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Gene: Atg4b (autophagy related 4B, cysteine peptidase) Rattus norvegicus

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Symbol:

Atg4b

Name:

autophagy related 4B, cysteine peptidase

RGD ID:

1309664

Description:

Predicted to enable cysteine-type endopeptidase activity; protein-phosphatidylethanolamide deconjugating activity; and scaffold protein binding activity. Involved in positive regulation of protein catabolic process. Predicted to be located in several cellular components, including autophagosome; endoplasmic reticulum; and mitochondrion. Predicted to be active in autophagosome membrane. Orthologous to human ATG4B (autophagy related 4B cysteine peptidase); PARTICIPATES IN autophagy pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; chromium(6+).

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

APG4 (ATG4) autophagy-related homolog B; APG4 (ATG4) autophagy-related homolog B (S. cerevisiae); Apg4b; ATG4 autophagy related 4 homolog B; ATG4 autophagy related 4 homolog B (S. cerevisiae); autophagy related 4 homolog B; autophagy related 4 homolog B (S. cerevisiae); autophagy related 4B; autophagy-related 4B; autophagy-related 4B (yeast); autophagy-related protein 4 homolog B; cysteine protease ATG4B; LOC316640; MGC112887

RGD Orthologs

Alliance Orthologs

More Info

more info ...

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	9	101,729,772 - 101,761,456 (+)	NCBI		GRCr8
mRatBN7.2	9	94,282,417 - 94,314,109 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	94,282,509 - 94,314,103 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	9	102,718,019 - 102,749,586 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	9	107,853,665 - 107,885,062 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	9	106,209,766 - 106,241,168 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	9	100,888,457 - 100,920,123 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	100,888,501 - 100,918,637 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	9	100,541,628 - 100,573,277 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	93,054,736 - 93,063,888 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	9	93,259,504 - 93,268,657 (+)	NCBI
Celera	9	91,839,255 - 91,848,407 (+)	NCBI		Celera
Cytogenetic Map	9	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Bethlem Myopathy 1A (ISO)

chromosome 2q37 deletion syndrome (ISO)

D-2-hydroxyglutaric aciduria 1 (ISO)

hereditary spastic paraplegia 30 (ISO)

intellectual disability (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-anisomycin (ISO)

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

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

2,4-dinitrotoluene (EXP)

2-deoxy-D-glucose (ISO)

2-methylcholine (ISO)

2-palmitoylglycerol (ISO)

3-methyladenine (ISO)

4-phenylbutyric acid (ISO)

acrolein (ISO)

alpha-pinene (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

atrazine (ISO)

cadmium dichloride (ISO)

cannabidiol (ISO)

Cannabidivarin (ISO)

carbon nanotube (ISO)

chlorpyrifos (ISO)

chromium(6+) (EXP)

clobetasol (ISO)

cocaine (EXP)

curcumin (ISO)

deoxynivalenol (ISO)

dieldrin (ISO)

dinitrogen (ISO)

doxorubicin (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

FR900359 (ISO)

iron dichloride (ISO)

ivermectin (ISO)

lycopene (ISO)

methotrexate (ISO)

oxaliplatin (EXP)

ozone (ISO)

paracetamol (ISO)

paraquat (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

potassium dichromate (EXP)

rotenone (ISO)

silicon dioxide (ISO)

sirolimus (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

tert-butyl hydroperoxide (ISO)

topotecan (EXP)

triphenyl phosphate (ISO)

triptonide (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aggrephagy (IBA)

autophagosome assembly (IBA,ISO)

autophagy (IEA,ISO)

cellular response to starvation (ISO)

microautophagy (IEA,ISO)

mitophagy (IBA,IEA,ISO)

otolith mineralization completed early in development (ISO)

piecemeal microautophagy of the nucleus (IBA)

positive regulation of protein catabolic process (IMP)

protein delipidation (ISO)

protein localization to phagophore assembly site (IEA,ISO)

protein processing (IBA)

protein transport (IEA)

proteolysis (IEA,ISO)

Cellular Component

autophagosome (IEA)

autophagosome membrane (IEA,ISO)

cytoplasm (IBA,ISO)

cytoplasmic vesicle (IEA)

cytosol (IEA)

endoplasmic reticulum (IEA)

mitochondrion (IEA)

Molecular Function

cysteine-type endopeptidase activity (IBA,IEA,ISO)

cysteine-type peptidase activity (IEA,ISO)

endopeptidase activity (ISO)

peptidase activity (ISO)

protein binding (ISO)

protein-phosphatidylethanolamide deconjugating activity (IBA,IEA,ISO)

scaffold protein binding (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

autophagy pathway (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	Comprehensive gene review and curation	RGD comprehensive gene curation
5.	LC3 conjugation system in mammalian autophagy.	Tanida I, etal., Int J Biochem Cell Biol. 2004 Dec;36(12):2503-18.
6.	Effects of RNA interference of Atg4B on the limited proteolysis of LC3 in PC12 cells and expression of Atg4B in various rat tissues.	Yoshimura K, etal., Autophagy. 2006 Jul-Sep;2(3):200-8. Epub 2006 Jul 28.

Additional References at PubMed

PMID:12477932	PMID:14530254	PMID:15169837	PMID:18387192	PMID:21177865	PMID:25327288	PMID:25578879

Genomics

Comparative Map Data

Atg4b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	9	101,729,772 - 101,761,456 (+)	NCBI		GRCr8
mRatBN7.2	9	94,282,417 - 94,314,109 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	94,282,509 - 94,314,103 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	9	102,718,019 - 102,749,586 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	9	107,853,665 - 107,885,062 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	9	106,209,766 - 106,241,168 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	9	100,888,457 - 100,920,123 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	100,888,501 - 100,918,637 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	9	100,541,628 - 100,573,277 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	93,054,736 - 93,063,888 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	9	93,259,504 - 93,268,657 (+)	NCBI
Celera	9	91,839,255 - 91,848,407 (+)	NCBI		Celera
Cytogenetic Map	9	q36	NCBI

ATG4B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	241,637,693 - 241,673,857 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	241,637,213 - 241,673,857 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	242,577,108 - 242,613,272 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	242,225,700 - 242,261,945 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	2	236,248,753 - 236,285,072 (+)	NCBI		Celera
Cytogenetic Map	2	q37.3	NCBI
HuRef	2	234,345,804 - 234,368,653 (+)	NCBI		HuRef
CHM1_1	2	242,583,163 - 242,619,336 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	242,141,021 - 242,177,191 (+)	NCBI		T2T-CHM13v2.0

Atg4b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	93,682,627 - 93,717,328 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	93,679,222 - 93,718,332 (+)	Ensembl		GRCm39 Ensembl
GRCm38	1	93,754,905 - 93,789,606 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	93,751,500 - 93,790,610 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	1	95,651,610 - 95,686,106 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	1	95,585,439 - 95,619,935 (+)	NCBI		MGSCv36	mm8
Celera	1	96,712,297 - 96,733,524 (+)	NCBI		Celera
Cytogenetic Map	1	D	NCBI
cM Map	1	47.32	NCBI

Atg4b
(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_004955542	166,365 - 193,006 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955542	164,969 - 192,498 (-)	NCBI	ChiLan1.0	ChiLan1.0

ATG4B
(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	13	144,345,296 - 144,382,195 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	144,360,352 - 144,395,867 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	128,913,323 - 128,950,112 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2B	247,702,880 - 247,738,985 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	247,702,880 - 247,738,977 (+)	Ensembl	panpan1.1		panPan2

ATG4B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	25	51,494,316 - 51,518,683 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	25	51,504,537 - 51,517,659 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	25	51,712,749 - 51,737,119 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	25	51,692,391 - 51,716,772 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	25	51,693,855 - 51,716,770 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	25	51,542,261 - 51,566,633 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	25	51,281,435 - 51,305,797 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	25	51,558,118 - 51,582,492 (+)	NCBI		UU_Cfam_GSD_1.0

Atg4b
(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_024405303	192,904,801 - 192,928,109 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936745	292,746 - 307,746 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936745	291,311 - 308,469 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ATG4B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	140,223,904 - 140,246,321 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	140,223,903 - 140,245,590 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

ATG4B
(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	10	127,689,577 - 127,720,232 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666040	71,603,345 - 71,632,928 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Atg4b
(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_004624847	5,605,844 - 5,629,891 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624847	5,605,818 - 5,629,729 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Atg4b
143 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	250
Count of miRNA genes:	155
Interacting mature miRNAs:	197
Transcripts:	ENSRNOT00000025529
Prediction methods:	Miranda, 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
1582203	Gluco19	Glucose level QTL 19	3.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	9	92491589	100929786	Rat
724515	Uae16	Urinary albumin excretion QTL 16	8		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	58163035	100929646	Rat
731171	Glom6	Glomerulus QTL 6	2.8	0.0003	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	9	64573531	109573531	Rat
724547	Cm21	Cardiac mass QTL 21	2.7		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	9	79271511	102910209	Rat
61385	Edpm9	Estrogen-dependent pituitary mass QTL 9	3.43	0.05	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	9	63869687	108869687	Rat
724544	Uae9	Urinary albumin excretion QTL 9	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	9	25268044	114175309	Rat
2290450	Scl57	Serum cholesterol level QTL 57	4.15		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	9	36962359	95410867	Rat
1578760	Cm53	Cardiac mass QTL 53	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	9	56771635	101771635	Rat
1581580	Uae34	Urinary albumin excretion QTL 34			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	62072275	96470995	Rat
1300134	Bp185	Blood pressure QTL 185	3.73		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	9	61381434	104821652	Rat
1354626	Bvd1	Brain ventricular dilatation QTL 1	3.73	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	9	75712843	111552878	Rat
4889852	Pur26	Proteinuria QTL 26	15	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	9	77813894	101597663	Rat
7794784	Mcs31	Mammary carcinoma susceptibility QTL 31	2.98		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	9	77813894	111552878	Rat
731164	Uae25	Urinary albumin excretion QTL 25	3.5	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	25661188	100929786	Rat
1578757	Pur6	Proteinuria QTL 6	3.3	0.005	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	9	62072275	96470995	Rat

Markers in Region

RH133414

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	9	94,313,835 - 94,314,048 (+)	MAPPER	mRatBN7.2
Rnor_6.0	9	100,919,849 - 100,920,061	NCBI	Rnor6.0
Rnor_5.0	9	100,573,004 - 100,573,216	UniSTS	Rnor5.0
RGSC_v3.4	9	93,063,617 - 93,063,829	UniSTS	RGSC3.4
Celera	9	91,848,136 - 91,848,348	UniSTS
RH 3.4 Map	9	810.5	UniSTS
Cytogenetic Map	9	q36	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_001399197	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006245534	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039083774	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039083775	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063267328	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC109427	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC098833	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473997	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000009	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000025529 ⟹ ENSRNOP00000025529

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	94,282,509 - 94,314,103 (+)	Ensembl
Rnor_6.0 Ensembl	9	100,888,501 - 100,918,637 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000102482 ⟹ ENSRNOP00000088154

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	94,294,542 - 94,314,103 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000116331 ⟹ ENSRNOP00000079449

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	9	94,282,509 - 94,314,103 (+)	Ensembl

RefSeq Acc Id:

NM_001399197 ⟹ NP_001386126

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	101,729,889 - 101,761,456 (+)	NCBI
mRatBN7.2	9	94,282,538 - 94,314,109 (+)	NCBI

RefSeq Acc Id:

XM_006245534 ⟹ XP_006245596

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	101,729,772 - 101,761,454 (+)	NCBI
mRatBN7.2	9	94,282,417 - 94,314,107 (+)	NCBI
Rnor_6.0	9	100,888,457 - 100,920,123 (+)	NCBI
Rnor_5.0	9	100,541,628 - 100,573,277 (+)	NCBI

Sequence:

show sequence

GCGAGATGGCGACGCCCGCGCTTCCGCTGCGCCGCGCTTGGCTACCTCGGCTTCCCGTCGCTGT
GTCGCGCAGTAGCCCGTCGGAGCGACAGCACGGTCAGTCGGCGGCCGGACAGGGAAGATGGACG
CAGCCACTTTGACATATGATACTCTCCGGTTTGCCGAATTTGAAGATTTCCCCGAGACCTCAGA
GCCTGTTTGGATTCTGGGCAGAAAATACAGCATTTTCACAGAGAAGGATGAGATCTTGTCTGAT
GTTGCATCCAGACTTTGGTTTACGTACAGGAGAAACTTTCCAGCTATTGATTGGAGATGGACTC
AGCGGAAGAGACAGCCTGACAGCTACTTCAGTGTCCTCAACGCTTTCCTCGACAGGAAGGACAG
CTACTATTCCATCCACCAGATAGCGCAAATGGGAGTTGGCGAAGGCAAGTCTATAGGCCAGTGG
TACGGGCCGAACACTGTTGCCCAGGTCCTCAAGAAACTGGCTGTATTCGACACATGGAGCTCCC
TGGCTGTTCACATAGCAATGGACAACACTGTGGTGATGGAGGAAATCAGAAGATTGTGCAGGGC
CAGCCTTCCCTGTGCCGGGGCCGCTGCACTATCCATGGAGTCAGAGAGGCACTGTAACGGGCTC
CCTGCTGGAGCTGAAGTCACCAACAGGCCCTTGGCCTGGAGACCATTAGTGCTTCTCATCCCTC
TTCGCCTGGGACTGACAGACATCAATGAGGCCTATGTGGAGACGCTGAAGCACTGTTTCATGAT
GCCCCAGTCCCTGGGTGTTATTGGAGGGAAGCCCAACAGTGCCCACTACTTTATTGGCTACGTT
GGTGAGGAGCTCATCTATCTGGATCCCCATACTACACAGCCTGCAGTGGAGCTGACAGACAGCT
GCTTTATCCCCGACGAGAGCTTCCACTGCCAACACCCTCCCTGTCGGATGGGCATTGGGGAGCT
TGACCCATCCATTGCCGTGGGGTTTTTCTGTAAGACCGAGGAAGACTTTAATGACTGGTGCCAG
CAAGTCAAAAAGCTGTCCCAGCTTGGAGGTGCCCTGCCCATGTTTGAGTTGGTGGAACAGCAGC
CTTCCCATCTGGCCTGCCAGGATGTCCTGAACCTGTCCCTAGATTCTTCTGATGTAGAGAGACT
GGAGAGGTTCTTTGACTCTGAGGATGAAGACTTTGAAATCTTATCCCTCTGAAAATCCTGGGGT
TGGGGGATGGCCTCCATGGCCCTCATTGGGGTGCGTTGAGAACCCAGACCTGCCTTGGGCACTC
AGTGTCACCGCATTCCATCCACCCAGCCCACCCTGCTGAGTGCTGTCCGCCTGTGCCACCTCTG
TCCCGAGGGCCTGCTCTGCTCATGGACCAAGGACTGTGGTGCCTGGAGGCCTTACTGCTTGGAG
TCAGACTGCCTAAGCCCAAACACACAAGGGCCTGTCCACATGAAGGCGCTCACCAGAAGGCCTA
GTCAGGAAGAGCAGTGGGTCGGGAGCGCCCAGCATTCTCCACTCGACACTGCCAGCCCTGGTCA
GCGCATCAGCTTGGTTCTGCTTTCTCCTGGGCACCTGGGTCTGTGGTTTATTTGGAATTAAAGC
CCTGTTTGAAGTTGTTTAACAAAGACATGAATTTCTGGGGCACTTCCCAGGTCAGTCTTAGAAG
ATCTGCAGGTTGGCGTGTACAGAGTGACAGCCACATCATGGCCTCATAACTGCTGGGCAGGGTG
AGCTTTTGTGCTGTCTCCTCTGCCCAGTGTGATTATCAAGGGCTACCTCAGTGGGAAAGCATAT
GGAGAGAATCCCAGCAAGGCTGCTATTTGCTTTGGAGAAAAAGTATTCTTGTGGGGCATTTGGA
AAATCCAAAGATACCAGTGTGCATGGGCACAATATGGACACCTGAACCTTGGAGCAGCTGACAA
GTTTCTAGTGCTTCTGGAGTTGTGGTCTTGAGGTTCTCCATTAGGCCCTCACTAGGGAAGAGCT
ATGTCTCCTATATGGGGTTGATGGGTTTCATGACACGCTGCCTGCTGCTGTTAGCTTGCCACCC
AGCTTCCCTCTGGGAGGAAAGGGAGGGGGGGAGCAGAGCTGTTCTTTGCTTGTGACACTGTGCC
CACTGGTAGTAGGGCACACACTGCTATTTGAGCCTTCCTCCATGTTCTTTCCCTTCTCAGAAAC
CCTCCTGGGACATAGGAAATTTTAGATGGTTTGGGGCCAACAAGGTAAAAGTACTGCAGCTTTC
GGTGCAGAGTAGACATTTAGACAGAGCAGGTAGCTCCAGGCACCAGTGGGTGAAGAGTTCAGCT
CTCCTTGGCACTCATTTCCATACCTGCCACCTAACCTTGGCTTCCTGGGCCTTCAAGCTTTGGG
TGCTCTAGGTCTGCTGTCTTAGAAAAGCACCTTTCCTCCCCCTAGATAGGAAACAGGGTATGGC
ATTGTGGGGAGGCCCATGCAACAAACAGCCTTTGCTAAAAATCCTCCCCAAGAGCCTGTAGATG
GGTGAGGCTGGAGCTACTCCAGATACAGCAGCTCTAAGTAGCCCACGAGGTAGCAAGAGATCCT
GCCTATCAACATCAGATATGTTGATGACATATTTATTTCATCTTATTCCTCTCTCCCGTATCTT
GTCCCTTGACTTCAGATGGGGTGGGACAGGAAGACTAGGGCAATTCCCATTCCTCTGGAGCTTG
CTTCCTGGTCCAGGAGCCATTGTGCTGTTGTCGACTAGGGTCTTGTTGTAACTCCTGCTGTTGG
TAGCAAGGGTGGATGTCTGGAACCCGACAACCTGAAGGACCTCTCAGGGCTCAAGAAAGGCCTC
CTGAGGTTGTTCATTCTTCGTAGTGTAGTTTGCAATCCTTAACAGTAAATAATAAGTTTCAGTA
GAAAACAG

hide sequence

RefSeq Acc Id:

XM_039083774 ⟹ XP_038939702

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	101,749,250 - 101,761,454 (+)	NCBI
mRatBN7.2	9	94,301,893 - 94,314,107 (+)	NCBI

RefSeq Acc Id:

XM_039083775 ⟹ XP_038939703

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	101,749,197 - 101,761,454 (+)	NCBI
mRatBN7.2	9	94,301,850 - 94,314,107 (+)	NCBI

RefSeq Acc Id:

XM_063267328 ⟹ XP_063123398

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	101,729,782 - 101,758,712 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001386126	(Get FASTA)	NCBI Sequence Viewer
	XP_006245596	(Get FASTA)	NCBI Sequence Viewer
	XP_038939702	(Get FASTA)	NCBI Sequence Viewer
	XP_038939703	(Get FASTA)	NCBI Sequence Viewer
	XP_063123398	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	A0A0G2QC33	(Get FASTA)	NCBI Sequence Viewer
	AAH98833	(Get FASTA)	NCBI Sequence Viewer
	EDL91904	(Get FASTA)	NCBI Sequence Viewer
	EDL91905	(Get FASTA)	NCBI Sequence Viewer
	EDL91906	(Get FASTA)	NCBI Sequence Viewer
	EDL91907	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000025529.6
	ENSRNOP00000079449.1
	ENSRNOP00000088154.1
	ENSRNOP00055014217
	ENSRNOP00060001275
	ENSRNOP00065027822

RefSeq Acc Id:	XP_006245596 ⟸ XM_006245534
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5ZQY4 (UniProtKB/TrEMBL), A0A8I6GGT0 (UniProtKB/TrEMBL)
- Sequence:	show sequence MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDVASRLWFTYRRNFPAIDWR WTQRKRQPDSYFSVLNAFLDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTW SSLAVHIAMDNTVVMEEIRRLCRASLPCAGAAALSMESERHCNGLPAGAEVTNRPLAWRPLVLL IPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIYLDPHTTQPAVELT DSCFIPDESFHCQHPPCRMGIGELDPSIAVGFFCKTEEDFNDWCQQVKKLSQLGGALPMFELVE QQPSHLACQDVLNLSLDSSDVERLERFFDSEDEDFEILSL hide sequence

Ensembl Acc Id:

ENSRNOP00000025529 ⟸ ENSRNOT00000025529

RefSeq Acc Id:	XP_038939703 ⟸ XM_039083775
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038939702 ⟸ XM_039083774
- Peptide Label:	isoform X3

Ensembl Acc Id:

ENSRNOP00000088154 ⟸ ENSRNOT00000102482

Ensembl Acc Id:

ENSRNOP00000079449 ⟸ ENSRNOT00000116331

RefSeq Acc Id:	NP_001386126 ⟸ NM_001399197
- UniProtKB:	F1LRG2 (UniProtKB/Swiss-Prot), A0A0G2QC33 (UniProtKB/Swiss-Prot), Q4KM36 (UniProtKB/Swiss-Prot)

RefSeq Acc Id:	XP_063123398 ⟸ XM_063267328
- Peptide Label:	isoform X2

Protein Domains

Peptidase C54 catalytic

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-A0A0G2QC33-F1-model_v2	AlphaFold	A0A0G2QC33	1-393	view protein structure

Transcriptome

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

Promoters

RGD ID:

13696883

Promoter ID:

EPDNEW_R7406

Type:

multiple initiation site

Name:

Atg4b_1

Description:

autophagy related 4B, cysteine peptidase

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	9	100,888,556 - 100,888,616	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1309664	AgrOrtholog
BioCyc Gene	G2FUF-26631	BioCyc
Ensembl Genes	ENSRNOG00000018403	Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOG00055010433	UniProtKB/Swiss-Prot
	ENSRNOG00060001414	UniProtKB/Swiss-Prot
	ENSRNOG00065020498	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000025529.8	UniProtKB/Swiss-Prot
	ENSRNOT00000102482.1	UniProtKB/TrEMBL
	ENSRNOT00000116331.1	UniProtKB/TrEMBL
	ENSRNOT00055017659	UniProtKB/Swiss-Prot
	ENSRNOT00060002079	UniProtKB/Swiss-Prot
	ENSRNOT00065034677	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7378703	IMAGE-MGC_LOAD
InterPro	ATG4_LIR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Papain-like_cys_pep_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Peptidase_C54	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Peptidase_C54_cat	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:112887	IMAGE-MGC_LOAD
NCBI Gene	316640	ENTREZGENE
PANTHER	PTHR22624	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR22624:SF39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	ATG4_LIR	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Peptidase_C54	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Atg4b	PhenoGen
RatGTEx	ENSRNOG00000018403	RatGTEx
	ENSRNOG00055010433	RatGTEx
	ENSRNOG00060001414	RatGTEx
	ENSRNOG00065020498	RatGTEx
Superfamily-SCOP	SSF54001	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2QC33	ENTREZGENE
	A0A8I5ZQY4	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6GGT0	ENTREZGENE, UniProtKB/TrEMBL
	A6JR30_RAT	UniProtKB/TrEMBL
	A6JR31_RAT	UniProtKB/TrEMBL
	A6JR32_RAT	UniProtKB/TrEMBL
	A6JR33_RAT	UniProtKB/TrEMBL
	ATG4B_RAT	UniProtKB/Swiss-Prot
	F1LRG2	ENTREZGENE
	Q4KM36	ENTREZGENE
UniProt Secondary	F1LRG2	UniProtKB/Swiss-Prot
	Q4KM36	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2012-06-07	Atg4b	autophagy related 4B, cysteine peptidase	Atg4b	autophagy related 4 homolog B (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-01-06	Atg4b	autophagy related 4 homolog B (S. cerevisiae)	Atg4b	ATG4 autophagy related 4 homolog B (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-12-03	Atg4b	ATG4 autophagy related 4 homolog B (S. cerevisiae)	Atg4b	autophagy-related 4B (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Atg4b	autophagy-related 4B (yeast)	Apg4b	APG4 (ATG4) autophagy-related homolog B (S. cerevisiae)	Symbol and Name updated	1299863	APPROVED
2005-12-06	Apg4b	APG4 (ATG4) autophagy-related homolog B (S. cerevisiae)	Apg4b_predicted	APG4 (ATG4) autophagy-related homolog B (S. cerevisiae) (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Apg4b_predicted	APG4 (ATG4) autophagy-related homolog B (S. cerevisiae) (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)

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Imported Annotations - KEGG (archival)

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