Alx4 (ALX homeobox 4) - Rat Genome Database

Name: Alx4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Alx4 (ALX homeobox 4) Ictidomys tridecemlineatus

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Symbol:

Alx4

Name:

ALX homeobox 4

RGD ID:

12456859

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity (inferred); INVOLVED IN anterior/posterior pattern specification (ortholog); digestive tract development (ortholog); embryonic digit morphogenesis (ortholog); ASSOCIATED WITH Adenomatous Polyps (ortholog); bronchiolo-alveolar adenocarcinoma (ortholog); colorectal cancer (ortholog); FOUND IN nucleoplasm (inferred); nucleus (inferred); transcription regulator complex (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein aristaless-like 4

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	ALX4 (ALX homeobox 4)	NCBI	Ortholog
Mus musculus (house mouse):	Alx4 (aristaless-like homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Alx4 (ALX homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Alx4 (ALX homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ALX4 (ALX homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ALX4 (ALX homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ALX4 (ALX homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ALX4 (ALX homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Alx4 (ALX homeobox 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	22,204,908 - 22,218,129 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936562	4,314,870 - 4,326,000 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936562	4,316,550 - 4,326,022 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Adenomatous Polyps (ISO)

bronchiolo-alveolar adenocarcinoma (ISO)

colorectal cancer (ISO)

Craniofacial Abnormalities (ISO)

craniosynostosis (ISO)

Craniosynostosis 5 (ISO)

frontonasal dysplasia (ISO)

frontonasal dysplasia 2 (ISO)

gastric adenocarcinoma (ISO)

genetic disease (ISO)

hepatocellular carcinoma (ISO)

intellectual disability (ISO)

lung adenocarcinoma (ISO)

lung cancer (ISO)

Lung Neoplasms (ISO)

optic nerve glioma (ISO)

parietal foramina (ISO)

Parietal Foramina 2 (ISO)

polydactyly (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (IEA,ISO)

digestive tract development (IEA,ISO)

embryonic digit morphogenesis (IEA,ISO)

embryonic forelimb morphogenesis (IEA,ISO)

embryonic hindlimb morphogenesis (IEA,ISO)

embryonic skeletal system morphogenesis (IEA,ISO)

hair follicle development (IEA)

limb morphogenesis (IEA,ISO)

muscle organ development (IEA,ISO)

pattern specification process (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

post-embryonic development (IEA,ISO)

regulation of apoptotic process (IEA,ISO)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IEA,ISO)

roof of mouth development (IEA,ISO)

skeletal system morphogenesis (IEA,ISO)

Cellular Component

nucleoplasm (IEA)

nucleus (IEA)

transcription regulator complex (IEA)

Molecular Function

DNA binding (IEA)

DNA-binding transcription activator activity, RNA polymerase II-specific (IEA)

DNA-binding transcription factor activity (IEA)

DNA-binding transcription factor activity, RNA polymerase II-specific (IEA)

HMG box domain binding (IEA)

protein binding (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IEA)

sequence-specific DNA binding (IEA)

sequence-specific double-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Alx4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	22,204,908 - 22,218,129 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936562	4,314,870 - 4,326,000 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936562	4,316,550 - 4,326,022 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ALX4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	44,260,440 - 44,310,139 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	11	44,260,440 - 44,310,139 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	11	44,281,990 - 44,331,689 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	44,242,734 - 44,288,292 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	11	44,242,733 - 44,288,292	NCBI
Celera	11	44,429,565 - 44,479,005 (-)	NCBI		Celera
Cytogenetic Map	11	p11.2	NCBI
HuRef	11	43,991,253 - 44,040,694 (-)	NCBI		HuRef
CHM1_1	11	44,281,300 - 44,330,733 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	11	44,415,783 - 44,465,465 (-)	NCBI		T2T-CHM13v2.0

Alx4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	93,472,779 - 93,511,686 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	93,472,729 - 93,511,684 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	93,642,434 - 93,681,341 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	93,642,384 - 93,681,339 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	93,482,591 - 93,521,496 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	93,443,273 - 93,478,775 (+)	NCBI		MGSCv36	mm8
Celera	2	95,046,101 - 95,085,009 (+)	NCBI		Celera
Cytogenetic Map	2	E1	NCBI
cM Map	2	51.62	NCBI

Alx4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	100,067,052 - 100,103,624 (+)	NCBI		GRCr8
mRatBN7.2	3	79,611,682 - 79,648,260 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	79,611,719 - 79,648,260 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	83,085,796 - 83,122,265 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	91,684,866 - 91,721,334 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	89,536,444 - 89,573,057 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	82,548,959 - 82,585,531 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	82,548,959 - 82,585,531 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	89,249,541 - 89,286,113 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	78,057,714 - 78,094,285 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	77,954,190 - 77,990,612 (+)	NCBI
Celera	3	78,814,063 - 78,850,575 (+)	NCBI		Celera
Cytogenetic Map	3	q31	NCBI

Alx4
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955422	3,278,615 - 3,291,714 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	3,278,615 - 3,290,799 (+)	NCBI	ChiLan1.0	ChiLan1.0

ALX4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	9	46,474,416 - 46,524,451 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	11	46,464,895 - 46,530,312 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	11	44,219,865 - 44,269,597 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	11	44,714,503 - 44,729,758 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

ALX4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	18	44,922,042 - 44,967,557 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	44,922,150 - 44,967,550 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	43,590,411 - 43,635,910 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	18	45,583,479 - 45,629,082 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	18	45,583,532 - 45,629,081 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	18	45,066,662 - 45,112,191 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	18	44,620,210 - 44,665,671 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	18	45,356,336 - 45,401,930 (+)	NCBI		UU_Cfam_GSD_1.0

ALX4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	18,037,401 - 18,085,683 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	18,070,726 - 18,085,685 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	19,626,044 - 19,627,294 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ALX4
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	1	21,051,413 - 21,099,159 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	1	21,051,580 - 21,097,605 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	118,279,875 - 118,329,166 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Alx4
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624767	3,770,762 - 3,805,323 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624767	3,770,755 - 3,808,511 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005330087	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000021489 ⟹ ENSSTOP00000022296

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936562	4,314,870 - 4,326,000 (+)	Ensembl

RefSeq Acc Id:

XM_005330087 ⟹ XP_005330144

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404947	22,204,908 - 22,218,129 (+)	NCBI
SpeTri2.0	NW_004936562	4,316,550 - 4,326,022 (+)	NCBI

Sequence:

show sequence

ATGGCCTCCAAAGCTGTCCCCAGACCTACTCTGGGCAGTCACCTCTGCCCGATTTTCCTCAATG
CCATGGAGACAGCGGGGGACAGAGCCAAAGAGAGCTCCCTGGGGGAGCCGGAGTTGCCCCCCGA
CCCTGACGCCGTGGGCATGGACAGCAGCTACCTCAGTGTGAAGGAGGCTGGGGTCAAGGGGCCC
CAGGACCGGGCCGGCTCCGAGCTCCCCAGCCCCCTGGAGAAGGCGGACTCGGAGAGCAACAAGG
GCAAGAAGCGGCGGAACCGCACCACCTTCACCAGCTACCAGCTGGAGGAGCTGGAGAAGGTCTT
CCAGAAGACGCACTACCCCGACGTGTACGCGCGCGAGCAGCTGGCCATGAGGACCGACCTCACC
GAGGCCCGCGTGCAGGTCTGGTTCCAGAACCGGAGGGCCAAGTGGAGGAAGAGGGAGCGCTTCG
GGCAGATGCAGCAGGTGCGGACCCACTTCTCCACGGCCTACGAGCTGCCCCTGCTCACCCGGGC
TGAGAACTACGCGCAGATTCAGAACCCGTCCTGGATCAGCAACAACGGGGCTGCCTCGCCGGTG
CCGGCCTGTGTGGTCCCCTGTGACCCGGTGCCTGCCTGCATGTCCCCTCACGCCCACCCCCCTG
GCTCTGGGGCCAGCGGTGTCACCGACTTCCTGAGTGTCTCTGGGGCTGGCAGCCACGTGGGCCA
GACGCACATGGGCAGCCTGTTCGGAGCGGCTGGCCTCAGCCCGGGCCTCAACGGCTATGAGCTC
AATGGCGAGCCGGACCGCAAGACCTCGAGCATCGCGGCGCTGCGCATGAAGGCCAAGGAGCACA
GTGCGGCCATCTCCTGGGCCACATGACAGGGCCCCTCCCGTCCGGCCC

hide sequence

Protein Sequences


Protein RefSeqs	XP_005330144	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000022296.2
GenBank Protein	KAG3285432	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005330144 ⟸ XM_005330087

- Sequence:

show sequence

MASKAVPRPTLGSHLCPIFLNAMETAGDRAKESSLGEPELPPDPDAVGMDSSYLSVKEAGVKGP
QDRAGSELPSPLEKADSESNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLT
EARVQVWFQNRRAKWRKRERFGQMQQVRTHFSTAYELPLLTRAENYAQIQNPSWISNNGAASPV
PACVVPCDPVPACMSPHAHPPGSGASGVTDFLSVSGAGSHVGQTHMGSLFGAAGLSPGLNGYEL
NGEPDRKTSSIAALRMKAKEHSAAISWAT

hide sequence

Ensembl Acc Id:

ENSSTOP00000022296 ⟸ ENSSTOT00000021489

Protein Domains

Homeobox OAR

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000029078	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000021489.2	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	OAR_dom	UniProtKB/TrEMBL
	Paired_Homeobox_TFs	UniProtKB/TrEMBL
NCBI Gene	Alx4	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN ARISTALESS	UniProtKB/TrEMBL
	PTHR24329:SF322	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
	OAR	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
	OAR	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	I3ND49_ICTTR	UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD

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