive regulation of BMP signaling pathway Source: UniProtKB
  • positive regulation of gene expression Source: UniProtKB
  • positive regulation of kidney development Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: NTNU_SB
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Forkhead box protein D1
Alternative name(s):
Brain factor 2
Short name:
BF-2
Forkhead-related protein FKHL8
Forkhead-related transcription factor 4
Short name:
FREAC-4
HFH-BF-2
Gene namesi
Name:Foxd1
Synonyms:Fkhl8, Freac4, Hfhbf2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1347463. Foxd1.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Mice show disrupted cell identity in the ventrotemporal area of the retina and aberrant morphogenesis of the optic chiasm. Their kidneys remain fused, have a disorganised ureteric tree and fail to ascend to a lumbar position.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 456456Forkhead box protein D1PRO_0000091812Add
BLAST

Proteomic databases

PaxDbiQ61345.
PRIDEiQ61345.

PTM databases

PhosphoSiteiQ61345.

Expressioni

Tissue specificityi

Predominantly expressed in the CNS and temporal half of the retina. Also expressed in the condensed head mesenchyme, metanephric blastema of the developing kidney, cortex of the adrenal gland, condensed mesenchyme at the base of the follicles of vibrassae and cartilage perichondrium of the developing vertebrate.

Developmental stagei

At E9.5 embryos, expressed in a limited region of the neuroepithelium and also in the temporal half of the primary optic cup and the optic stalk. At E10.5, seen in the hypothalamus, temporal half of the optic stalk, and temporal hemiretina. At E12.5 and E13.5 a high expression is seen in regions of condensed mesenchyme of the head, and as neuroepithelial cells begin to differentiate and migrate outward from the ventricular zone, expression declines markedly. By E16.5 levels are diminished and restricted to unfused pockets along the exhausted ventricular zone.

Gene expression databases

BgeeiQ61345.
CleanExiMM_FOXD1.
GenevisibleiQ61345. MM.

Interactioni

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000100725.

Structurei

3D structure databases

ProteinModelPortaliQ61345.
SMRiQ61345. Positions 129-225.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi29 – 324Poly-Glu
Compositional biasi33 – 364Poly-Asp
Compositional biasi38 – 469Poly-Gly
Compositional biasi55 – 584Poly-Arg
Compositional biasi73 – 764Poly-Asp
Compositional biasi261 – 2677Poly-Pro
Compositional biasi293 – 30210Poly-Ala
Compositional biasi308 – 31912Poly-ProAdd
BLAST
Compositional biasi395 – 4006Poly-Gly
Compositional biasi420 – 4256Poly-Ala

Sequence similaritiesi

Contains 1 fork-head DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2294. Eukaryota.
COG5025. LUCA.
GeneTreeiENSGT00760000118904.
HOGENOMiHOG000231285.
HOVERGENiHBG051641.
InParanoidiQ61345.
KOiK09397.
OMAiMTLSTEM.
OrthoDBiEOG7C8GHD.
TreeFamiTF316127.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR001766. Fork_head_dom.
IPR018122. TF_fork_head_CS_1.
IPR030456. TF_fork_head_CS_2.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00250. Forkhead. 1 hit.
[Graphical view]
PRINTSiPR00053. FORKHEAD.
SMARTiSM00339. FH. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS00657. FORK_HEAD_1. 1 hit.
PS00658. FORK_HEAD_2. 1 hit.
PS50039. FORK_HEAD_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q61345-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTLSTEMSDA SGLAEETDID VVGEGEDDEE EEDDDDEGGG GRGGGGSRLP
60 70 80 90 100
SSAQRRRRSY AGEDDLEDLE EEDDDDLLLA SRPAASPAPP GPAPAPGTGS
110 120 130 140 150
GGCSGAGAGG GAGGGTGAGT GGGAKNPLVK PPYSYIALIT MAILQSPKKR
160 170 180 190 200
LTLSEICEFI SSRFPYYREK FPAWQNSIRH NLSLNDCFVK IPREPGNPGK
210 220 230 240 250
GNYWTLDPES ADMFDNGSFL RRRKRFKRQP LLAPHAAAEA LLLRGAGPAA
260 270 280 290 300
GAGDPGAALF PPPPPPPACG YGAYGCAYGL QLPPCAPPSA LFAAAAAAAA
310 320 330 340 350
AAFHPHSPPP PPPPPPPPPG AAAELARTAF GYRSHALAAA LPGPLQAAAV
360 370 380 390 400
KAGGPGAAAL ARSPFSIESL IGRTRGPAAA GAHVSSGAAS GTAPGPGGGG
410 420 430 440 450
CAVQAAAGPA VALTRSLVVA AAAAASSVSS SAALGTLHQG TALSSVENFT

ARISNC
Length:456
Mass (Da):45,371
Last modified:July 27, 2011 - v2
Checksum:i3153172991DC99A4
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti355 – 3551P → R in AAC42042 (PubMed:7815060).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L38607 mRNA. Translation: AAC42042.1.
AK132390 mRNA. Translation: BAE21140.1.
AK142034 mRNA. Translation: BAE24920.1.
CCDSiCCDS36759.1.
RefSeqiNP_032268.2. NM_008242.2.
UniGeneiMm.347441.

Genome annotation databases

EnsembliENSMUST00000105098; ENSMUSP00000100725; ENSMUSG00000078302.
GeneIDi15229.
KEGGimmu:15229.
UCSCiuc009van.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L38607 mRNA. Translation: AAC42042.1.
AK132390 mRNA. Translation: BAE21140.1.
AK142034 mRNA. Translation: BAE24920.1.
CCDSiCCDS36759.1.
RefSeqiNP_032268.2. NM_008242.2.
UniGeneiMm.347441.

3D structure databases

ProteinModelPortaliQ61345.
SMRiQ61345. Positions 129-225.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000100725.

PTM databases

PhosphoSiteiQ61345.

Proteomic databases

PaxDbiQ61345.
PRIDEiQ61345.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000105098; ENSMUSP00000100725; ENSMUSG00000078302.
GeneIDi15229.
KEGGimmu:15229.
UCSCiuc009van.1. mouse.

Organism-specific databases

CTDi2297.
MGIiMGI:1347463. Foxd1.

Phylogenomic databases

eggNOGiKOG2294. Eukaryota.
COG5025. LUCA.
GeneTreeiENSGT00760000118904.
HOGENOMiHOG000231285.
HOVERGENiHBG051641.
InParanoidiQ61345.
KOiK09397.
OMAiMTLSTEM.
OrthoDBiEOG7C8GHD.
TreeFamiTF316127.

Miscellaneous databases

PROiQ61345.
SOURCEiSearch...

Gene expression databases

BgeeiQ61345.
CleanExiMM_FOXD1.
GenevisibleiQ61345. MM.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR001766. Fork_head_dom.
IPR018122. TF_fork_head_CS_1.
IPR030456. TF_fork_head_CS_2.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00250. Forkhead. 1 hit.
[Graphical view]
PRINTSiPR00053. FORKHEAD.
SMARTiSM00339. FH. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS00657. FORK_HEAD_1. 1 hit.
PS00658. FORK_HEAD_2. 1 hit.
PS50039. FORK_HEAD_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Expression of winged helix genes, BF-1 and BF-2, define adjacent domains within the developing forebrain and retina."
    Hatini V., Tao W., Lai E.
    J. Neurobiol. 25:1293-1309(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: BALB/cJ.
    Tissue: Embryo.
  2. "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].
    Strain: C57BL/6J.
    Tissue: Eye and Head.
  3. "XBF-2 is a transcriptional repressor that converts ectoderm into neural tissue."
    Mariani F.V., Harland R.M.
    Development 125:5019-5031(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "Foxd1 is required for proper formation of the optic chiasm."
    Herrera E., Marcus R., Li S., Williams S.E., Erskine L., Lai E., Mason C.
    Development 131:5727-5739(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  5. "Foxd1-dependent signals control cellularity in the renal capsule, a structure required for normal renal development."
    Levinson R.S., Batourina E., Choi C., Vorontchikhina M., Kitajewski J., Mendelsohn C.L.
    Development 132:529-539(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiFOXD1_MOUSE
AccessioniPrimary (citable) accession number: Q61345
Secondary accession number(s): Q3UQW8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: July 27, 2011
Last modified: July 6, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Caution

Was originally assigned to be BF-2 (FOXG1).1 Publication

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

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 one 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.