Atg4a (autophagy related 4A, cysteine peptidase) - Rat Genome Database

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Gene: Atg4a (autophagy related 4A, cysteine peptidase) Rattus norvegicus
Analyze
Symbol: Atg4a (Ensembl: AABR07040864.1)
Name: autophagy related 4A, cysteine peptidase
RGD ID: 1596915
Description: Predicted to enable cysteine-type peptidase activity and protein-phosphatidylethanolamide deconjugating activity. Predicted to be involved in autophagosome assembly and proteolysis. Predicted to be located in cytoplasm. Orthologous to human ATG4A (autophagy related 4A cysteine peptidase); PARTICIPATES IN autophagy pathway; INTERACTS WITH bisphenol A; vinclozolin; (-)-epigallocatechin 3-gallate (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Agt4a; Atg4al1; autophagy related 4 homolog A; autophagy related 4 homolog A (S. cerevisiae); autophagy related 4A, cysteine peptidase-like 1; cysteine protease ATG4A; cysteine protease ATG4A-like; hypothetical protein LOC678769; LOC100910507; LOC678769; RGD1588268; similar to Cysteine protease ATG4A; similar to Cysteine protease ATG4A (Autophagy-related protein 4 homolog A) (Autophagin-2) (Autophagy-related cysteine endopeptidase 2) (AUT-like 2 cysteine endopeptidase); uncharacterized protein LOC678769
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X109,453,712 - 109,553,758 (+)NCBIGRCr8
mRatBN7.2X104,665,345 - 104,765,271 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX104,665,345 - 104,765,268 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX106,794,654 - 106,894,585 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X110,294,013 - 110,393,796 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X107,848,029 - 107,952,306 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X112,328,907 - 112,403,157 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0352,231,912 - 52,273,743 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX104,178,429 - 104,184,592 (+)NCBICelera
Cytogenetic MapXq33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Comprehensive gene review and curation RGD comprehensive gene curation
3. LC3 conjugation system in mammalian autophagy. Tanida I, etal., Int J Biochem Cell Biol. 2004 Dec;36(12):2503-18.
Additional References at PubMed
PMID:12473658   PMID:12477932   PMID:15169837   PMID:15632090   PMID:21177865   PMID:21873635  


Genomics

Comparative Map Data
Atg4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X109,453,712 - 109,553,758 (+)NCBIGRCr8
mRatBN7.2X104,665,345 - 104,765,271 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX104,665,345 - 104,765,268 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX106,794,654 - 106,894,585 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X110,294,013 - 110,393,796 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X107,848,029 - 107,952,306 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X112,328,907 - 112,403,157 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0352,231,912 - 52,273,743 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX104,178,429 - 104,184,592 (+)NCBICelera
Cytogenetic MapXq33NCBI
ATG4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X108,088,829 - 108,154,671 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX108,091,668 - 108,154,671 (+)EnsemblGRCh38hg38GRCh38
GRCh37X107,335,008 - 107,397,901 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X107,221,590 - 107,284,552 (+)NCBINCBI36Build 36hg18NCBI36
CeleraX107,806,406 - 107,869,363 (+)NCBICelera
Cytogenetic MapXq22.3NCBI
HuRefX96,957,585 - 97,020,331 (+)NCBIHuRef
CHM1_1X107,245,775 - 107,308,734 (+)NCBICHM1_1
T2T-CHM13v2.0X106,526,530 - 106,592,262 (+)NCBIT2T-CHM13v2.0
Atg4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X139,854,594 - 139,947,190 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX139,857,656 - 139,947,266 (+)EnsemblGRCm39 Ensembl
GRCm38X140,953,845 - 141,164,194 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX140,956,907 - 141,164,270 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X137,593,241 - 137,598,813 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv37X137,491,456 - 137,529,979 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X136,303,271 - 136,342,019 (+)NCBIMGSCv36mm8
CeleraX124,212,154 - 124,250,668 (+)NCBICelera
CeleraX125,167,353 - 125,172,805 (+)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX61.67NCBI
Atg4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554907,762,623 - 7,788,705 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554907,765,145 - 7,825,126 (-)NCBIChiLan1.0ChiLan1.0
ATG4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X107,572,779 - 107,636,591 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X107,576,410 - 107,640,195 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X97,189,556 - 97,253,371 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X107,559,639 - 107,623,389 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX107,559,639 - 107,623,389 (+)Ensemblpanpan1.1panPan2
ATG4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X81,629,346 - 81,688,086 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX81,629,465 - 81,688,099 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX67,753,046 - 67,808,661 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X83,281,769 - 83,337,418 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX83,279,008 - 83,337,403 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X80,740,818 - 80,796,428 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X82,453,368 - 82,509,012 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X82,244,510 - 82,299,838 (+)NCBIUU_Cfam_GSD_1.0
Atg4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X80,966,279 - 81,016,771 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364996,640,957 - 6,691,995 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364996,641,192 - 6,691,685 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATG4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX88,548,751 - 88,633,321 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X88,545,924 - 88,633,328 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X103,050,536 - 103,071,241 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATG4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X95,936,385 - 96,011,541 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX95,983,662 - 96,010,578 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606521,037,553 - 21,109,912 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Atg4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248038,337,042 - 8,407,222 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248038,336,123 - 8,407,354 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Atg4a
772 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat

Markers in Region
ATG4A  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X104,764,338 - 104,764,488 (+)MAPPERmRatBN7.2
Rnor_6.0X112,402,227 - 112,402,376NCBIRnor6.0
Rnor_5.0X110,864,184 - 110,864,333UniSTSRnor5.0
CeleraX104,183,662 - 104,183,811UniSTS


Expression


Sequence


RefSeq Acc Id: ENSRNOT00000074776   ⟹   ENSRNOP00000066137
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX104,693,433 - 104,765,268 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105654   ⟹   ENSRNOP00000077804
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX104,665,345 - 104,765,268 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108208   ⟹   ENSRNOP00000088348
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX104,693,255 - 104,765,184 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111058   ⟹   ENSRNOP00000096469
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX104,695,726 - 104,765,184 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111607   ⟹   ENSRNOP00000089027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX104,665,345 - 104,765,268 (+)Ensembl
RefSeq Acc Id: NM_001126298   ⟹   NP_001119770
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X109,453,828 - 109,553,751 (+)NCBI
mRatBN7.2X104,665,345 - 104,765,269 (+)NCBI
Rnor_6.0X112,328,907 - 112,403,157 (+)NCBI
Rnor_5.0352,231,912 - 52,273,743 (-)NCBI
CeleraX104,178,429 - 104,184,592 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100045   ⟹   XP_038955973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X109,454,143 - 109,553,758 (+)NCBI
mRatBN7.2X104,665,671 - 104,765,271 (+)NCBI
RefSeq Acc Id: XM_039100047   ⟹   XP_038955975
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X109,454,142 - 109,553,758 (+)NCBI
mRatBN7.2X104,665,669 - 104,765,271 (+)NCBI
RefSeq Acc Id: XM_063280293   ⟹   XP_063136363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X109,453,942 - 109,553,758 (+)NCBI
RefSeq Acc Id: XM_063280294   ⟹   XP_063136364
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X109,453,712 - 109,553,758 (+)NCBI
RefSeq Acc Id: XR_005498060
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X109,454,142 - 109,548,841 (+)NCBI
mRatBN7.2X104,665,669 - 104,760,357 (+)NCBI
RefSeq Acc Id: XR_005498061
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X109,454,142 - 109,552,117 (+)NCBI
mRatBN7.2X104,665,669 - 104,763,634 (+)NCBI
RefSeq Acc Id: NP_001119770   ⟸   NM_001126298
- UniProtKB: B1H274 (UniProtKB/TrEMBL),   M0R9G9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038955975   ⟸   XM_039100047
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZJL0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955973   ⟸   XM_039100045
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AIP9 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000089027   ⟸   ENSRNOT00000111607
RefSeq Acc Id: ENSRNOP00000077804   ⟸   ENSRNOT00000105654
RefSeq Acc Id: ENSRNOP00000096469   ⟸   ENSRNOT00000111058
RefSeq Acc Id: ENSRNOP00000066137   ⟸   ENSRNOT00000074776
RefSeq Acc Id: ENSRNOP00000088348   ⟸   ENSRNOT00000108208
RefSeq Acc Id: XP_063136364   ⟸   XM_063280294
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063136363   ⟸   XM_063280293
- Peptide Label: isoform X3
Protein Domains
Peptidase C54 catalytic

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R9G9-F1-model_v2 AlphaFold M0R9G9 1-408 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596915 AgrOrtholog
BioCyc Gene G2FUF-1529 BioCyc
Ensembl Genes ENSRNOG00000050960 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074776.3 UniProtKB/TrEMBL
  ENSRNOT00000105654.1 UniProtKB/TrEMBL
  ENSRNOT00000108208.1 UniProtKB/TrEMBL
  ENSRNOT00000111058.1 UniProtKB/TrEMBL
  ENSRNOT00000111607 ENTREZGENE
  ENSRNOT00000111607.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7442516 IMAGE-MGC_LOAD
InterPro ATG4_LIR UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Peptidase_C54 UniProtKB/TrEMBL
  Peptidase_C54_cat UniProtKB/TrEMBL
KEGG Report rno:678769 UniProtKB/TrEMBL
MGC_CLONE MGC:188313 IMAGE-MGC_LOAD
NCBI Gene Atg4al1 ENTREZGENE
PANTHER Peptidase_C54 UniProtKB/TrEMBL
  PTHR22624:SF35 UniProtKB/TrEMBL
Pfam ATG4_LIR UniProtKB/TrEMBL
  Peptidase_C54 UniProtKB/TrEMBL
PhenoGen Atg4al1 PhenoGen
RatGTEx ENSRNOG00000050960 RatGTEx
Superfamily-SCOP SSF54001 UniProtKB/TrEMBL
UniProt A0A8I5ZJL0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AIP9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AQT0_RAT UniProtKB/TrEMBL
  B1H274 ENTREZGENE, UniProtKB/TrEMBL
  M0R9G9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-11-11 Atg4al1  autophagy related 4A, cysteine peptidase-like 1  Atg4a  autophagy related 4A, cysteine peptidase  Data merged from RGD:6498436 737654 APPROVED
2014-11-11 Atg4a  autophagy related 4A, cysteine peptidase  Atg4al1  autophagy related 4A, cysteine peptidase-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-07-31 Atg4a  autophagy related 4A, cysteine peptidase  Agt4a  autophagy related 4A, cysteine peptidase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-15 Agt4a  autophagy related 4A, cysteine peptidase  LOC100910507  cysteine protease ATG4A-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-15 Atg4al1  autophagy related 4A, cysteine peptidase-like 1  Atg4a  autophagy related 4A, cysteine peptidase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100910507  cysteine protease ATG4A-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-06-07 Atg4a  autophagy related 4A, cysteine peptidase  Atg4a  autophagy related 4 homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-06-01 Atg4a  autophagy related 4 homolog A (S. cerevisiae)  LOC678769  similar to Cysteine protease ATG4A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-02-22 Atg4a  Autophagy related 4 A (S. cerevisiae)  LOC678769  similar to Cysteine protease ATG4A (Autophagy-related protein 4 homolog A) (Autophagin-2) (Autophagy-related cysteine endopeptidase 2) (AUT-like 2 cysteine endopeptidase)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC678769  similar to Cysteine protease ATG4A (Autophagy-related protein 4 homolog A) (Autophagin-2) (Autophagy-related cysteine endopeptidase 2) (AUT-like 2 cysteine endopeptidase)      Symbol and Name status set to provisional 70820 PROVISIONAL