Atg2b (autophagy related 2B) - Rat Genome Database

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Gene: Atg2b (autophagy related 2B) Rattus norvegicus
Analyze
Symbol: Atg2b
Name: autophagy related 2B
RGD ID: 1304878
Description: Predicted to enable lipid transfer activity; phosphatidylinositol-3-phosphate binding activity; and protein-membrane adaptor activity. Predicted to be involved in autophagy of mitochondrion and macroautophagy. Predicted to be located in endoplasmic reticulum. Predicted to be active in phagophore and phagophore assembly site. Orthologous to human ATG2B (autophagy related 2B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: autophagy-related protein 2 homolog B; LOC314415; RGD1304878; similar to 2410024A21Rik protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86130,286,979 - 130,357,109 (-)NCBIGRCr8
mRatBN7.26124,522,283 - 124,592,412 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6124,525,523 - 124,592,015 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06129,449,451 - 129,519,599 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6129,449,449 - 129,509,720 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06138,642,749 - 138,712,529 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46129,773,507 - 129,841,598 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.16129,778,695 - 129,803,238 (-)NCBI
Celera6122,089,232 - 122,159,479 (-)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Atg2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86130,286,979 - 130,357,109 (-)NCBIGRCr8
mRatBN7.26124,522,283 - 124,592,412 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6124,525,523 - 124,592,015 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06129,449,451 - 129,519,599 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6129,449,449 - 129,509,720 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06138,642,749 - 138,712,529 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46129,773,507 - 129,841,598 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.16129,778,695 - 129,803,238 (-)NCBI
Celera6122,089,232 - 122,159,479 (-)NCBICelera
Cytogenetic Map6q32NCBI
ATG2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381496,279,195 - 96,363,341 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1496,279,195 - 96,363,341 (-)EnsemblGRCh38hg38GRCh38
GRCh371496,745,532 - 96,829,678 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361495,817,348 - 95,899,431 (-)NCBINCBI36Build 36hg18NCBI36
Build 341495,820,836 - 95,853,254NCBI
Celera1476,803,312 - 76,885,404 (-)NCBICelera
Cytogenetic Map14q32.2NCBI
HuRef1476,932,696 - 77,014,765 (-)NCBIHuRef
CHM1_11496,686,513 - 96,768,523 (-)NCBICHM1_1
T2T-CHM13v2.01490,510,437 - 90,594,937 (-)NCBIT2T-CHM13v2.0
Atg2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912105,579,798 - 105,651,554 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12105,582,395 - 105,651,470 (-)EnsemblGRCm39 Ensembl
GRCm3812105,613,539 - 105,685,297 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12105,616,136 - 105,685,211 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712106,851,749 - 106,923,451 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612106,017,186 - 106,047,879 (-)NCBIMGSCv36mm8
Celera12106,848,151 - 106,919,764 (-)NCBICelera
Cytogenetic Map12ENCBI
cM Map1255.82NCBI
Atg2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543818,078,685 - 18,153,098 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543818,080,641 - 18,153,490 (-)NCBIChiLan1.0ChiLan1.0
ATG2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21597,441,258 - 97,523,352 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11496,657,763 - 96,739,856 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01476,910,943 - 76,992,969 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11496,233,322 - 96,314,881 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1496,237,825 - 96,314,881 (-)Ensemblpanpan1.1panPan2
ATG2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1865,039,960 - 65,110,811 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl865,044,194 - 65,110,796 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha864,555,847 - 64,626,693 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0865,311,353 - 65,382,558 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl865,314,912 - 65,382,482 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1864,984,413 - 65,055,244 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0865,045,745 - 65,116,666 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0865,369,420 - 65,440,283 (-)NCBIUU_Cfam_GSD_1.0
Atg2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086409,441,264 - 9,502,872 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936604584,480 - 641,183 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936604583,391 - 641,217 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATG2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7117,506,302 - 117,586,545 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17117,506,298 - 117,586,651 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27124,763,437 - 124,844,551 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATG2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12474,163,750 - 74,246,131 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2474,163,442 - 74,246,116 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605361,314,998 - 61,397,385 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Atg2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247347,015,672 - 7,096,348 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247347,015,356 - 7,097,392 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Atg2b
325 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:201
Count of miRNA genes:156
Interacting mature miRNAs:174
Transcripts:ENSRNOT00000006131
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6122549046140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6122549046137801795Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6116506292130245370Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1300076Glom8Glomerulus QTL 879e-09kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6122549046140286318Rat

Markers in Region
RH133729  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26124,525,839 - 124,526,020 (+)MAPPERmRatBN7.2
Rnor_6.06129,453,018 - 129,453,198NCBIRnor6.0
Rnor_5.06138,646,309 - 138,646,489UniSTSRnor5.0
RGSC_v3.46129,774,989 - 129,775,169UniSTSRGSC3.4
Celera6122,092,789 - 122,092,969UniSTS
RH 3.4 Map6819.0UniSTS
Cytogenetic Map6q32UniSTS
RH143805  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26124,524,862 - 124,525,007 (+)MAPPERmRatBN7.2
Rnor_6.06129,452,041 - 129,452,185NCBIRnor6.0
Rnor_5.06138,645,332 - 138,645,476UniSTSRnor5.0
RGSC_v3.46129,774,012 - 129,774,156UniSTSRGSC3.4
Celera6122,091,822 - 122,091,966UniSTS
RH 3.4 Map6833.1UniSTS
Cytogenetic Map6q32UniSTS
BF387587  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26124,524,173 - 124,524,332 (+)MAPPERmRatBN7.2
Rnor_6.06129,451,352 - 129,451,510NCBIRnor6.0
Rnor_5.06138,644,643 - 138,644,801UniSTSRnor5.0
RGSC_v3.46129,773,323 - 129,773,481UniSTSRGSC3.4
Celera6122,091,133 - 122,091,291UniSTS
RH 3.4 Map6818.2UniSTS
Cytogenetic Map6q32UniSTS
RH134739  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26124,524,991 - 124,525,209 (+)MAPPERmRatBN7.2
Rnor_6.06129,452,170 - 129,452,387NCBIRnor6.0
Rnor_5.06138,645,461 - 138,645,678UniSTSRnor5.0
RGSC_v3.46129,774,141 - 129,774,358UniSTSRGSC3.4
Celera6122,091,951 - 122,092,168UniSTS
RH 3.4 Map6819.5UniSTS
Cytogenetic Map6q32UniSTS
AI503411  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26124,524,968 - 124,525,074 (+)MAPPERmRatBN7.2
Rnor_6.06129,452,147 - 129,452,252NCBIRnor6.0
Rnor_5.06138,645,438 - 138,645,543UniSTSRnor5.0
RGSC_v3.46129,774,118 - 129,774,223UniSTSRGSC3.4
Celera6122,091,928 - 122,092,033UniSTS
Cytogenetic Map6q32UniSTS


Expression

RNA-SEQ Expression

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


Ensembl Acc Id: ENSRNOT00000006131   ⟹   ENSRNOP00000006131
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6124,525,523 - 124,592,015 (-)Ensembl
Rnor_6.0 Ensembl6129,449,449 - 129,509,720 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108549   ⟹   ENSRNOP00000079513
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6124,525,523 - 124,576,151 (-)Ensembl
RefSeq Acc Id: NM_001427775   ⟹   NP_001414704
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86130,286,986 - 130,357,109 (-)NCBI
RefSeq Acc Id: XM_063261999   ⟹   XP_063118069
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86130,286,979 - 130,356,702 (-)NCBI
RefSeq Acc Id: XM_063262000   ⟹   XP_063118070
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86130,286,979 - 130,316,834 (-)NCBI
Ensembl Acc Id: ENSRNOP00000006131   ⟸   ENSRNOT00000006131
Ensembl Acc Id: ENSRNOP00000079513   ⟸   ENSRNOT00000108549
RefSeq Acc Id: XP_063118069   ⟸   XM_063261999
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZR47 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063118070   ⟸   XM_063262000
- Peptide Label: isoform X2
- UniProtKB: A6KBD0 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001414704   ⟸   NM_001427775
- UniProtKB: A0A8I5ZR47 (UniProtKB/TrEMBL),   F1MAF8 (UniProtKB/TrEMBL)
Protein Domains
Atg2/VPS13 C-terminal   Autophagy-related protein 2 middle RBG module   Chorein N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1MAF8-F1-model_v2 AlphaFold F1MAF8 1-1977 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:1304878 AgrOrtholog
BioCyc Gene G2FUF-36331 BioCyc
Ensembl Genes ENSRNOG00000004519 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006131 ENTREZGENE
  ENSRNOT00000006131.7 UniProtKB/TrEMBL
  ENSRNOT00000108549 ENTREZGENE
  ENSRNOT00000108549.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7368501 IMAGE-MGC_LOAD
InterPro ATG2 UniProtKB/TrEMBL
  ATG2_mid_RBG UniProtKB/TrEMBL
  autophagy-related_C UniProtKB/TrEMBL
  VPS13-like_N UniProtKB/TrEMBL
MGC_CLONE MGC:109047 IMAGE-MGC_LOAD
NCBI Gene Atg2b ENTREZGENE
PANTHER AUTOPHAGY-RELATED PROTEIN 2 HOMOLOG B UniProtKB/TrEMBL
  PTHR13190 UniProtKB/TrEMBL
Pfam ATG2_CAD UniProtKB/TrEMBL
  ATG_C UniProtKB/TrEMBL
  Chorein_N UniProtKB/TrEMBL
PhenoGen Atg2b PhenoGen
RatGTEx ENSRNOG00000004519 RatGTEx
UniProt A0A8I5ZR47 ENTREZGENE, UniProtKB/TrEMBL
  A6KBD0 ENTREZGENE, UniProtKB/TrEMBL
  F1MAF8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-20 Atg2b  autophagy related 2B  Atg2b  autophagy related 2B  Type changed (type changed from [gene] to [protein-coding]) 629549 APPROVED
2014-07-29 Atg2b  autophagy related 2B  RGD1304878  similar to 2410024A21Rik protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1304878  similar to 2410024A21Rik protein  RGD1304878_predicted  similar to 2410024A21Rik protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1304878_predicted  similar to 2410024A21Rik protein (predicted)  LOC314415_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC314415_predicted  similar to 2410024A21Rik protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL