Foxd1 MGI Mouse Gene Detail - MGI:1347463

Symbol

Foxd1
Name

forkhead box D1
Synonyms

BF-2, FREAC4, Hfh10, Hfhbf2

Feature Type

protein coding gene
IDs

MGI:1347463
NCBI Gene: 15229
Alliance

gene page
Transcription Start Sites

10 TSS

Sequence Map

Chr13:98490753-98493213 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 13, 51.96 cM
Mapping Data

3 experiments

SNPs within 2kb

115 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1347463	protein coding gene	Chr13:98490750-98495813 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0020866	protein coding gene	Chr13:100058151-100060612 (+)
A/J	MGP_AJ_G0020820	protein coding gene	Chr13:96243440-96245901 (+)
AKR/J	MGP_AKRJ_G0020794	protein coding gene	Chr13:99182306-99184764 (+)
BALB/cJ	MGP_BALBcJ_G0020818	protein coding gene	Chr13:96948942-96951403 (+)
C3H/HeJ	MGP_C3HHeJ_G0020609	protein coding gene	Chr13:98920926-98923387 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0021252	protein coding gene	Chr13:103071075-103073566 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018822	protein coding gene	Chr13:91991411-91993885 (+)
CAST/EiJ	MGP_CASTEiJ_G0020128	protein coding gene	Chr13:98289792-98292259 (+)
CBA/J	MGP_CBAJ_G0020569	protein coding gene	Chr13:107174196-107176654 (+)
DBA/2J	MGP_DBA2J_G0020694	protein coding gene	Chr13:96017192-96019650 (+)
FVB/NJ	MGP_FVBNJ_G0020675	protein coding gene	Chr13:94777312-94779673 (+)
LP/J	MGP_LPJ_G0020769	protein coding gene	Chr13:100162485-100164946 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0020703	protein coding gene	Chr13:107484011-107486472 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0021293	protein coding gene	Chr13:98639089-98641550 (+)
PWK/PhJ	MGP_PWKPhJ_G0019881	protein coding gene	Chr13:94824283-94835237 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0019704	protein coding gene	Chr13:94909046-94911503 (+)
WSB/EiJ	MGP_WSBEiJ_G0020185	protein coding gene	Chr13:99078471-99080929 (+)

Human Ortholog

FOXD1, forkhead box D1

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FOXD1, forkhead box D1
Synonyms

FKHL8, FREAC-4, FREAC4
Links

HGNC:3802

NCBI Gene ID: 2297

neXtProt AC: NX_Q16676

UniProt: Q16676
Chr Location

5q13.2; chr5:73444827-73448777 (-) GRCh38

MGI Vertebrate Homology

Foxd1 stringent orthology
1 human;1 mouse;1 zebrafish
HCOP

vertebrate homology predictions: FOXD1
Gene Tree

Foxd1

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Phenotype Summary

23 phenotypes from 1 allele in 1 genetic background
4 phenotypes from multigenic genotypes
103 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

8
Endonuclease-mediated

4
Targeted

4
Find Mice (IMSR)

13 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Mice homozygous for this targeted mutation die within 24 hours after birth with severe defects in nephrogenesis, and abnormal development of the renal collecting system.

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All GO Annotations

29
GO References

10

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1383
Tissues

358
cDNA Data

28
Literature Summary

145

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase foxd1

ZFIN foxd1

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All Sequences

33
RefSeq

2
UniProt

2
CCDS

CCDS36759.1

Ensembl

ENSMUSG00000078302 (Evidence)
NCBI Gene

15229

			Length	Strain/Species	Flank
genomic	15229	NCBI Gene Model \| MGI Sequence Detail	2461	C57BL/6J	± kb
transcript	NM_008242	RefSeq \| MGI Sequence Detail	2461	ZRU/MplStud
polypeptide	Q61345	UniProt \| EBI \| MGI Sequence Detail	456	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000007609 forkhead box protein D1

(term hierarchy)
InterPro Domains

IPR050211 Forkhead box domain-containing protein

IPR001766 Fork head domain

IPR018122 Fork head domain conserved site1

IPR030456 Fork head domain conserved site 2

IPR036390 Winged helix DNA-binding domain superfamily

IPR036388 Winged helix-like DNA-binding domain superfamily

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All nucleic 45

cDNA 29

Primer pair 4

Other 12

Microarray probesets 2

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MGD-MRK-16691, MGI:2145223, MGI:99895

Summaries

All 240

Developmental Gene Expression 145

Gene Ontology 10

Phenotypes 103
Earliest

J:20863 Clevidence DE, et al., Identification of nine tissue-specific transcription factors of the hepatocyte nuclear factor 3/forkhead DNA-binding-domain family. Proc Natl Acad Sci U S A. 1993 May 1;90(9):3948-52
Latest

J:350438 Hampl M, et al., Early embryogenesis in CHDFIDD mouse model reveals facial clefts and altered cranial neurogenesis. Dis Model Mech. 2024 Jun 1;17(6)

TSS for Foxd1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr120803	Chr13:98490742-98490758 (+)	-3 bp
Tssr120804	Chr13:98490789-98490796 (+)	40 bp
Tssr120805	Chr13:98490896-98490907 (+)	149 bp
Tssr120806	Chr13:98490948-98490959 (+)	201 bp
Tssr120807	Chr13:98491282-98491298 (+)	537 bp
Tssr120808	Chr13:98491310-98491317 (+)	561 bp
Tssr120809	Chr13:98491489-98491505 (+)	744 bp
Tssr120810	Chr13:98491592-98491604 (+)	845 bp
Tssr120811	Chr13:98491610-98491622 (+)	863 bp
Tssr120812	Chr13:98492743-98492746 (+)	1,992 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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