Lmo4 (LIM domain only 4) - Rat Genome Database

Name: Lmo4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Lmo4 (LIM domain only 4) Chinchilla lanigera

Analyze

Symbol:

Lmo4

Name:

LIM domain only 4

RGD ID:

8869745

Description:

ENCODES a protein that exhibits DNA-binding transcription factor binding (ortholog); transcription corepressor activity (ortholog); INVOLVED IN motor neuron axon guidance (ortholog); negative regulation of protein-containing complex assembly (ortholog); negative regulation of transcription by RNA polymerase II (ortholog); PARTICIPATES IN interleukin-6 signaling pathway; ASSOCIATED WITH anencephaly (ortholog); genetic disease (ortholog); FOUND IN cell leading edge (ortholog); nucleus (ortholog); RNA polymerase II transcription regulator complex (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

LIM domain transcription factor LMO4

RGD Orthologs

Alliance Genes

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):	LMO4 (LIM domain only 4)	NCBI	Ortholog
Mus musculus (house mouse):	Lmo4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Lmo4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LMO4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LMO4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lmo4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LMO4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LMO4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lmo4 (LIM domain only 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955423	6,849,555 - 6,866,137 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955423	6,849,542 - 6,865,928 (-)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

anencephaly (ISO)

genetic disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

motor neuron axon guidance (ISO)

negative regulation of protein-containing complex assembly (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

neural tube closure (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of cell activation (ISO)

regulation of cell fate specification (ISO)

regulation of cell migration (ISO)

regulation of transcription by RNA polymerase II (ISO)

spinal cord association neuron differentiation (ISO)

spinal cord motor neuron cell fate specification (ISO)

spinal cord motor neuron differentiation (ISO)

thymus development (ISO)

ventral spinal cord interneuron differentiation (ISO)

ventricular septum development (ISO)

Cellular Component

cell leading edge (ISO)

nucleus (ISO)

RNA polymerase II transcription regulator complex (ISO)

Molecular Function

DNA-binding transcription factor binding (ISO)

protein binding (ISO)

transcription corepressor activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

interleukin-6 signaling pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Genomics

Comparative Map Data

Lmo4
(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_004955423	6,849,555 - 6,866,137 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955423	6,849,542 - 6,865,928 (-)	NCBI	ChiLan1.0	ChiLan1.0

LMO4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	87,328,880 - 87,348,923 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	87,328,880 - 87,348,923 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	87,794,563 - 87,814,606 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	87,566,739 - 87,583,851 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	87,506,171 - 87,523,283	NCBI
Celera	1	86,039,830 - 86,060,286 (+)	NCBI		Celera
Cytogenetic Map	1	p22.3	NCBI
HuRef	1	85,907,757 - 85,928,201 (+)	NCBI		HuRef
CHM1_1	1	87,909,001 - 87,929,485 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	87,171,579 - 87,191,625 (+)	NCBI		T2T-CHM13v2.0

Lmo4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	143,894,291 - 143,911,016 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	3	143,894,291 - 143,910,981 (-)	Ensembl		GRCm39 Ensembl
GRCm38	3	144,188,530 - 144,205,255 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	144,188,530 - 144,205,220 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	143,851,494 - 143,868,219 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	3	144,125,916 - 144,142,357 (-)	NCBI		MGSCv36	mm8
Celera	3	150,625,911 - 150,643,008 (-)	NCBI		Celera
Cytogenetic Map	3	H2	NCBI
cM Map	3	68.61	NCBI

Lmo4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	2	235,924,574 - 235,941,609 (-)	NCBI		GRCr8
mRatBN7.2	2	233,264,180 - 233,280,881 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	233,264,182 - 233,280,880 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	2	241,048,779 - 241,065,526 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	238,943,176 - 238,959,923 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	233,806,381 - 233,823,133 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	250,218,635 - 250,235,435 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	250,218,641 - 250,241,673 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	268,752,222 - 268,769,170 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	242,498,074 - 242,515,160 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	2	242,484,813 - 242,501,899 (+)	NCBI
Celera	2	225,256,943 - 225,273,636 (-)	NCBI		Celera
Cytogenetic Map	2	q44	NCBI

LMO4
(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	1	139,625,326 - 139,642,026 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	138,780,899 - 138,797,699 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	119,848,323 - 119,867,007 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	88,698,962 - 88,718,760 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	88,698,962 - 88,718,760 (+)	Ensembl	panpan1.1		panPan2

LMO4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	60,892,478 - 60,909,910 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	60,727,270 - 60,941,058 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	63,606,359 - 63,623,679 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	6	61,432,227 - 61,449,629 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	6	61,430,188 - 61,446,484 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	6	60,967,016 - 60,984,353 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	6	60,923,303 - 60,940,624 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	6	61,421,332 - 61,438,711 (-)	NCBI		UU_Cfam_GSD_1.0

Lmo4
(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_024405058	97,881,311 - 97,900,916 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936732	1,541,515 - 1,555,735 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936732	1,541,511 - 1,557,845 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LMO4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	4	128,894,113 - 128,910,648 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	141,341,687 - 141,354,291 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LMO4
(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	20	46,105,755 - 46,126,291 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	46,105,699 - 46,126,399 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666033	71,708,190 - 71,726,923 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lmo4
(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_004624742	10,207,899 - 10,225,209 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624742	10,207,901 - 10,224,807 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005385115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01023588	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AGCD01023589	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDJ01075782	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDK01018084	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCLAT00000006705 ⟹ ENSCLAP00000006596

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955423	6,849,555 - 6,866,137 (-)	Ensembl

RefSeq Acc Id:

ENSCLAT00000006706 ⟹ ENSCLAP00000006597

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955423	6,849,699 - 6,863,327 (-)	Ensembl

RefSeq Acc Id:

ENSCLAT00000006707 ⟹ ENSCLAP00000006598

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955423	6,850,309 - 6,862,963 (-)	Ensembl

RefSeq Acc Id:

XM_005385115 ⟹ XP_005385172

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955423	6,849,542 - 6,865,928 (-)	NCBI

Sequence:

show sequence

CTCATTCACAGCTCTGCCGTCCGGGCCGGGCGCTTCCTCTGCGGGACCGAAATAACCGAGCACT
GTCACATCGGGTGTGATGCAGCGATCCTCCTTCGGAGGCTCTTCTTTTTCCTAAGCAATAAAAA
ACAACACGCGATTAAAAAAAAAAAAAAGCATCCCTTAGCCCCCTCCTCCCCTTTCCTGCTTCTG
CGAGAACTCCCTCCCTCCCTCCAGCTCCGCCAGCCGAGGCGCCCCTTCCTTCCCTGGAAGCCGA
GCGGCTGCGCTCGCATTCGCCTTCGCCGCCGCCTCGCAGTATTGCAATATAGGGGAGAAGCAGA
CCATGGTGAATCCGGGCAGCAGCTCGCAGCCGCCCCCCGTGACGGCCGGCTCCCTCTCCTGGAA
GCGGTGCGCAGGCTGCGGGGGCAAGATTGCAGACCGCTTTCTGCTCTATGCCATGGACAGCTAC
TGGCACAGCCGGTGCCTCAAGTGCTCCTGCTGCCAGGCGCAGCTGGGCGACATCGGCACGTCCT
GTTACACCAAGAGCGGCATGATTCTTTGCAGAAACGACTACATTAGGTTATTTGGGAATAGCGG
TGCTTGCAGTGCTTGTGGACAGTCGATTCCTGCGAGCGAGCTCGTCATGAGGGCGCAAGGCAAT
GTGTATCATCTTAAGTGTTTCACATGCTCTACCTGCCGGAATCGCCTGGTCCCGGGAGATCGGT
TTCACTACATCAATGGCAGTTTATTCTGTGAACATGATAGACCTACAGCTCTCATCAATGGCCA
TTTGAATTCACTTCAGAGCAATCCACTACTGCCAGACCAGAAGGTCTGCTAAAAGGTCAGAGTA
ATGCAGAATGCGTGCCTTCATCTCAGATTTTGTTCATCACAGGTGGATCCCATGTGTCTTCAGT
AGACAAGTCACCTTTGTAGCTAGCACCAGTGCCAGCTCCATGCCATTGCACCTTCTTTAGTCTT
GATTGCCCTTCCCGCATTTATTGGTGTATTAAAATGACTGAATATGAACATTAAGGACTCCGTG
AACCTGGGCTAATGGGAGACTGTAGAGAAAATGAAAAAAGATCCACCGGAGGACATCTTTGGGG
GGGAGGGAGCTTAGGGGGAGGGAAGTGACTAATGAAGCTAATTAAAAGAAGCATTCAAATCTGC
TTTCTACCCTCATTAACAATTAGCAGGGCACTGGCCGGAGTTTGTACCCTGTGTTTTACCTTAA
CAACATTCTATTTGCTCTTTGTATATTTAAGTGTTGTAAGGAAATGTGTTTCAATCAAAACTGA
ACATGAGATAAAGGAAAGAGATGTGGCTTTTGTGATATTCTATCACAAACACTTTTATTGTATC
TCTGTAAAATACAATGTATGTATGCATGTAAGTGTTTTTGTCCTAATGTTGCTACTCCCATGGC
AAAGATTAAAAAAAAAAAAAAAAAAAACAAAAAAAGAGAAAAAAAATCAGGCTCATAGCAGCTA
CTGTGTAGAAATTTCCCCCTACTTCTAATTTGCTGAATGAAGAAAAAAAATCTTTTATTTGTGA
TATTTTCAGAGACATTTGCTCTAGTATGGTGTATTTAAATAATAAAAACTTAAAAGAAAAAATA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005385172	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000006596
	ENSCLAP00000006596.1
	ENSCLAP00000006597.1
	ENSCLAP00000006598.1

RefSeq Acc Id:	XP_005385172 ⟸ XM_005385115
- UniProtKB:	A0A8C2UWU6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MVNPGSSSQPPPVTAGSLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSCCQAQLGDIGTSC YTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRF HYINGSLFCEHDRPTALINGHLNSLQSNPLLPDQKVC hide sequence

RefSeq Acc Id:

ENSCLAP00000006598 ⟸ ENSCLAT00000006707

RefSeq Acc Id:

ENSCLAP00000006597 ⟸ ENSCLAT00000006706

RefSeq Acc Id:

ENSCLAP00000006596 ⟸ ENSCLAT00000006705

Protein Domains

LIM zinc-binding

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000004652	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000006705	ENTREZGENE
	ENSCLAT00000006705.1	UniProtKB/TrEMBL
	ENSCLAT00000006706.1	UniProtKB/TrEMBL
	ENSCLAT00000006707.1	UniProtKB/TrEMBL
Gene3D-CATH	Cysteine Rich Protein	UniProtKB/TrEMBL
InterPro	Znf_LIM	UniProtKB/TrEMBL
NCBI Gene	Lmo4	ENTREZGENE
PANTHER	LD11652P	UniProtKB/TrEMBL
	LIM DOMAIN TRANSCRIPTION FACTOR LMO4	UniProtKB/TrEMBL
Pfam	LIM	UniProtKB/TrEMBL
PROSITE	LIM_DOMAIN_1	UniProtKB/TrEMBL
	LIM_DOMAIN_2	UniProtKB/TrEMBL
SMART	LIM	UniProtKB/TrEMBL
Superfamily-SCOP	Glucocorticoid receptor-like (DNA-binding domain)	UniProtKB/TrEMBL
UniProt	A0A8C2UWU6	ENTREZGENE, UniProtKB/TrEMBL
	A0A8C2YL37_CHILA	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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - MGI

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - MGI

Imported Annotations - PID (archival)