Lig4 (DNA ligase 4) - Rat Genome Database

Name: Lig4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Lig4 (DNA ligase 4) Rattus norvegicus

Analyze

Symbol:

Lig4

Name:

DNA ligase 4

RGD ID:

1304639

Description:

Enables ATP binding activity; DNA binding activity; and DNA ligase (ATP) activity. Involved in DNA ligation and cellular response to lithium ion. Predicted to be located in condensed chromosome and nucleoplasm. Predicted to be part of DNA ligase IV complex and DNA-dependent protein kinase-DNA ligase 4 complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in several diseases, including DNA ligase IV deficiency; colorectal cancer; multiple myeloma; pancreatic cancer; and prostate cancer. Orthologous to human LIG4 (DNA ligase 4); PARTICIPATES IN non-homologous end joining pathway of double-strand break repair; INTERACTS WITH 17beta-estradiol; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

DNA ligase (ATP) 4; ligase IV, DNA, ATP-dependent; LOC290907

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):	LIG4 (DNA ligase 4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Lig4 (ligase IV, DNA, ATP-dependent)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lig4 (DNA ligase 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LIG4 (DNA ligase 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LIG4 (DNA ligase 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lig4 (DNA ligase 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LIG4 (DNA ligase 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LIG4 (DNA ligase 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lig4 (DNA ligase 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	BRDT (bromodomain testis associated)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	LIG4 (DNA ligase 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Lig4 (ligase IV, DNA, ATP-dependent)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	lig4 (ligase IV, DNA, ATP-dependent)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	DNL4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	DNAlig4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	lig-4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	lig4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	16	79,518,393 - 79,526,956 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	79,518,312 - 79,527,040 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	84,798,850 - 84,805,611 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	88,251,496 - 88,258,257 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	83,493,568 - 83,499,498 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	85,331,771 - 85,339,496 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	85,331,866 - 85,337,769 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	84,770,824 - 84,778,539 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	84,881,880 - 84,888,448 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	84,871,561 - 84,874,322 (+)	NCBI
Celera	16	77,305,627 - 77,312,388 (+)	NCBI		Celera
Cytogenetic Map	16	q12.5	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Anal Atresia, Hypospadias, and Penoscrotal Inversion (ISO)

colorectal cancer (ISO)

DNA ligase IV deficiency (ISO,ISS)

genetic disease (ISO)

high grade glioma (ISO)

multiple myeloma (ISO)

pancreatic cancer (ISO)

prostate cancer (ISO)

severe combined immunodeficiency (ISO)

severe combined immunodeficiency with sensitivity to ionizing radiation (ISO)

thyroid gland papillary carcinoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-quinic acid (ISO)

(S)-nicotine (ISO)

1,2-dimethylhydrazine (ISO)

1-nitropyrene (ISO)

17beta-estradiol (EXP)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-acetamidofluorene (EXP)

2-butoxyethanol (ISO)

6-propyl-2-thiouracil (EXP)

acrolein (ISO)

aflatoxin B1 (EXP,ISO)

aflatoxin M1 (ISO)

alpha-pinene (ISO)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

barium sulfate (EXP)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

biphenyl-4-amine (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP)

bortezomib (ISO)

carbon nanotube (ISO)

ceric oxide (EXP)

chlordecone (ISO)

clorgyline (ISO)

copper atom (EXP)

copper(0) (EXP)

coumestrol (ISO)

crocidolite asbestos (ISO)

curcumin (ISO)

cyclosporin A (ISO)

cylindrospermopsin (ISO)

dioxygen (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

fonofos (ISO)

gallic acid (ISO)

gold atom (ISO)

gold(0) (ISO)

hydrogen peroxide (ISO)

inulin (ISO)

lead diacetate (EXP)

lead(0) (ISO)

lithium chloride (EXP)

methylmercury chloride (ISO)

nickel dichloride (ISO)

nicotine (ISO)

ozone (ISO)

paracetamol (EXP,ISO)

parathion (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenylmercury acetate (ISO)

propiconazole (ISO)

resveratrol (ISO)

SB 431542 (ISO)

succimer (ISO)

terbufos (ISO)

thioacetamide (EXP)

trichloroethene (EXP)

trichostatin A (ISO)

urethane (ISO)

valproic acid (EXP,ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to ionizing radiation (ISO)

cellular response to lithium ion (IEP)

central nervous system development (ISO)

chromosome organization (ISO)

DN2 thymocyte differentiation (ISO)

DNA biosynthetic process (IEA)

DNA ligation (IDA,ISO)

DNA ligation involved in DNA recombination (ISO)

DNA ligation involved in DNA repair (ISO)

DNA repair (ISO)

DNA replication (IEA)

double-strand break repair (ISO)

double-strand break repair via classical nonhomologous end joining (ISO)

double-strand break repair via nonhomologous end joining (IBA,ISO)

fibroblast proliferation (ISO)

immunoglobulin V(D)J recombination (IBA,ISO)

in utero embryonic development (ISO)

isotype switching (ISO)

negative regulation of neuron apoptotic process (ISO)

neurogenesis (ISO)

neuron apoptotic process (ISO)

nucleotide-excision repair, DNA gap filling (IBA,ISO)

positive regulation of chromosome organization (ISO)

positive regulation of fibroblast proliferation (ISO)

positive regulation of neurogenesis (ISO)

pro-B cell differentiation (ISO)

response to gamma radiation (ISO)

response to ionizing radiation (ISO)

response to X-ray (ISO)

single strand break repair (ISO)

somatic stem cell population maintenance (ISO)

stem cell proliferation (ISO)

T cell receptor V(D)J recombination (ISO)

V(D)J recombination (ISO)

Cellular Component

condensed chromosome (ISO)

DNA ligase IV complex (IBA,ISO)

DNA-dependent protein kinase-DNA ligase 4 complex (IBA,ISO)

intracellular membrane-bounded organelle (ISO)

nonhomologous end joining complex (ISO)

nucleoplasm (IEA,ISO)

nucleus (ISO)

Molecular Function

ATP binding (IBA,IDA,ISO)

DNA binding (IBA,IDA,ISO)

DNA ligase (ATP) activity (IBA,IDA,ISO)

DNA ligase activity (ISO)

ligase activity (ISO)

magnesium ion binding (IEA,ISO)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

non-homologous end joining pathway of double-strand break repair (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Association of DNA repair and steroid metabolism gene polymorphisms with clinical late toxicity in patients treated with conformal radiotherapy for prostate cancer.	Damaraju S, etal., Clin Cancer Res. 2006 Apr 15;12(8):2545-54.
2.	Ligase-4 Deficiency Causes Distinctive Immune Abnormalities in Asymptomatic Individuals.	Felgentreff K, etal., J Clin Immunol. 2016 May;36(4):341-53. doi: 10.1007/s10875-016-0266-5. Epub 2016 Apr 11.
3.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
5.	Altered regulation of DNA ligase IV activity by aberrant promoter DNA methylation and gene amplification in colorectal cancer.	Kuhmann C, etal., Hum Mol Genet. 2014 Apr 15;23(8):2043-54. doi: 10.1093/hmg/ddt599. Epub 2013 Nov 26.
6.	DNA repair gene polymorphisms and risk of pancreatic cancer.	Li D, etal., Clin Cancer Res. 2009 Jan 15;15(2):740-6.
7.	The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway.	Lieber MR Annu Rev Biochem. 2010;79:181-211. doi: 10.1146/annurev.biochem.052308.093131.
8.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
9.	Non-histone chromosomal proteins HMG1 and 2 enhance ligation reaction of DNA double-strand breaks.	Nagaki S, etal., Biochem Biophys Res Commun. 1998 May 8;246(1):137-41.
10.	Impaired lymphocyte development and antibody class switching and increased malignancy in a murine model of DNA ligase IV syndrome.	Nijnik A, etal., J Clin Invest. 2009 Jun;119(6):1696-705. doi: 10.1172/JCI32743. Epub 2009 May 18.
11.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
12.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
13.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
15.	Comprehensive gene review and curation	RGD comprehensive gene curation
16.	Genetic variants of NHEJ DNA ligase IV can affect the risk of developing multiple myeloma, a tumour characterised by aberrant class switch recombination.	Roddam PL, etal., J Med Genet. 2002 Dec;39(12):900-5.
17.	Homozygous DNA ligase IV R278H mutation in mice leads to leaky SCID and represents a model for human LIG4 syndrome.	Rucci F, etal., Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3024-9. doi: 10.1073/pnas.0914865107. Epub 2010 Feb 1.
18.	Genetic polymorphisms of DNA double-strand break repair pathway genes and glioma susceptibility.	Zhao P, etal., BMC Cancer. 2013 May 10;13:234. doi: 10.1186/1471-2407-13-234.
19.	Lithium chloride protects retinal neurocytes from nutrient deprivation by promoting DNA non-homologous end-joining.	Zhuang J, etal., Biochem Biophys Res Commun. 2009 Mar 13;380(3):650-4. Epub 2009 Jan 31.

Additional References at PubMed

PMID:8798671	PMID:9242410	PMID:9809069	PMID:9823897	PMID:9875844	PMID:9889105	PMID:10716994	PMID:10823907	PMID:10911993	PMID:11248063	PMID:11779495	PMID:12361565
PMID:12517771	PMID:12531011	PMID:12589063	PMID:15175260	PMID:15194694	PMID:15968270	PMID:16777961	PMID:17554302	PMID:17713479	PMID:19589734	PMID:20383123	PMID:21390131
PMID:22192310	PMID:23275564	PMID:24837021	PMID:25941166	PMID:29463814

Genomics

Comparative Map Data

Lig4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	16	79,518,393 - 79,526,956 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	79,518,312 - 79,527,040 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	84,798,850 - 84,805,611 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	88,251,496 - 88,258,257 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	83,493,568 - 83,499,498 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	85,331,771 - 85,339,496 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	85,331,866 - 85,337,769 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	84,770,824 - 84,778,539 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	84,881,880 - 84,888,448 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	84,871,561 - 84,874,322 (+)	NCBI
Celera	16	77,305,627 - 77,312,388 (+)	NCBI		Celera
Cytogenetic Map	16	q12.5	NCBI

LIG4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	13	108,207,442 - 108,218,349 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	13	108,207,439 - 108,218,368 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	13	108,859,790 - 108,870,697 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	107,657,791 - 107,668,717 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	13	107,657,791 - 107,665,883	NCBI
Celera	13	89,704,529 - 89,715,460 (-)	NCBI		Celera
Cytogenetic Map	13	q33.3	NCBI
HuRef	13	89,450,570 - 89,461,621 (-)	NCBI		HuRef
CHM1_1	13	108,828,932 - 108,839,838 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	13	107,433,544 - 107,444,540 (-)	NCBI		T2T-CHM13v2.0

Lig4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	10,020,020 - 10,027,680 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	10,019,049 - 10,027,686 (-)	Ensembl		GRCm39 Ensembl
GRCm38	8	9,970,020 - 9,977,680 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	9,969,049 - 9,977,686 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	9,970,020 - 9,976,323 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	8	9,969,992 - 9,976,295 (-)	NCBI		MGSCv36	mm8
Celera	8	10,145,430 - 10,151,733 (-)	NCBI		Celera
Cytogenetic Map	8	A1.1	NCBI
cM Map	8	4.52	NCBI

Lig4
(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_004955404	3,606,077 - 3,615,193 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955404	3,606,077 - 3,615,193 (+)	NCBI	ChiLan1.0	ChiLan1.0

LIG4
(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	13	108,374,564 - 108,385,554 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	13	89,336,434 - 89,347,418 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	13	108,474,718 - 108,485,421 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	13	108,475,820 - 108,478,555 (-)	Ensembl	panpan1.1		panPan2

LIG4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	22	56,980,333 - 56,987,636 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	22	56,980,622 - 56,983,357 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	22	56,752,066 - 56,759,380 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	22	57,500,830 - 57,508,151 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	22	57,500,745 - 57,510,390 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	22	57,101,978 - 57,109,289 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	22	57,090,156 - 57,097,580 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	22	57,127,280 - 57,134,599 (-)	NCBI		UU_Cfam_GSD_1.0

Lig4
(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_024404945	192,083,762 - 192,090,382 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936472	3,861,866 - 3,867,933 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936472	3,861,833 - 3,867,943 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LIG4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	75,537,036 - 75,547,716 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	11	75,537,027 - 75,547,711 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	11	82,953,056 - 82,962,185 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LIG4
(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	3	86,576,200 - 86,587,097 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	3	86,577,304 - 86,580,039 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666046	43,235,759 - 43,246,667 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lig4
(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_004624793	3,699,506 - 3,706,073 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624793	3,699,394 - 3,706,591 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Lig4
91 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	26
Count of miRNA genes:	25
Interacting mature miRNAs:	26
Transcripts:	ENSRNOT00000019615
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1600378	Arunc4	Aerobic running capacity QTL 4		0.03	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	16	380245	80345693	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor depth of invasion (CMO:0001888)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor depth of invasion (CMO:0001888)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor diameter (CMO:0001889)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor diameter (CMO:0001889)	16	17696791	82635055	Rat
1578768	Stresp22	Stress response QTL 22	2.8		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	16	35288870	80288870	Rat
2293690	Bss45	Bone structure and strength QTL 45	5.13	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	16	37752156	82752156	Rat
2300163	Bmd64	Bone mineral density QTL 64	5.3	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	16	37752156	82752156	Rat
7205510	Activ5	Activity QTL 5	3.78	0.00028	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	16	42396345	84729064	Rat
8694429	Bw164	Body weight QTL 164	5	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	16	52726464	84729064	Rat
8694364	Abfw7	Abdominal fat weight QTL 7	12.22	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	16	52726464	84729064	Rat
7411648	Foco22	Food consumption QTL 22	15	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	16	52726464	84729064	Rat
631525	Pia14	Pristane induced arthritis QTL 14	4.4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	16	55711087	83402471	Rat

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2	30	28	16	19	16			73	30	35	11
Low	1	13	29	25		25	8	11	1	5	6		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106095	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006253477	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017600050	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473970	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000283	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000019615 ⟹ ENSRNOP00000019615

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,518,399 - 79,527,040 (+)	Ensembl
Rnor_6.0 Ensembl	16	85,331,866 - 85,337,769 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000097537 ⟹ ENSRNOP00000095406

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,518,312 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000101750 ⟹ ENSRNOP00000093705

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,518,462 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000106603 ⟹ ENSRNOP00000092486

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,518,451 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000111224 ⟹ ENSRNOP00000078250

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,518,412 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000111250 ⟹ ENSRNOP00000079496

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,518,423 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000112670 ⟹ ENSRNOP00000077244

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,518,420 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000116261 ⟹ ENSRNOP00000076669

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,521,846 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000116266 ⟹ ENSRNOP00000091637

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	79,521,699 - 79,527,040 (+)	Ensembl

RefSeq Acc Id:

NM_001106095 ⟹ NP_001099565

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	79,518,468 - 79,525,229 (+)	NCBI
Rnor_6.0	16	85,331,866 - 85,337,769 (+)	NCBI
Rnor_5.0	16	84,770,824 - 84,778,539 (+)	NCBI
RGSC_v3.4	16	84,881,880 - 84,888,448 (+)	RGD
Celera	16	77,305,627 - 77,312,388 (+)	RGD

Sequence:

show sequence

TAGGCAAGTCGTGTGGCGGGCTGTCAGGTCCTAGCGTCACCACCCCGGAGCTTCTCGTGGGGCG
ACGCCTTCCGCGGTGCAGCCGGCTCGCTGCGGACTCGTTTCAGGTGGCAGCCACCGGGTGAGGA
AATCTTGTTCTGATAATTAGTTGTGTACATTCTGAAAGTGAAGCCTCCCTCTGCCGCCTAGCTA
CCTAGGACGGCCGCACTCCTCCAGCTTCCTTCGGCTGGACTGGGATTTACAGGTTGCTTAGTTA
AAACCGGAGGATTTGTTGTCGTTTCTATGGCTTCCTCACAAGCCTCACGAACTGTCGCAGCTCA
TGTCCCCTTTGCAGACTTGTGCTCCACCTTAGAACGAATACAGAAAGGTAAAGACCGTGCAGAA
AAAATCAGGCACTTCAAGGAGTTTCTGGATTCTTGGAGAAAATTTCATGATGCCCTTCATAAGA
ACAAGAAGGATGTTCCGGACTCTTTTTACCCAGCAATGAGACTTATTCTCCCTCAGCTAGAGAG
AGAGAGGATGGCTTACGGAATCAAAGAAACCATGCTGGCTAAGCTTTACATCGAATTGCTCAAT
TTACCAAGAGAAGGCAAGGATGCCCAGAAGCTCCTGAATTACCGAACCCCCAGTGGAGCTCGCT
CAGATGCTGGGGACTTTGCCACGATTGCATACTTTGTTTTGAAGCCAAGGTGCTTACAGAAAGG
AAGCTTAACCATACAGAAGGTGAATGAACTCTTAGACTTAGTTGCCAGCAATAACTCTGGCAAA
AGAAAAGATCTAGTGAAAAAGAGCCTTCTTCAGTTAATAACCCAGTGTTCAGCACTCGAGCAAA
AGTGGCTGATTCGCATGATTATTAAGGACTTAAAGCTTGGTGTCAGTCAGCACACGATATTGTC
CATCTTCCACAATGATGCAGTCGAGTTGCACAATGTCACCACAGATCTGGAAAAGGTCTGTAGG
CAGCTACATGACCCCTCCGTAGGGCTCAGCGACATCTCCATCACTTTGTTCTCTGCCTTTAGGC
CAATGCTAGCTGCTGTAGCAGATGTGGAGCGTGTGGAGAAGGACATGAAGCAGCAGAGTTTCTA
CATCGAAACTAAGCTCGATGGCGAGCGCATGCAGATGCACAAGGATGGCGCCCTGTACCGGTAC
TTCTCCAGAAATGGTTACAACTACACCGATCAGTTCGGCGAATCTCCACAGGAAGGCTCTCTCA
CCCCGTTTATTCACAACGCATTCAAGACAGATGTGCAAGTGTGCATCCTTGATGGCGAGATGAT
GGCCTACAACCCAACGACACAGACTTTCATGCAGAAGGGGGTCAAGTTTGATATCAAAAGGATG
GTCGAAGATTCTGACCTACAGACATGCTACTGTGTTTTCGATGTGCTGATGGTTAATAATAAGA
AGCTAGGGCGTGAGACTCTCAGGAAGAGGTATGATATCCTTAGTAGCACTTTCACACCCATACA
AGGTCGAATAGAGATAGTGCAGAAAACTCAAGCTCAGACAAAGCAGGAAGTAGTGGATGCATTA
AATGATGCCATAGACAAGAGAGAAGAGGGGATCATGGTTAAACACCCTCTGTCCATTTACAAGC
CAGACAAAAGAGGTGAAGGGTGGCTAAAGATTAAACCAGAGTATGTCACTGGATTGATGGATGA
ATTAGACCTCTTAATTGTTGGGGGCTACTGGGGTAAAGGTTCTCGAGGTGGCATGATGTCTCAC
TTTCTGTGTGCAGTGGCAGAGACACCACCTCCTGGTGACAAGCCATCTGTGTTCCACACTCTGT
GCCGTGTTGGGTCGGGTTACACGATGAAAGAACTCTATGACCTGGGCTTGAAATTGGCAAAATA
CTGGAAGCCTTTCCAAAGAAAATCTCCACCAAGCTGTATTTTGTGTGGCACAGAGAAGCCAGAA
GTGTACATTGAACCCCAGAACTCTGTCATCGTTCAGATCAAGGCGGCAGAGATCGTCCCCAGTG
ACATGTACAAGACTGGCTCTACCTTGCGCTTCCCACGCATCGAGAAGATCAGAGATGACAAAGA
GTGGCATGACTGTATGACGCTGGATGACCTGGAGCAGCTGAGGGGGAAAGCATCTGGGAAGCTT
GCCACAAAACACCTTCACATAGGTGACGATGACGAACCCAGAGAAAAAAGGCGGAAACCCATCT
CTAAGACGAAGAAAACCATTGGAATCATTGAACACCTAAAAGCGCCTAACCTTTCTAACATAAA
CAAAGTTTCTAATGTATTTGAAGATGTTGAGTTTTGTGTCATGAGTGGATTAGATGGTTATCCA
AAGCCTGACCTAGAGAACAAAATTGCAGAATTTGGTGGTTATATAGTCCAGAATCCAGGCCCAG
ATACATACTGTGTGATTGCAGGTTCTGAGAACATTAGGGTCAGAAACATCATCTCTTCAGATAG
GCATGATGTTGTCAAGCCCGAGTGGCTTTTAGAGTGTTTTAAAACAAAAACATGTGTGCCATGG
CAACCCCGCTTTATGATTCACATGTGCCCATCAACAAAGCAGCATTTTGCCCGTGAATATGACT
GCTATGGTGATAGCTATTTCGTTGATGCAGATTTGGATCAATTGAAAGAAGTGTTTTTAAGAAT
TAAACCCAGTGAGCAGCAGACTCCTGAAGAAATGGCCCCTGTGATTGCTGACCTAGAATGTCGT
TATTCCTGGGATCACTCTCCTCTCAGTATGTTTCGACACTACACCGTTTATTTGGACTTGTATG
CTGTTATTAATGACTTAAGTTCCAAAATCGAAGCCACAAGGTTAGGTGTTACAGCACTTGAGCT
GCGGTTTCGTGGAGCAAAGGTGGTTTCCCGCTTATCTGAAGGGGTGTCTCACGTAATCATCGGG
GAAGATCAGAGACGAGTCAGTGACTTTAAAACGTTCAGAAGAACGCTTAAGAAAAAGTTTAAAA
TCCTGCAGGAACGTTGGGTGATCGATTCAGTAGACAAGTGTGAACTGCAGGAAGAAAACCTGTA
TTTGCTTTAGAGGAAAATGTTAACCGTGTCAGACAACAGCAGGCAGTGATGATGGAATAGCCAG
TGGCCTTCATTTTATCTCCTAATACTTCAAAAGGATTAGTTACCAGAAGGCAATACTTTTCAAG
TAGAAAGGAAACTGAATAGGCCAAAGCCAAAAAAACCCTTTTCCCAACATAACTTA

hide sequence

RefSeq Acc Id:

XM_006253477 ⟹ XP_006253539

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	79,518,393 - 79,526,956 (+)	NCBI
Rnor_6.0	16	85,331,771 - 85,339,496 (+)	NCBI
Rnor_5.0	16	84,770,824 - 84,778,539 (+)	NCBI

Sequence:

show sequence

CTGCGCAATAAACAGCTGGCGGAAACGCGGGTTTGGCCTCCGACGGTGACGTTTTCCGGTCGGA
ATGAAAGTGGGCGACTTCTCGGGAGGCTGCCTAGGCAAGTCGTGTGGCGGGCTGTCAGGTCCTA
GCGTCACCACCCCGGAGCTTCTCGTGGGGCGACGCCTTCCGCGGTGCAGCCGGCTCGCTGCGGA
CTCGTTTCAGGTGGCAGCCACCGGTTAAAACCGGAGGATTTGTTGTCGTTTCTATGGCTTCCTC
ACAAGCCTCACGAACTGTCGCAGCTCATGTCCCCTTTGCAGACTTGTGCTCCACCTTAGAACGA
ATACAGAAAGGTAAAGACCGTGCAGAAAAAATCAGGCACTTCAAGGAGTTTCTGGATTCTTGGA
GAAAATTTCATGATGCCCTTCATAAGAACAAGAAGGATGTTCCGGACTCTTTTTACCCAGCAAT
GAGACTTATTCTCCCTCAGCTAGAGAGAGAGAGGATGGCTTACGGAATCAAAGAAACCATGCTG
GCTAAGCTTTACATCGAATTGCTCAATTTACCAAGAGAAGGCAAGGATGCCCAGAAGCTCCTGA
ATTACCGAACCCCCAGTGGAGCTCGCTCAGATGCTGGGGACTTTGCCACGATTGCATACTTTGT
TTTGAAGCCAAGGTGCTTACAGAAAGGAAGCTTAACCATACAGAAGGTGAATGAACTCTTAGAC
TTAGTTGCCAGCAATAACTCTGGCAAAAGAAAAGATCTAGTGAAAAAGAGCCTTCTTCAGTTAA
TAACCCAGTGTTCAGCACTCGAGCAAAAGTGGCTGATTCGCATGATTATTAAGGACTTAAAGCT
TGGTGTCAGTCAGCACACGATATTGTCCATCTTCCACAATGATGCAGTCGAGTTGCACAATGTC
ACCACAGATCTGGAAAAGGTCTGTAGGCAGCTACATGACCCCTCCGTAGGGCTCAGCGACATCT
CCATCACTTTGTTCTCTGCCTTTAGGCCAATGCTAGCTGCTGTAGCAGATGTGGAGCGTGTGGA
GAAGGACATGAAGCAGCAGAGTTTCTACATCGAAACTAAGCTCGATGGCGAGCGCATGCAGATG
CACAAGGATGGCGCCCTGTACCGGTACTTCTCCAGAAATGGTTACAACTACACCGATCAGTTCG
GCGAATCTCCACAGGAAGGCTCTCTCACCCCGTTTATTCACAACGCATTCAAGACAGATGTGCA
AGTGTGCATCCTTGATGGCGAGATGATGGCCTACAACCCAACGACACAGACTTTCATGCAGAAG
GGGGTCAAGTTTGATATCAAAAGGATGGTCGAAGATTCTGACCTACAGACATGCTACTGTGTTT
TCGATGTGCTGATGGTTAATAATAAGAAGCTAGGGCGTGAGACTCTCAGGAAGAGGTATGATAT
CCTTAGTAGCACTTTCACACCCATACAAGGTCGAATAGAGATAGTGCAGAAAACTCAAGCTCAG
ACAAAGCAGGAAGTAGTGGATGCATTAAATGATGCCATAGACAAGAGAGAAGAGGGGATCATGG
TTAAACACCCTCTGTCCATTTACAAGCCAGACAAAAGAGGTGAAGGGTGGCTAAAGATTAAACC
AGAGTATGTCACTGGATTGATGGATGAATTAGACCTCTTAATTGTTGGGGGCTACTGGGGTAAA
GGTTCTCGAGGTGGCATGATGTCTCACTTTCTGTGTGCAGTGGCAGAGACACCACCTCCTGGTG
ACAAGCCATCTGTGTTCCACACTCTGTGCCGTGTTGGGTCGGGTTACACGATGAAAGAACTCTA
TGACCTGGGCTTGAAATTGGCAAAATACTGGAAGCCTTTCCAAAGAAAATCTCCACCAAGCTGT
ATTTTGTGTGGCACAGAGAAGCCAGAAGTGTACATTGAACCCCAGAACTCTGTCATCGTTCAGA
TCAAGGCGGCAGAGATCGTCCCCAGTGACATGTACAAGACTGGCTCTACCTTGCGCTTCCCACG
CATCGAGAAGATCAGAGATGACAAAGAGTGGCATGACTGTATGACGCTGGATGACCTGGAGCAG
CTGAGGGGGAAAGCATCTGGGAAGCTTGCCACAAAACACCTTCACATAGGTGACGATGACGAAC
CCAGAGAAAAAAGGCGGAAACCCATCTCTAAGACGAAGAAAACCATTGGAATCATTGAACACCT
AAAAGCGCCTAACCTTTCTAACATAAACAAAGTTTCTAATGTATTTGAAGATGTTGAGTTTTGT
GTCATGAGTGGATTAGATGGTTATCCAAAGCCTGACCTAGAGAACAAAATTGCAGAATTTGGTG
GTTATATAGTCCAGAATCCAGGCCCAGATACATACTGTGTGATTGCAGGTTCTGAGAACATTAG
GGTCAGAAACATCATCTCTTCAGATAGGCATGATGTTGTCAAGCCCGAGTGGCTTTTAGAGTGT
TTTAAAACAAAAACATGTGTGCCATGGCAACCCCGCTTTATGATTCACATGTGCCCATCAACAA
AGCAGCATTTTGCCCGTGAATATGACTGCTATGGTGATAGCTATTTCGTTGATGCAGATTTGGA
TCAATTGAAAGAAGTGTTTTTAAGAATTAAACCCAGTGAGCAGCAGACTCCTGAAGAAATGGCC
CCTGTGATTGCTGACCTAGAATGTCGTTATTCCTGGGATCACTCTCCTCTCAGTATGTTTCGAC
ACTACACCGTTTATTTGGACTTGTATGCTGTTATTAATGACTTAAGTTCCAAAATCGAAGCCAC
AAGGTTAGGTGTTACAGCACTTGAGCTGCGGTTTCGTGGAGCAAAGGTGGTTTCCCGCTTATCT
GAAGGGGTGTCTCACGTAATCATCGGGGAAGATCAGAGACGAGTCAGTGACTTTAAAACGTTCA
GAAGAACGCTTAAGAAAAAGTTTAAAATCCTGCAGGAACGTTGGGTGATCGATTCAGTAGACAA
GTGTGAACTGCAGGAAGAAAACCTGTATTTGCTTTAGAGGAAAATGTTAACCGTGTCAGACAAC
AGCAGGCAGTGATGATGGAATAGCCAGTGGCCTTCATTTTATCTCCTAATACTTCAAAAGGATT
AGTTACCAGAAGGCAATACTTTTCAAGTAGAAAGGAAACTGAATAGGCCAAAGCCAAAAAAACC
CTTTTCCCAACATAACTTACAATTGACATACAATGACAACTTGAAGAGGTGCTTGTGTGGTATT
CATGTTGAAGCTAGAATTTTGACTTGGATATTAAGGAAAGTATATTTGGAACCTTTTAGAACCG
TTGCTGCTATTGACTTTCTAAATAGAATTTCCCAGAGTTAAAGATTAAAGTTTTTAGCTAATAA
AAGGCTTATACCAAAATTGTTACAATTAGACTTATAAGAATAAGCCTTTTTATTTGAGGTCTCA
AATGCCCCCTATAAGCATGAAATATTTTAATAAGTTTTTAAGGTTTGCCAAATGTGCTTTGATA
ATATGGGGAAAGTTGAGAGATAATCATCTAAACACCAAACACTTTAGATGTTAATTAATTTTAT
TTAAAAAAAAATCCTTACAAGTATAAGTTAGCTAAGAATTTTTTTTTTTTGAAGATACGTTTCA
TGGGGAAGTTTTCTGCGTGAATTTGCACTCCAGTATTAACAATGTTGACAGAACTTGTCTCCTT
TGATGAGCCATTGAGTAGCTGTCCATACAATGAACCTGTTGTCAATTTCATTAGAGACTAGGTG
CTGTCGCTTTTAGAGATGGCTTTTATGATTGTGTTGAAGTCACAGTGATGTATGTATTAGATCT
GTTCAGAATTATTCTTCCATGGCAGCACTGACATGGAGGGATGTGGGGCCTGAAGTAGTGGGTA
TAAACTATTTAAGTAATTAGACTTCTTTTTAAAGCAATTGAGATGTTTGTGATTATTGTAACTT
AAATAAAATTATTAAATATTTAATGTAATACCAACATTATTTATGTTCTTTTTATTTTAAAACG
ATTCATCATAATTCTTTTAATCAGATTTAATAATGTCATTACACTTTGTGTCCTTGTGTGAGGC
GGTGTCCAGGATGACTGTGAATTTACAGTATTGCACCTCTAACCTCCCAAGTACCGAGACTGTA
GAAGACAGCCATTGCTCTTGTCTTGGTATACCTACAGACGAGCTTTAGTCACAGCTCCTCCTGG
ATCCTTTGGGTTTCACATTACCAAGCGAGCTTTAATGATTTAAGTGTGTACTGCTTTGTGTTCA
GAGAGACATGTCTCAAAGCACAAGTATAGTTGAAGATTTGTAACTTTATAATTTAAATGTATAT
GAATTAAAAGTTTATAATTTTCCTACTTAAAGGTAATACTCAGGGTACCCATGGTAAAGGACTC
ATAAAGCCATTGTTTGGGGTAACAATACTAAAGCTTACTGTGTTTTCCTTATTTTCTTATTAAG
TTGTGAGAATACTTGCAGGCCACAAAAGTACCTCATCGGTTTTCACTGCGGCACAGCACTCCAC
TGAATGCACCTAATGTGCCTTTTGCAGCATTTAAATTAGCTCCTTGTACTCCATTCACATTTTC
CTTCTCCTGTCCTGATAAATCTTTTACCTGGTCTGTGTACATTTGTTATGGGTAATCTTGGTTG
TCAGTTTGAATGCACCTGGAATCAACTAAAACACAAGCTGCTGGGCATTCTCTTTAGGGGTTTT
TAAAGTCAGAAGACACCTTAAGTGAGTGGCACCTTCTGGTCATGGAAGACAGAAACATGTAGGT
TGAAAACCAGCAGTCCAGGATTCCTCAGAGACATCCGCCTTCATGGACTAAACGACTACTATAA
TCAGTCTCCAGTATGAGGTGGCCATTTTTGGACTCTGTGAAACACTTTTGTACTTCAGTCTAAT
AAATCCCTTTGCAATACA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099565	(Get FASTA)	NCBI Sequence Viewer
	XP_006253539	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM08799	(Get FASTA)	NCBI Sequence Viewer
	EDM08800	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000019615
	ENSRNOP00000019615.4
	ENSRNOP00000076669
	ENSRNOP00000076669.1
	ENSRNOP00000077244.1
	ENSRNOP00000078250.1
	ENSRNOP00000079496.1
	ENSRNOP00000091637.1
	ENSRNOP00000092486.1
	ENSRNOP00000093705.1
	ENSRNOP00000095406.1

RefSeq Acc Id:

NP_001099565 ⟸ NM_001106095

- UniProtKB:

D4A0U6 (UniProtKB/TrEMBL), A6IWS2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MASSQASRTVAAHVPFADLCSTLERIQKGKDRAEKIRHFKEFLDSWRKFHDALHKNKKDVPDSF
YPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPREGKDAQKLLNYRTPSGARSDAGDFATI
AYFVLKPRCLQKGSLTIQKVNELLDLVASNNSGKRKDLVKKSLLQLITQCSALEQKWLIRMIIK
DLKLGVSQHTILSIFHNDAVELHNVTTDLEKVCRQLHDPSVGLSDISITLFSAFRPMLAAVADV
ERVEKDMKQQSFYIETKLDGERMQMHKDGALYRYFSRNGYNYTDQFGESPQEGSLTPFIHNAFK
TDVQVCILDGEMMAYNPTTQTFMQKGVKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGRETLRK
RYDILSSTFTPIQGRIEIVQKTQAQTKQEVVDALNDAIDKREEGIMVKHPLSIYKPDKRGEGWL
KIKPEYVTGLMDELDLLIVGGYWGKGSRGGMMSHFLCAVAETPPPGDKPSVFHTLCRVGSGYTM
KELYDLGLKLAKYWKPFQRKSPPSCILCGTEKPEVYIEPQNSVIVQIKAAEIVPSDMYKTGSTL
RFPRIEKIRDDKEWHDCMTLDDLEQLRGKASGKLATKHLHIGDDDEPREKRRKPISKTKKTIGI
IEHLKAPNLSNINKVSNVFEDVEFCVMSGLDGYPKPDLENKIAEFGGYIVQNPGPDTYCVIAGS
ENIRVRNIISSDRHDVVKPEWLLECFKTKTCVPWQPRFMIHMCPSTKQHFAREYDCYGDSYFVD
ADLDQLKEVFLRIKPSEQQTPEEMAPVIADLECRYSWDHSPLSMFRHYTVYLDLYAVINDLSSK
IEATRLGVTALELRFRGAKVVSRLSEGVSHVIIGEDQRRVSDFKTFRRTLKKKFKILQERWVID
SVDKCELQEENLYLL

hide sequence

RefSeq Acc Id:	XP_006253539 ⟸ XM_006253477
- Peptide Label:	isoform X1
- UniProtKB:	D4A0U6 (UniProtKB/TrEMBL), A6IWS2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MASSQASRTVAAHVPFADLCSTLERIQKGKDRAEKIRHFKEFLDSWRKFHDALHKNKKDVPDSF YPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPREGKDAQKLLNYRTPSGARSDAGDFATI AYFVLKPRCLQKGSLTIQKVNELLDLVASNNSGKRKDLVKKSLLQLITQCSALEQKWLIRMIIK DLKLGVSQHTILSIFHNDAVELHNVTTDLEKVCRQLHDPSVGLSDISITLFSAFRPMLAAVADV ERVEKDMKQQSFYIETKLDGERMQMHKDGALYRYFSRNGYNYTDQFGESPQEGSLTPFIHNAFK TDVQVCILDGEMMAYNPTTQTFMQKGVKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGRETLRK RYDILSSTFTPIQGRIEIVQKTQAQTKQEVVDALNDAIDKREEGIMVKHPLSIYKPDKRGEGWL KIKPEYVTGLMDELDLLIVGGYWGKGSRGGMMSHFLCAVAETPPPGDKPSVFHTLCRVGSGYTM KELYDLGLKLAKYWKPFQRKSPPSCILCGTEKPEVYIEPQNSVIVQIKAAEIVPSDMYKTGSTL RFPRIEKIRDDKEWHDCMTLDDLEQLRGKASGKLATKHLHIGDDDEPREKRRKPISKTKKTIGI IEHLKAPNLSNINKVSNVFEDVEFCVMSGLDGYPKPDLENKIAEFGGYIVQNPGPDTYCVIAGS ENIRVRNIISSDRHDVVKPEWLLECFKTKTCVPWQPRFMIHMCPSTKQHFAREYDCYGDSYFVD ADLDQLKEVFLRIKPSEQQTPEEMAPVIADLECRYSWDHSPLSMFRHYTVYLDLYAVINDLSSK IEATRLGVTALELRFRGAKVVSRLSEGVSHVIIGEDQRRVSDFKTFRRTLKKKFKILQERWVID SVDKCELQEENLYLL hide sequence

RefSeq Acc Id:

ENSRNOP00000019615 ⟸ ENSRNOT00000019615

RefSeq Acc Id:

ENSRNOP00000092486 ⟸ ENSRNOT00000106603

RefSeq Acc Id:

ENSRNOP00000076669 ⟸ ENSRNOT00000116261

RefSeq Acc Id:

ENSRNOP00000095406 ⟸ ENSRNOT00000097537

RefSeq Acc Id:

ENSRNOP00000091637 ⟸ ENSRNOT00000116266

RefSeq Acc Id:

ENSRNOP00000093705 ⟸ ENSRNOT00000101750

RefSeq Acc Id:

ENSRNOP00000079496 ⟸ ENSRNOT00000111250

RefSeq Acc Id:

ENSRNOP00000078250 ⟸ ENSRNOT00000111224

RefSeq Acc Id:

ENSRNOP00000077244 ⟸ ENSRNOT00000112670

Protein Domains

ATP-dependent DNA ligase family profile BRCT

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A0U6-F1-model_v2	AlphaFold	D4A0U6	1-911	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13700249

Promoter ID:

EPDNEW_R10772

Type:

initiation region

Name:

Lig4_1

Description:

DNA ligase 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	16	85,331,847 - 85,331,907	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1304639	AgrOrtholog
BioCyc Gene	G2FUF-10614	BioCyc
Ensembl Genes	ENSRNOG00000014605	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000019615	ENTREZGENE
	ENSRNOT00000019615.6	UniProtKB/TrEMBL
	ENSRNOT00000097537.1	UniProtKB/TrEMBL
	ENSRNOT00000101750.1	UniProtKB/TrEMBL
	ENSRNOT00000106603.1	UniProtKB/TrEMBL
	ENSRNOT00000111224.1	UniProtKB/TrEMBL
	ENSRNOT00000111250.1	UniProtKB/TrEMBL
	ENSRNOT00000112670.1	UniProtKB/TrEMBL
	ENSRNOT00000116261	ENTREZGENE
	ENSRNOT00000116261.1	UniProtKB/TrEMBL
	ENSRNOT00000116266.1	UniProtKB/TrEMBL
Gene3D-CATH	1.10.3260.10	UniProtKB/TrEMBL
	2.40.50.140	UniProtKB/TrEMBL
	3.40.50.10190	UniProtKB/TrEMBL
	6.10.250.520	UniProtKB/TrEMBL
	DNA ligase/mRNA capping enzyme	UniProtKB/TrEMBL
InterPro	Adenylation_DNA_ligase_IV	UniProtKB/TrEMBL
	BRCT	UniProtKB/TrEMBL
	BRCT_dom_sf	UniProtKB/TrEMBL
	DNA_ligase	UniProtKB/TrEMBL
	DNA_ligase_A_C	UniProtKB/TrEMBL
	DNA_ligase_A_M	UniProtKB/TrEMBL
	DNA_ligase_A_N	UniProtKB/TrEMBL
	DNA_ligase_CS	UniProtKB/TrEMBL
	DNA_ligase_IV	UniProtKB/TrEMBL
	DNA_ligase_N_sf	UniProtKB/TrEMBL
	LIG4	UniProtKB/TrEMBL
	NA-bd_OB-fold	UniProtKB/TrEMBL
KEGG Report	rno:290907	UniProtKB/TrEMBL
NCBI Gene	290907	ENTREZGENE
PANTHER	DNA LIGASE 4	UniProtKB/TrEMBL
	PTHR45997	UniProtKB/TrEMBL
Pfam	BRCT	UniProtKB/TrEMBL
	DNA_ligase_A_C	UniProtKB/TrEMBL
	DNA_ligase_A_M	UniProtKB/TrEMBL
	DNA_ligase_A_N	UniProtKB/TrEMBL
	DNA_ligase_IV	UniProtKB/TrEMBL
PhenoGen	Lig4	PhenoGen
PROSITE	BRCT	UniProtKB/TrEMBL
	DNA_LIGASE_A1	UniProtKB/TrEMBL
	DNA_LIGASE_A2	UniProtKB/TrEMBL
	DNA_LIGASE_A3	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000014605	RatGTEx
SMART	BRCT	UniProtKB/TrEMBL
Superfamily-SCOP	BRCT	UniProtKB/TrEMBL
	DNA ligase/mRNA capping enzyme, catalytic domain	UniProtKB/TrEMBL
	Nucleic_acid_OB	UniProtKB/TrEMBL
	SSF117018	UniProtKB/TrEMBL
UniProt	A6IWS2	ENTREZGENE, UniProtKB/TrEMBL
	D4A0U6	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-05-04	Lig4	DNA ligase 4	Lig4	ligase IV, DNA, ATP-dependent	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Lig4	ligase IV, DNA, ATP-dependent	Lig4_predicted	ligase IV, DNA, ATP-dependent (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Lig4_predicted	ligase IV, DNA, ATP-dependent (predicted)			Symbol and Name status set to approved	70820	APPROVED

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 - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - KEGG (archival)