Atg12 (autophagy related 12) - Rat Genome Database

Name: Atg12
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Atg12 (autophagy related 12) Ictidomys tridecemlineatus

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Symbol:

Atg12

Name:

autophagy related 12

RGD ID:

12655767

Description:

ENCODES a protein that exhibits Atg8-family ligase activity (inferred); INVOLVED IN autophagy (ortholog); PARTICIPATES IN autophagy pathway; ASSOCIATED WITH autistic disorder (ortholog); Brain Injuries (ortholog); familial adenomatous polyposis 1 (ortholog); FOUND IN protein-containing complex (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

autophagy related 12, transcript variant X1; autophagy related 12, transcript variant X2; ubiquitin-like protein ATG12

RGD Orthologs

Alliance Orthologs

More Info

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More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	ATG12 (autophagy related 12)	NCBI	Ortholog
Mus musculus (house mouse):	Atg12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Atg12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Atg12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ATG12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ATG12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ATG12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ATG12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Atg12 (autophagy related 12)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024407213	128,299,258 - 128,306,932 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936742	999,771 - 1,007,885 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936742	1,000,029 - 1,007,885 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

Brain Injuries (ISO)

familial adenomatous polyposis 1 (ISO)

Hereditary Neoplastic Syndromes (ISO)

metabolic dysfunction-associated steatohepatitis (ISO)

Neurodevelopmental Disorders (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

autophagosome assembly (IEA)

autophagosome maturation (IEA)

autophagy (IEA,ISO)

autophagy of mitochondrion (IEA)

glycophagy (IEA)

macroautophagy (IEA)

negative regulation of defense response to virus (IEA)

negative regulation of innate immune response (IEA)

negative regulation of type I interferon production (IEA)

piecemeal microautophagy of the nucleus (IEA)

positive regulation of viral translation (IEA)

regulation of autophagosome maturation (IEA)

Cellular Component

Atg12-Atg5-Atg16 complex (IEA)

autophagosome (IEA)

autophagosome membrane (IEA)

cytoplasm (IEA)

intracellular membrane-bounded organelle (IEA)

membrane (IEA)

nucleoplasm (IEA)

phagophore assembly site membrane (IEA)

protein-containing complex (ISO)

transferase complex (IEA)

Molecular Function

Atg8-family ligase activity (IEA)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

autophagy pathway (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Atg12
(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_024407213	128,299,258 - 128,306,932 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936742	999,771 - 1,007,885 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936742	1,000,029 - 1,007,885 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ATG12
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	115,828,200 - 115,841,565 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	115,828,200 - 115,841,837 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	5	115,163,897 - 115,177,262 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	115,193,714 - 115,205,398 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	5	115,193,713 - 115,205,398	NCBI
Celera	5	111,112,297 - 111,125,961 (-)	NCBI		Celera
Cytogenetic Map	5	q22.3	NCBI
HuRef	5	110,344,587 - 110,358,250 (-)	NCBI		HuRef
CHM1_1	5	114,596,527 - 114,610,191 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	5	116,340,597 - 116,353,961 (-)	NCBI		T2T-CHM13v2.0

Atg12
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	46,865,484 - 46,874,683 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	18	46,863,211 - 46,874,647 (-)	Ensembl		GRCm39 Ensembl
GRCm38	18	46,732,417 - 46,741,724 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	46,730,144 - 46,741,580 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	18	46,892,071 - 46,901,233 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	18	46,857,758 - 46,866,888 (-)	NCBI		MGSCv36	mm8
Celera	18	48,091,663 - 48,100,825 (-)	NCBI		Celera
Cytogenetic Map	18	C	NCBI
cM Map	18	24.76	NCBI

Atg12
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	18	41,638,841 - 41,649,311 (-)	NCBI		GRCr8
mRatBN7.2	18	39,452,247 - 39,462,424 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	18	39,452,191 - 39,462,418 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	18	41,485,451 - 41,495,628 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	18	42,187,696 - 42,197,873 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	18	39,980,798 - 39,990,975 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	18	40,721,799 - 40,732,143 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	40,721,800 - 40,732,126 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	18	40,367,826 - 40,378,153 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	40,933,793 - 40,943,970 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	18	40,971,333 - 40,981,496 (-)	NCBI
Celera	18	37,703,672 - 37,713,849 (-)	NCBI		Celera
Cytogenetic Map	18	q11	NCBI

Atg12
(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_004955408	35,607,541 - 35,620,878 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	35,607,541 - 35,620,878 (-)	NCBI	ChiLan1.0	ChiLan1.0

ATG12
(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	4	111,074,139 - 111,086,535 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	5	109,227,800 - 109,240,196 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	5	111,184,617 - 111,196,038 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	5	116,979,738 - 116,992,288 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

ATG12
(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	5,531,062 - 5,543,034 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	11	5,531,759 - 5,542,743 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	11	5,681,691 - 5,693,659 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	11	5,522,868 - 5,534,845 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	11	5,522,246 - 5,534,875 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	11	5,478,061 - 5,490,016 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	11	5,549,224 - 5,561,188 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	11	5,801,442 - 5,813,410 (-)	NCBI		UU_Cfam_GSD_1.0

ATG12
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	119,941,997 - 119,965,696 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	119,948,443 - 119,965,702 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	124,835,748 - 124,851,487 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ATG12
(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	23	19,073,545 - 19,087,603 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	23	19,072,401 - 19,087,625 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666034	59,321,234 - 59,334,961 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Atg12
(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_004624733	6,045,432 - 6,060,784 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624733	6,046,073 - 6,056,321 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005339491	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_021736037	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010002273	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000011750 ⟹ ENSSTOP00000010542

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936742	999,771 - 1,007,885 (-)	Ensembl

RefSeq Acc Id:

XM_005339491 ⟹ XP_005339548

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	128,299,258 - 128,306,932 (-)	NCBI
SpeTri2.0	NW_004936742	1,000,029 - 1,007,885 (-)	NCBI

Sequence:

show sequence

CCGACTTACCGGAGGGGTGCTTTTCACTTGGCGGCTCATGGGAATGTTGCCCGTGGAACCCGTC
CTTAAGTTTATCTCAGTAAGAAAACATCAGATGCCATAGTAACAGCCAGGGGTCCTAGACAGTT
TCCATATGGAGAGCTAGCCGGAAGCTCCAACGTTCACCGTTGGGTTAGATCCCCCTTTGGCGCG
TCCTTTGCGATTCTCCTCAGCGCTGAGCCCGCCCTCTGCACGCTCTCAGCTGCCACTTCCGCTC
TCGCTTTCCACCGTGCAATATGGCGGAGGAGCCTGAGTCGGTGTTGCAACTCCCTTCAACTGCT
GCTGCCGGCGGTGAAGGACTTACGGATGTCTCCCCAGAAACAGCCACTCCAGAGCCCCCATCTT
CTGCTGCAGTCTCGCCGGGGACAGAGGAGCCTTCAGGCGACACCAAGAAAAAAATTGACATCCT
ACTGAAGGCTGTGGGAGACACCCCTATAATGAAAACAAAGAAGTGGGCTGTAGAGCGAACCCGA
ACCATCCAAGGACTCATTGACTTCATCAAGAAGTTCCTTAAACTTGTGGCCTCGGAACAGTTGT
TTATTTATGTGAATCAGTCCTTTGCTCCTTCCCCAGACCAGGAAGTCGGGACCCTCTATGAGTG
TTTTGGCAGTGATGGTAAACTGGTCCTACATTACTGCAAATCTCAGGCCTGGGGATGAGCCACA
GAGAAAAACAGCTTGCTACTCAAGATGATGTTTTCACAGAGGAAAAAGCTCCATAAAGTTCTTA
TGCTGTGACGAGACTTAACAGATATCAACTACTCAGCATGTGTCTACTGTAACTCATATTCATA
CATAAGAAAACCTCTGTAGAGTGAATAGACTAACAAAAATATGATTTGTGTTATTACACAAGTC
TTCATAAAAGATTGACATCACAGTATGCCTGTTACTCCTGCCTACTACCATTGTTTCAGATCTG
CCTCCAAGATTGAGAAGATTGAAACTACATGAACTTTCATTACCTGTTTTCAAAATGATTGAAA
TTGTTTACTTATAGAACTAGTACTCTGCTGATTTCTTTCATGGTAAAAATTAATTTACTAATAG
GTTTTTCCATTTCTTTTTAACTCATTCAAGGAAACGTCAGGGGTATAAGAGGTTTATATTTTTT
CTGTTGAATTACCTTGTCAAACCAAGTCGCATTGACCTCTTAGCTGAATACCTTACATAGTCCA
TTAGAGGGCAGTCCAGCTGATAAAAAGGGTTTGGTTAATCCGGTTCTACATCTTTGCCAGGTGA
ATGGAAATAAGACTTTTCTTGTTAATTTCTGGCCAATATGTAGCCAAGAAAGCAAGTATGTTGA
TAAACTGGAAGACTTTGAGAAAATAATCACAATTTAATTATGCTTGGAAACAGAAACAATTTTA
CAAATTCTAGACAAATGAGTTTTATAGGATTTTTTTTTTTTTTTGGTACTATCATTTAAGATTG
AGTTCCAGTGTTGTGCTGCTTATTTAAATATCACTTATTTAAACAATGTCCAAAGAACTTGCTG
AGTAAACCTAAAATCATTGTGTACTTCATATTATATTCAGATTGAAAGTATTCAAAGAATAATT
GTAAAATAGCCTCAAATTTTATGTGTATGTCATGCCTTGACTAAAAGAGTACCATTTTTACTGG
TGTGGTTAGAGTGCTCATTGCTTGAAGTGAGATTTAACTTTTTTTTCTTTTGTACTTTATTTAT
CATGCATAATATTTAAAGCCATTCCATAAATGGAATAGAATGTTCAAACAGGTTTTGTGACATG
TACTATAATTTCAAGTGTTTGTTTTCAAAGATAATATGGTAGGAAGGATGTGATTTTTATGAAA
GTATTTGAGCTACACTTACATCCTTTAAATCCCAGAGTGCACTTTATGGCTAGGGTTCAGCCAC
ATATTAGCATGAGGATATGCTAAATAACAATTCACTTTACAGTGAAGAAATTGCTATTCAGTTC
TCATTTTTTGCCTAAGAATGTGAATTCTTGATTTCCCTTATACCAATGACCCTTTATAATAAAT
GAATATGGCTAATAGCAGTGGAAAA

hide sequence

RefSeq Acc Id:

XM_021736037 ⟹ XP_021591712

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	128,301,601 - 128,306,867 (-)	NCBI
SpeTri2.0	NW_004936742	1,002,372 - 1,007,632 (-)	NCBI

Sequence:

show sequence

CTCTCGCTTTCCACCGTGCAATATGGCGGAGGAGCCTGAGTCGGTGTTGCAACTCCCTTCAACT
GCTGCTGCCGGCGGTGAAGGACTTACGGATGTCTCCCCAGAAACAGCCACTCCAGAGCCCCCAT
CTTCTGCTGCAGTCTCGCCGGGGACAGAGGAGCCTTCAGGCGACACCAAGAAAAAAATTTATTT
ATGTGAATCAGTCCTTTGCTCCTTCCCCAGACCAGGAAGTCGGGACCCTCTATGA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005339548	(Get FASTA)	NCBI Sequence Viewer
	XP_021591712	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000010542.3
GenBank Protein	KAG3265849	(Get FASTA)	NCBI Sequence Viewer
	KAG3265850	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_005339548 ⟸ XM_005339491
- Peptide Label:	isoform X1
- UniProtKB:	I3MHX5 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAEEPESVLQLPSTAAAGGEGLTDVSPETATPEPPSSAAVSPGTEEPSGDTKKKIDILLKAVGD TPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGK LVLHYCKSQAWG hide sequence

RefSeq Acc Id:	XP_021591712 ⟸ XM_021736037
- Peptide Label:	isoform X2
- Sequence:	show sequence MAEEPESVLQLPSTAAAGGEGLTDVSPETATPEPPSSAAVSPGTEEPSGDTKKKIYLCESVLCS FPRPGSRDPL hide sequence

Ensembl Acc Id:

ENSSTOP00000010542 ⟸ ENSSTOT00000011750

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000011755	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000011750.3	UniProtKB/TrEMBL
InterPro	Atg12	UniProtKB/TrEMBL
	Ubiquitin-like_domsf	UniProtKB/TrEMBL
NCBI Gene	Atg12	ENTREZGENE
PANTHER	PTHR13385	UniProtKB/TrEMBL
	UBIQUITIN-LIKE PROTEIN ATG12	UniProtKB/TrEMBL
Pfam	APG12	UniProtKB/TrEMBL
Superfamily-SCOP	SSF54236	UniProtKB/TrEMBL
UniProt	I3MHX5	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

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Imported Disease Annotations - ClinVar

RGD Manual Annotations