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Gene: Clta (clathrin, light chain A) Rattus norvegicus

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Symbol:

Clta

Name:

clathrin, light chain A

RGD ID:

70919

Description:

Enables GTPase binding activity and peptide binding activity. Involved in synaptic vesicle endocytosis. Located in clathrin-coated pit and clathrin-coated vesicle. Part of clathrin coat. Is active in postsynaptic endocytic zone; presynaptic endocytic zone membrane; and synaptic vesicle membrane. Orthologous to human CLTA (clathrin light chain A); PARTICIPATES IN Arf family mediated signaling pathway; clathrin-dependent synaptic vesicle endocytosis; endocytosis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-amino-2-deoxy-D-glucopyranose; 4,4'-sulfonyldiphenol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

clathrin light chain; clathrin light chain A; clathrin, light chain (Lca); clathrin, light polypeptide (Lca); lca; LCA1; LCA2; LCA3; MGC105384

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):	CLTA (clathrin light chain A)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Clta (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Clta (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CLTA (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CLTA (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Clta (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CLTA (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CLTA (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Clta (clathrin light chain A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	HPS6 (HPS6 biogenesis of lysosomal organelles complex 2 subunit 3)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	CLTA (clathrin light chain A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Clta (clathrin light chain A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	clta (clathrin, light chain A)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	CLC1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	Clc	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	clic-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	clta	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

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
GRCr8	5	63,022,046 - 63,059,223 (+)	NCBI		GRCr8
mRatBN7.2	5	58,244,253 - 58,263,480 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	58,245,442 - 58,263,472 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	60,227,391 - 60,245,248 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	62,046,199 - 62,064,056 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	62,015,336 - 62,033,490 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	59,490,689 - 59,509,139 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	59,491,096 - 59,509,138 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	64,012,881 - 64,031,657 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	60,484,437 - 60,502,432 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	60,484,615 - 60,502,611 (+)	NCBI
Celera	5	56,823,904 - 56,841,911 (+)	NCBI		Celera
Cytogenetic Map	5	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

acromesomelic dysplasia, Maroteaux type (ISO)

anauxetic dysplasia (ISO)

autosomal recessive distal hereditary motor neuronopathy 2 (ISO)

COVID-19 (ISO)

distal arthrogryposis type 1A (ISO)

frontotemporal dementia and/or amyotrophic lateral sclerosis 6 (ISO)

galactosemia (ISO)

hyperphosphatasia with impaired intellectual development syndrome 2 (ISO)

paraplegia (ISO)

primary ciliary dyskinesia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,4,6-tribromophenol (ISO)

2-amino-2-deoxy-D-glucopyranose (EXP)

3,3',5,5'-tetrabromobisphenol A (ISO)

4,4'-sulfonyldiphenol (EXP,ISO)

4-hydroxyphenyl retinamide (ISO)

aconitine (EXP)

actinomycin D (ISO)

aldehydo-D-glucosamine (EXP)

ammonium chloride (EXP)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

beta-D-glucosamine (EXP)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (EXP)

cadmium dichloride (EXP,ISO)

calcidiol (EXP)

CGP 52608 (ISO)

clozapine (EXP)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

decabromodiphenyl ether (ISO)

diarsenic trioxide (ISO)

Dibutyl phosphate (ISO)

disodium selenite (ISO)

disulfiram (ISO)

folic acid (ISO)

FR900359 (ISO)

gamma-linolenic acid (ISO)

gentamycin (EXP)

haloperidol (EXP)

hypochlorous acid (ISO)

ivermectin (ISO)

lead(0) (ISO)

methidathion (ISO)

N-methyl-N'-nitro-N-nitrosoguanidine (ISO)

Nutlin-3 (ISO)

okadaic acid (ISO)

paracetamol (ISO)

perfluorooctanoic acid (ISO)

phenylmercury acetate (ISO)

phorbol 13-acetate 12-myristate (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

succimer (ISO)

sunitinib (ISO)

tetrachloromethane (ISO)

thiram (ISO)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell division (IEA)

clathrin coat assembly (ISO)

clathrin-dependent endocytosis (IBA)

endocytosis (IEP)

intracellular protein transport (IEA)

synaptic vesicle endocytosis (EXP,IDA,IMP)

vesicle-mediated transport (IEA)

Cellular Component

clathrin coat (IDA,ISO)

clathrin coat of coated pit (IEA,NAS)

clathrin coat of trans-Golgi network vesicle (IEA)

clathrin complex (ISO)

clathrin vesicle coat (IBA,NAS)

clathrin-coated endocytic vesicle membrane (TAS)

clathrin-coated pit (IDA)

clathrin-coated vesicle (IDA)

cytoplasmic vesicle (ISO)

endosome (IEA,ISO)

glutamatergic synapse (ISO)

Golgi apparatus (ISO)

intracellular membrane-bounded organelle (ISO)

lysosome (IEA,ISO)

plasma membrane (IBA)

postsynaptic endocytic zone (IDA,IMP,ISO)

presynaptic endocytic zone membrane (IDA,IEP)

spindle (IEA)

synaptic vesicle membrane (IBA,IDA,IEP)

Molecular Function

clathrin heavy chain binding (IBA,ISO)

GTPase binding (IPI)

peptide binding (IDA)

protein binding (IPI,ISO)

protein-containing complex binding (IPI)

structural molecule activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

Arf family mediated signaling pathway (ISO)

clathrin-dependent synaptic vesicle endocytosis (ISO)

endocytosis pathway (IEA)

Huntington's disease pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Dynamics and nanoscale organization of the postsynaptic endocytic zone at excitatory synapses.	Catsburg LA, etal., Elife. 2022 Jan 24;11:e74387. doi: 10.7554/eLife.74387.
2.	Epsin binds to clathrin by associating directly with the clathrin-terminal domain. Evidence for cooperative binding through two discrete sites.	Drake MT, etal., J Biol Chem. 2000 Mar 3;275(9):6479-89.
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.	Non-stoichiometric relationship between clathrin heavy and light chains revealed by quantitative comparative proteomics of clathrin-coated vesicles from brain and liver.	Girard M, etal., Mol Cell Proteomics. 2005 Aug;4(8):1145-54. Epub 2005 Jun 2.
5.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
6.	KEGG: Kyoto Encyclopedia of Genes and Genomes	KEGG
7.	Clathrin light chains LCA and LCB are similar, polymorphic, and share repeated heptad motifs.	Kirchhausen T, etal., Science 1987 Apr 17;236(4799):320-4.
8.	A Bcl-xL-Drp1 complex regulates synaptic vesicle membrane dynamics during endocytosis.	Li H, etal., Nat Cell Biol. 2013 Jul;15(7):773-85. doi: 10.1038/ncb2791. Epub 2013 Jun 23.
9.	Clathrin-coated vesicles in nervous tissue are involved primarily in synaptic vesicle recycling.	Maycox PR, etal., J Cell Biol. 1992 Sep;118(6):1379-88.
10.	Gene Data Set	MGD Curation, June 12, 2002
11.	Monitoring clathrin-mediated endocytosis during synaptic activity.	Mueller VJ, etal., J Neurosci. 2004 Feb 25;24(8):2004-12.
12.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
13.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
14.	PID Annotation Import Pipeline	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
15.	A motif in the clathrin heavy chain required for the Hsc70/auxilin uncoating reaction.	Rapoport I, etal., Mol Biol Cell. 2008 Jan;19(1):405-13. Epub 2007 Oct 31.
16.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
17.	Comprehensive gene review and curation	RGD comprehensive gene curation
18.	The NECAP PHear domain increases clathrin accessory protein binding potential.	Ritter B, etal., EMBO J. 2007 Sep 19;26(18):4066-77. Epub 2007 Aug 30.
19.	Synaptic vesicle endocytosis.	Saheki Y and De Camilli P, Cold Spring Harb Perspect Biol. 2012 Sep 1;4(9):a005645. doi: 10.1101/cshperspect.a005645.
20.	Possible involvement of clathrin in neuritogenesis induced by a protease inhibitor (benzyloxycarbonyl-Leu-Leu-Leu-aldehyde) in PC12 cells.	Saito Y, etal., J Biochem. 1992 Oct;112(4):448-55.

Additional References at PubMed

PMID:4066749	PMID:8413590	PMID:9188501	PMID:10908605	PMID:11382783	PMID:11756460	PMID:12234931	PMID:12477932	PMID:16025302	PMID:16854843	PMID:17228368	PMID:17880892
PMID:19144635	PMID:19946888	PMID:20231386	PMID:20730103	PMID:22871113	PMID:25002582	PMID:25427558	PMID:29476059	PMID:31672988

Genomics

Comparative Map Data

Clta
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	63,022,046 - 63,059,223 (+)	NCBI		GRCr8
mRatBN7.2	5	58,244,253 - 58,263,480 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	58,245,442 - 58,263,472 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	60,227,391 - 60,245,248 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	62,046,199 - 62,064,056 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	62,015,336 - 62,033,490 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	59,490,689 - 59,509,139 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	59,491,096 - 59,509,138 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	64,012,881 - 64,031,657 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	60,484,437 - 60,502,432 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	60,484,615 - 60,502,611 (+)	NCBI
Celera	5	56,823,904 - 56,841,911 (+)	NCBI		Celera
Cytogenetic Map	5	q22	NCBI

CLTA
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	36,190,874 - 36,212,059 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	36,190,856 - 36,304,781 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	36,190,918 - 36,212,056 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	36,180,892 - 36,202,056 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	36,180,988 - 36,202,055	NCBI
Celera	9	36,124,438 - 36,145,644 (+)	NCBI		Celera
Cytogenetic Map	9	p13.3	NCBI
HuRef	9	36,144,777 - 36,166,054 (+)	NCBI		HuRef
CHM1_1	9	36,191,259 - 36,212,465 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	9	36,212,880 - 36,234,065 (+)	NCBI		T2T-CHM13v2.0

Clta
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	44,003,816 - 44,032,846 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	44,004,452 - 44,032,846 (+)	Ensembl		GRCm39 Ensembl
GRCm38	4	44,003,816 - 44,032,846 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	44,004,452 - 44,032,846 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	44,025,515 - 44,045,718 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	44,033,784 - 44,053,946 (+)	NCBI		MGSCv36	mm8
Celera	4	44,033,842 - 44,054,042 (+)	NCBI		Celera
Cytogenetic Map	4	B1	NCBI
cM Map	4	23.09	NCBI

Clta
(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_004955472	97,235 - 117,144 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955472	96,958 - 117,230 (-)	NCBI	ChiLan1.0	ChiLan1.0

CLTA
(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	11	88,377,550 - 88,398,727 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	88,383,487 - 88,404,664 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	36,040,566 - 36,061,744 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	36,841,477 - 36,862,528 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	36,840,868 - 36,862,528 (+)	Ensembl	panpan1.1		panPan2

CLTA
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	11	52,636,328 - 52,681,258 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	11	52,615,039 - 52,681,270 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	11	51,227,019 - 51,271,906 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	11	53,742,643 - 53,787,381 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	11	53,765,885 - 53,789,703 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	11	52,245,564 - 52,290,214 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	11	52,267,619 - 52,312,459 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	11	52,969,170 - 53,014,020 (+)	NCBI		UU_Cfam_GSD_1.0

Clta
(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	167,622,904 - 167,644,372 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936524	4,169,732 - 4,191,951 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936524	4,170,425 - 4,191,951 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLTA
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	236,971,505 - 237,001,731 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	236,971,317 - 236,993,291 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	264,772,770 - 264,783,359 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLTA
(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	12	44,346,169 - 44,367,626 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	44,344,395 - 44,367,619 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	41,437,200 - 41,458,568 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Clta
(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_004624868	4,419,554 - 4,443,477 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624868	4,419,554 - 4,443,475 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Clta
109 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	108
Count of miRNA genes:	45
Interacting mature miRNAs:	54
Transcripts:	ENSRNOT00000019737, ENSRNOT00000036366
Prediction methods:	Miranda, Rnahybrid, Targetscan
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
1578776	Stresp18	Stress response QTL 18	2.9		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	5	27955440	72955440	Rat
1298067	Scl15	Serum cholesterol level QTL 15	4.8	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	33215665	78215665	Rat
1300115	Hrtrt7	Heart rate QTL 7	2.76		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	5	47869062	90099692	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40128307	148607290	Rat
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	131345958	Rat
1358353	Srcrtb2	Stress Responsive Cort Basal QTL 2	3.48	0.003	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	18873947	74251464	Rat
634305	Mamtr1	Mammary tumor resistance QTL 1		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	12789751	113558310	Rat
1331801	Rf33	Renal function QTL 33	4.149		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	43726656	129132602	Rat
1598807	Glom12	Glomerulus QTL 12	2.7		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	5	33215665	78215665	Rat
1302786	Kidm8	Kidney mass QTL 8	28.15		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	5	33215665	78215665	Rat
6903292	Stl28	Serum triglyceride level QTL 28	2.6	0.0073	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	5	28515489	73515489	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	46711509	161317411	Rat
1578767	Stresp17	Stress response QTL 17	4.3	0.01	blood aldosterone amount (VT:0005346)	plasma aldosterone level (CMO:0000551)	5	27955440	72955440	Rat
7411561	Bw134	Body weight QTL 134	24	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	49463600	94463600	Rat
1641922	Alcrsp8	Alcohol response QTL 8			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	5	35189153	68564008	Rat
2303615	Vencon7	Ventilatory control QTL 7		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	5	50983895	95983895	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	50328551	141643988	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35189153	141643988	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
6903306	Scl35	Serum cholesterol QTL 35	2.6	0.0073	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	28515489	73515489	Rat
1576317	Eutr2	Estrogen induced uterine response QTL 2		0.01	uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	34730116	104251008	Rat
7394712	Emca13	Estrogen-induced mammary cancer QTL 13			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	9823266	99753708	Rat
1331773	Scl26	Serum cholesterol level QTL 26	3.065		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	43726656	86724018	Rat
70189	Mcs5	Mammary carcinoma susceptibility QTL 5	10.51		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	55805606	132207589	Rat
1331771	Rf35	Renal function QTL 35	4.36965		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	729470	86724018	Rat
61359	Eaex	Experimental allergic encephalomyelitis QTL x	3		nervous system integrity trait (VT:0010566)	post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)	5	55715622	100715622	Rat
8662454	Vetf3	Vascular elastic tissue fragility QTL 3	27.4		artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	5	2282226	69540447	Rat
2290448	Scl54	Serum cholesterol level QTL 54	2.93		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	31663789	131345958	Rat
9589025	Epfw7	Epididymal fat weight QTL 7	20.66	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	5	49463600	94463600	Rat
2303574	Gluco42	Glucose level QTL 42	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	53496719	98496719	Rat
1331756	Rf34	Renal function QTL 34	4.16275		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	1	90450412	Rat
8552954	Pigfal14	Plasma insulin-like growth factor 1 level QTL 14	9		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	21226744	66226744	Rat
2316959	Gluco59	Glucose level QTL 59	4.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	34944474	113558310	Rat
1600358	Mamtr5	Mammary tumor resistance QTL 5			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	18873947	63873947	Rat

Markers in Region

BI282730

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	58,263,218 - 58,263,407 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	59,508,878 - 59,509,066	NCBI	Rnor6.0
Rnor_5.0	5	64,031,396 - 64,031,584	UniSTS	Rnor5.0
RGSC_v3.4	5	60,502,179 - 60,502,367	UniSTS	RGSC3.4
Celera	5	56,841,658 - 56,841,846	UniSTS
Cytogenetic Map	5	q22	UniSTS

AV026556

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	58,263,354 - 58,263,444 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	59,509,014 - 59,509,103	NCBI	Rnor6.0
Rnor_5.0	5	64,031,532 - 64,031,621	UniSTS	Rnor5.0
RGSC_v3.4	5	60,502,315 - 60,502,404	UniSTS	RGSC3.4
Celera	5	56,841,794 - 56,841,883	UniSTS
Cytogenetic Map	5	q22	UniSTS

RH79677

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	58,263,164 - 58,263,443 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	59,508,824 - 59,509,102	NCBI	Rnor6.0
Rnor_5.0	5	64,031,342 - 64,031,620	UniSTS	Rnor5.0
RGSC_v3.4	5	60,502,125 - 60,502,403	UniSTS	RGSC3.4
Celera	5	56,841,604 - 56,841,882	UniSTS
Cytogenetic Map	5	q22	UniSTS

RH74929

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	58,263,201 - 58,263,434 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	59,508,861 - 59,509,093	NCBI	Rnor6.0
Rnor_5.0	5	64,031,379 - 64,031,611	UniSTS	Rnor5.0
RGSC_v3.4	5	60,502,162 - 60,502,394	UniSTS	RGSC3.4
Celera	5	56,841,641 - 56,841,873	UniSTS
Cytogenetic Map	5	q22	UniSTS

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.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031974	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238104	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238105	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238106	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC127935	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC087577	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473962	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213034	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213766	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220908	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230032	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M15882	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M19260	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M19261	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000019737 ⟹ ENSRNOP00000019737

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	58,245,467 - 58,263,472 (+)	Ensembl
Rnor_6.0 Ensembl	5	59,491,096 - 59,509,138 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000036366 ⟹ ENSRNOP00000035138

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	58,245,442 - 58,263,472 (+)	Ensembl
Rnor_6.0 Ensembl	5	59,491,103 - 59,509,131 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000083068 ⟹ ENSRNOP00000070814

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	58,245,474 - 58,263,472 (+)	Ensembl
Rnor_6.0 Ensembl	5	59,491,136 - 59,509,131 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000101159 ⟹ ENSRNOP00000089530

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	58,245,467 - 58,263,472 (+)	Ensembl

RefSeq Acc Id:

NM_031974 ⟹ NP_114180

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	63,041,220 - 63,059,215 (+)	NCBI
mRatBN7.2	5	58,245,475 - 58,263,472 (+)	NCBI
Rnor_6.0	5	59,491,136 - 59,509,131 (+)	NCBI
Rnor_5.0	5	64,012,881 - 64,031,657 (+)	NCBI
RGSC_v3.4	5	60,484,437 - 60,502,432 (+)	RGD
Celera	5	56,823,904 - 56,841,911 (+)	RGD

Sequence:

show sequence

TCTCCGCTCGTCCTCCGGTAGCAGCCGCCAGCACAGTGTCCGCTGCTGGGCGGGGTGTCGGCGG
ATCGGTCGGTTGGTTTCGGCTTCGGTGTCGCTGCGTTTGAGTTGGGCCGTCATGGCTGAGTTGG
ATCCATTTGGCGCTCCCGCCGGTGCGCCCGGTGGCCCCGCGCTCGGGAACGGGGTGGCGGGCGC
CGGCGAGGAAGACCCGGCCGCGGCCTTCTTGGCGCAGCAGGAGAGTGAGATTGCGGGCATAGAG
AACGACGAGGCCTTCGCCATCCTAGACGGCGGCGCCCCCGGGCCGCAGGCACACGGCGAGCCGC
CGGGGGGTCCTGATGCGGTTGATGGAGTGATGAATGGCGAATACTACCAGGAGAGCAATGGTCC
AACAGACAGTTACGCAGCCATTTCAGAAGTGGATCGGTTGCAGTCAGAGCCTGAAAGTATCCGT
AAGTGGAGAGAAGAGCAGACAGAGCGCCTGGAAGCCCTCGATGCCAATTCTCGGAAGCAGGAAG
CAGAGTGGAAAGAAAAGGCAGTGAAGGAGCTGGAAGAGTGGTACGCAAGGCAGGATGAGCAGCT
ACAGAAGACAAAAGCCAGCAACAGGGTGGCAGATGAAGCTTTCTACAAACAACCCTTCGCTGAC
GTGATTGGTTATGTCACAAACATAAACCATCCTTGCTACAGCCTAGAACAGGCAGCAGAAGAAG
CCTTTGTAAACGACATTGACGAGTCATCCCCAGGCACTGAGTGGGAGCGGGTGGCCCGCCTGTG
TGACTTTAACCCCAAGTCCAGCAAACAGGCCAAAGATGTCTCTCGCATGCGCTCAGTCCTCATC
TCCCTGAAGCAGGCGCCCCTGGTGCATTGAAGAGCCACCCTGTGGAAACACTACGTCTCCGATC
TTAATCCTACTCAGTGAAGCTGTTCACGCAATTGGATTAATTATGCCGAGTTCTTTTGGACCAA
ACCTTTTGTCTTTAGAGTTGATCATTGTTTGTGATTGCATGTTTCCTTCAACTGTGTTCTCCCT
GGCATTCAGAGAAGAGAGAGGAAGAGGAAGGGAGGGGAGCTCCCAACAGTAGCCTCAACCTGTG
CTTTTGTGCATTATTCTGAGAATAAATTTCTGTTTC

hide sequence

RefSeq Acc Id:

XM_006238104 ⟹ XP_006238166

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	63,022,046 - 63,059,223 (+)	NCBI
mRatBN7.2	5	58,244,253 - 58,263,480 (+)	NCBI
Rnor_6.0	5	59,490,689 - 59,509,139 (+)	NCBI
Rnor_5.0	5	64,012,881 - 64,031,657 (+)	NCBI

Sequence:

show sequence

TTCTTTCTTTTTAGGGCGGTGACATTAAATGGTAAATGCACTTCTCTTGGTCTATGTACCCATA
AAATTTTTCAATTATCCAGGAGGGAAACAATGTAAGATTCTTCTACCAGTCTTCCAAGCAAGGA
CACTGAGGTTCAGAAACACCAAGTGGTTGCGTGTTGAGTAGTCCGGAAGAGCTCATATCCCTGG
TCCCCGCAAACTCCTCAAACCCTACTAACGGCTGTTCCAGGTCACTCAGGCTCCGGACGCTCGA
CGACTCCCAGCTTTCCAAAGTGGGCATTTCCGCTGGCTCCTCCCTCCGCTCCGGGTCACGAGTT
GTCTCCAGGACTCCACCCCTTTGCCGGCTGATAGGGTAACTTTCACCTTCTGATTGGCTGTTCT
TTTTGTGGCTCGCCAACCTAACCGGATATAGAAGCAAGGCTTCCGCTTCCACCTTCTCCCTCCT
CTCCGCTCGTCCTCCGGTAGCAGCCGCCAGCACAGTGTCCGCTGCTGGGCGGGGTGTCGGCGGA
TCGGTCGGTTGGTTTCGGCTTCGGTGTCGCTGCGTTTGAGTTGGGCCGTCATGGCTGAGTTGGA
TCCATTTGGCGCTCCCGCCGGTGCGCCCGGTGGCCCCGCGCTCGGGAACGGGGTGGCGGGCGCC
GGCGAGGAAGACCCGGCCGCGGCCTTCTTGGCGCAGCAGGAGAGTGAGATTGCGGGCATAGAGA
ACGACGAGGCCTTCGCCATCCTAGACGGCGGCGCCCCCGGGCCGCAGGCACACGGCGAGCCGCC
GGGGGGTCCTGATGCGGTTGATGGAGTGATGAATGGCGAATACTACCAGGAGAGCAATGGTCCA
ACAGACAGTTACGCAGCCATTTCAGAAGTGGATCGGTTGCAGTCAGAGCCTGAAAGTATCCGTA
AGTGGAGAGAAGAGCAGACAGAGCGCCTGGAAGCCCTCGATGCCAATTCTCGGAAGCAGGAAGC
AGAGTGGAAAGAAAAGGCCGTGAAGGAGCTGGAAGAGTGGTACGCAAGGCAGGACGAGCAGCTA
CAGAAGACAAAAGCCAGCAACAGGGTGGCAGATGAAGCTTTCTACAAACAACCCTTCGCTGACG
TGATTGGTTATGTGGCAGCAGAAGAAGCCTTTGTAAACGACATTGACGAGTCATCCCCAGGCAC
TGAGTGGGAGCGGGTGGCCCGCCTGTGTGACTTTAACCCCAAGTCCAGCAAACAGGCCAAAGAT
GTCTCTCGCATGCGCTCAGTCCTCATCTCCCTGAAGCAGGCGCCCCTGGTGCATTGAAGAGCCA
CCCTGTGGAAACACTACGTCTCCGATCTTAATCCTACTCAGTGAAGCTGTTCACGCAATTGGAT
TAATTATGCCGAGTTCTTTTGGACCAAACCTTTTGTCTTTAGAGTTGATCATTGTTTGTGATTG
CATGTTTCCTTCAACTGTGTTCTCCCTGGCATTCAGAGAAGAGAGAGGAAGAGGAAGGGAGGGG
AGCTCCCAACAGTAGCCTCAACCTGTGCTTTTGTGCATTATTCTGAGAATAAATTTCTGTTTCA
AACAATA

hide sequence

RefSeq Acc Id:

XM_006238105 ⟹ XP_006238167

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	63,022,046 - 63,059,223 (+)	NCBI
mRatBN7.2	5	58,244,253 - 58,263,480 (+)	NCBI
Rnor_6.0	5	59,490,689 - 59,509,139 (+)	NCBI
Rnor_5.0	5	64,012,881 - 64,031,657 (+)	NCBI

Sequence:

show sequence

TTCTTTCTTTTTAGGGCGGTGACATTAAATGGTAAATGCACTTCTCTTGGTCTATGTACCCATA
AAATTTTTCAATTATCCAGGAGGGAAACAATGTAAGATTCTTCTACCAGTCTTCCAAGCAAGGA
CACTGAGGTTCAGAAACACCAAGTGGTTGCGTGTTGAGTAGTCCGGAAGAGCTCATATCCCTGG
TCCCCGCAAACTCCTCAAACCCTACTAACGGCTGTTCCAGGTCACTCAGGCTCCGGACGCTCGA
CGACTCCCAGCTTTCCAAAGTGGGCATTTCCGCTGGCTCCTCCCTCCGCTCCGGGTCACGAGTT
GTCTCCAGGACTCCACCCCTTTGCCGGCTGATAGGGTAACTTTCACCTTCTGATTGGCTGTTCT
TTTTGTGGCTCGCCAACCTAACCGGATATAGAAGCAAGGCTTCCGCTTCCACCTTCTCCCTCCT
CTCCGCTCGTCCTCCGGTAGCAGCCGCCAGCACAGTGTCCGCTGCTGGGCGGGGTGTCGGCGGA
TCGGTCGGTTGGTTTCGGCTTCGGTGTCGCTGCGTTTGAGTTGGGCCGTCATGGCTGAGTTGGA
TCCATTTGGCGCTCCCGCCGGTGCGCCCGGTGGCCCCGCGCTCGGGAACGGGGTGGCGGGCGCC
GGCGAGGAAGACCCGGCCGCGGCCTTCTTGGCGCAGCAGGAGAGTGAGATTGCGGGCATAGAGA
ACGACGAGGCCTTCGCCATCCTAGACGGCGGCGCCCCCGGGCCGCAGGCACACGGCGAGCCGCC
GGGGGGTCCTGATGCGGTTGATGGAGTGATGAATGGCGAATACTACCAGGAGAGCAATGGTCCA
ACAGACAGTTACGCAGCCATTTCAGAAGTGGATCGGTTGCAGTCAGAGCCTGAAAGTATCCGTA
AGTGGAGAGAAGAGCAGACAGAGCGCCTGGAAGCCCTCGATGCCAATTCTCGGAAGCAGGAAGC
AGAGTGGAAAGAAAAGGCCGTGAAGGAGCTGGAAGAGTGGTACGCAAGGCAGGACGAGCAGCTA
CAGAAGACAAAAGCCAGCAACAGCACAAACATAAACCATCCTTGCTACAGCCTAGAACAGGCAG
CAGAAGAAGCCTTTGTAAACGACATTGACGAGTCATCCCCAGGCACTGAGTGGGAGCGGGTGGC
CCGCCTGTGTGACTTTAACCCCAAGTCCAGCAAACAGGCCAAAGATGTCTCTCGCATGCGCTCA
GTCCTCATCTCCCTGAAGCAGGCGCCCCTGGTGCATTGAAGAGCCACCCTGTGGAAACACTACG
TCTCCGATCTTAATCCTACTCAGTGAAGCTGTTCACGCAATTGGATTAATTATGCCGAGTTCTT
TTGGACCAAACCTTTTGTCTTTAGAGTTGATCATTGTTTGTGATTGCATGTTTCCTTCAACTGT
GTTCTCCCTGGCATTCAGAGAAGAGAGAGGAAGAGGAAGGGAGGGGAGCTCCCAACAGTAGCCT
CAACCTGTGCTTTTGTGCATTATTCTGAGAATAAATTTCTGTTTCAAACAATA

hide sequence

RefSeq Acc Id:

XM_006238106 ⟹ XP_006238168

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	63,022,046 - 63,059,223 (+)	NCBI
mRatBN7.2	5	58,244,253 - 58,263,480 (+)	NCBI
Rnor_6.0	5	59,490,689 - 59,509,139 (+)	NCBI
Rnor_5.0	5	64,012,881 - 64,031,657 (+)	NCBI

Sequence:

show sequence

TTCTTTCTTTTTAGGGCGGTGACATTAAATGGTAAATGCACTTCTCTTGGTCTATGTACCCATA
AAATTTTTCAATTATCCAGGAGGGAAACAATGTAAGATTCTTCTACCAGTCTTCCAAGCAAGGA
CACTGAGGTTCAGAAACACCAAGTGGTTGCGTGTTGAGTAGTCCGGAAGAGCTCATATCCCTGG
TCCCCGCAAACTCCTCAAACCCTACTAACGGCTGTTCCAGGTCACTCAGGCTCCGGACGCTCGA
CGACTCCCAGCTTTCCAAAGTGGGCATTTCCGCTGGCTCCTCCCTCCGCTCCGGGTCACGAGTT
GTCTCCAGGACTCCACCCCTTTGCCGGCTGATAGGGTAACTTTCACCTTCTGATTGGCTGTTCT
TTTTGTGGCTCGCCAACCTAACCGGATATAGAAGCAAGGCTTCCGCTTCCACCTTCTCCCTCCT
CTCCGCTCGTCCTCCGGTAGCAGCCGCCAGCACAGTGTCCGCTGCTGGGCGGGGTGTCGGCGGA
TCGGTCGGTTGGTTTCGGCTTCGGTGTCGCTGCGTTTGAGTTGGGCCGTCATGGCTGAGTTGGA
TCCATTTGGCGCTCCCGCCGGTGCGCCCGGTGGCCCCGCGCTCGGGAACGGGGTGGCGGGCGCC
GGCGAGGAAGACCCGGCCGCGGCCTTCTTGGCGCAGCAGGAGAGTGAGATTGCGGGCATAGAGA
ACGACGAGGCCTTCGCCATCCTAGACGGCGGCGCCCCCGGGCCGCAGGCACACGGCGAGCCGCC
GGGGGGTCCTGATGCGGTTGATGGAGTGATGAATGGCGAATACTACCAGGAGAGCAATGGTCCA
ACAGACAGTTACGCAGCCATTTCAGAAGTGGATCGGTTGCAGTCAGAGCCTGAAAGTATCCGTA
AGTGGAGAGAAGAGCAGACAGAGCGCCTGGAAGCCCTCGATGCCAATTCTCGGAAGCAGGAAGC
AGAGTGGAAAGAAAAGGCCGTGAAGGAGCTGGAAGAGTGGTACGCAAGGCAGGACGAGCAGCTA
CAGAAGACAAAAGCCAGCAACAGGGCAGCAGAAGAAGCCTTTGTAAACGACATTGACGAGTCAT
CCCCAGGCACTGAGTGGGAGCGGGTGGCCCGCCTGTGTGACTTTAACCCCAAGTCCAGCAAACA
GGCCAAAGATGTCTCTCGCATGCGCTCAGTCCTCATCTCCCTGAAGCAGGCGCCCCTGGTGCAT
TGAAGAGCCACCCTGTGGAAACACTACGTCTCCGATCTTAATCCTACTCAGTGAAGCTGTTCAC
GCAATTGGATTAATTATGCCGAGTTCTTTTGGACCAAACCTTTTGTCTTTAGAGTTGATCATTG
TTTGTGATTGCATGTTTCCTTCAACTGTGTTCTCCCTGGCATTCAGAGAAGAGAGAGGAAGAGG
AAGGGAGGGGAGCTCCCAACAGTAGCCTCAACCTGTGCTTTTGTGCATTATTCTGAGAATAAAT
TTCTGTTTCAAACAATA

hide sequence

Protein Sequences


Protein RefSeqs	NP_114180	(Get FASTA)	NCBI Sequence Viewer
	XP_006238166	(Get FASTA)	NCBI Sequence Viewer
	XP_006238167	(Get FASTA)	NCBI Sequence Viewer
	XP_006238168	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40868	(Get FASTA)	NCBI Sequence Viewer
	AAA40869	(Get FASTA)	NCBI Sequence Viewer
	AAA40870	(Get FASTA)	NCBI Sequence Viewer
	AAH87577	(Get FASTA)	NCBI Sequence Viewer
	EDL98783	(Get FASTA)	NCBI Sequence Viewer
	EDL98784	(Get FASTA)	NCBI Sequence Viewer
	EDL98785	(Get FASTA)	NCBI Sequence Viewer
	EDL98786	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000019737.2
	ENSRNOP00000035138.4
	ENSRNOP00000070814.1
	ENSRNOP00000089530.1
	ENSRNOP00055028673
	ENSRNOP00060005609
	ENSRNOP00065012375
GenBank Protein	P08081	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_114180 ⟸ NM_031974

- UniProtKB:

P08081 (UniProtKB/Swiss-Prot), A6IJ63 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAELDPFGAPAGAPGGPALGNGVAGAGEEDPAAAFLAQQESEIAGIENDEAFAILDGGAPGPQA
HGEPPGGPDAVDGVMNGEYYQESNGPTDSYAAISEVDRLQSEPESIRKWREEQTERLEALDANS
RKQEAEWKEKAVKELEEWYARQDEQLQKTKASNRVADEAFYKQPFADVIGYVTNINHPCYSLEQ
AAEEAFVNDIDESSPGTEWERVARLCDFNPKSSKQAKDVSRMRSVLISLKQAPLVH

hide sequence

RefSeq Acc Id:	XP_006238166 ⟸ XM_006238104
- Peptide Label:	isoform X1
- UniProtKB:	A0A0G2JYW3 (UniProtKB/TrEMBL), A6IJ64 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAELDPFGAPAGAPGGPALGNGVAGAGEEDPAAAFLAQQESEIAGIENDEAFAILDGGAPGPQA HGEPPGGPDAVDGVMNGEYYQESNGPTDSYAAISEVDRLQSEPESIRKWREEQTERLEALDANS RKQEAEWKEKAVKELEEWYARQDEQLQKTKASNRVADEAFYKQPFADVIGYVAAEEAFVNDIDE SSPGTEWERVARLCDFNPKSSKQAKDVSRMRSVLISLKQAPLVH hide sequence

RefSeq Acc Id:	XP_006238167 ⟸ XM_006238105
- Peptide Label:	isoform X2
- UniProtKB:	A0A8I6A7H3 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAELDPFGAPAGAPGGPALGNGVAGAGEEDPAAAFLAQQESEIAGIENDEAFAILDGGAPGPQA HGEPPGGPDAVDGVMNGEYYQESNGPTDSYAAISEVDRLQSEPESIRKWREEQTERLEALDANS RKQEAEWKEKAVKELEEWYARQDEQLQKTKASNSTNINHPCYSLEQAAEEAFVNDIDESSPGTE WERVARLCDFNPKSSKQAKDVSRMRSVLISLKQAPLVH hide sequence

RefSeq Acc Id:	XP_006238168 ⟸ XM_006238106
- Peptide Label:	isoform X3
- UniProtKB:	Q5PPP1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAELDPFGAPAGAPGGPALGNGVAGAGEEDPAAAFLAQQESEIAGIENDEAFAILDGGAPGPQA HGEPPGGPDAVDGVMNGEYYQESNGPTDSYAAISEVDRLQSEPESIRKWREEQTERLEALDANS RKQEAEWKEKAVKELEEWYARQDEQLQKTKASNRAAEEAFVNDIDESSPGTEWERVARLCDFNP KSSKQAKDVSRMRSVLISLKQAPLVH hide sequence

Ensembl Acc Id:

ENSRNOP00000070814 ⟸ ENSRNOT00000083068

Ensembl Acc Id:

ENSRNOP00000035138 ⟸ ENSRNOT00000036366

Ensembl Acc Id:

ENSRNOP00000019737 ⟸ ENSRNOT00000019737

Ensembl Acc Id:

ENSRNOP00000089530 ⟸ ENSRNOT00000101159

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P08081-F1-model_v2	AlphaFold	P08081	1-248	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693690

Promoter ID:

EPDNEW_R4212

Type:

initiation region

Name:

Clta_1

Description:

clathrin, light chain A

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	5	59,491,128 - 59,491,188	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:70919	AgrOrtholog
BioCyc Gene	G2FUF-41479	BioCyc
Ensembl Genes	ENSRNOG00000014635	Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOG00055020710	UniProtKB/Swiss-Prot
	ENSRNOG00060004393	UniProtKB/Swiss-Prot
	ENSRNOG00065010119	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000019737.6	UniProtKB/Swiss-Prot
	ENSRNOT00000036366.7	UniProtKB/Swiss-Prot
	ENSRNOT00000083068.2	UniProtKB/TrEMBL
	ENSRNOT00000101159.1	UniProtKB/TrEMBL
	ENSRNOT00055035371	UniProtKB/Swiss-Prot
	ENSRNOT00060007397	UniProtKB/Swiss-Prot
	ENSRNOT00065016316	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7307624	IMAGE-MGC_LOAD
InterPro	Clathrin_L-chain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:83800	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:105384	IMAGE-MGC_LOAD
NCBI Gene	83800	ENTREZGENE
PANTHER	CLATHRIN LIGHT CHAIN A	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR10639	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Clathrin_lg_ch	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Clta	PhenoGen
PROSITE	CLATHRIN_LIGHT_CHN_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CLATHRIN_LIGHT_CHN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000014635	RatGTEx
	ENSRNOG00055020710	RatGTEx
	ENSRNOG00060004393	RatGTEx
	ENSRNOG00065010119	RatGTEx
UniProt	A0A0G2JYW3	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6A7H3	ENTREZGENE, UniProtKB/TrEMBL
	A6IJ63	ENTREZGENE, UniProtKB/TrEMBL
	A6IJ64	ENTREZGENE, UniProtKB/TrEMBL
	A6IJ66_RAT	UniProtKB/TrEMBL
	CLCA_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q5PPP1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2011-08-01	Clta	clathrin, light chain A	Clta	clathrin, light chain (Lca)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-09	Clta	clathrin, light chain (Lca)	Clta	clathrin, light polypeptide (Lca)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-07-09	Clta	clathrin, light polypeptide (Lca)			Symbol and Name updated to reflect Human and Mouse nomenclature	70877	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains ten heptad elements that may form alpha-helical coiled coils	70686

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

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)