Atg9b (autophagy related 9B) - Rat Genome Database

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Gene: Atg9b (autophagy related 9B) Rattus norvegicus
Analyze
Symbol: Atg9b
Name: autophagy related 9B
RGD ID: 1560887
Description: Predicted to be involved in autophagy of mitochondrion and macroautophagy. Predicted to act upstream of or within autophagosome assembly. Predicted to be located in cytoplasm. Predicted to be active in autophagosome and phagophore assembly site. Orthologous to human ATG9B (autophagy related 9B); PARTICIPATES IN autophagy pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; copper atom.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ATG9 autophagy related 9 homolog B; ATG9 autophagy related 9 homolog B (S. cerevisiae); autophagy-related protein 9B; LOC499973; RGD1560887; similar to autophagy 9-like 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8411,678,548 - 11,686,097 (+)NCBIGRCr8
mRatBN7.2410,784,934 - 10,793,832 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl410,786,114 - 10,793,651 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx415,932,374 - 15,939,036 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0411,752,565 - 11,759,227 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0410,104,349 - 10,111,011 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.047,314,369 - 7,322,095 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,314,369 - 7,321,029 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,325,733 - 7,332,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,151,128 - 6,157,788 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera46,400,691 - 6,407,351 (+)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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
4. Comprehensive gene review and curation RGD comprehensive gene curation
5. Autophagy in the heart and liver during normal aging and calorie restriction. Wohlgemuth SE, etal., Rejuvenation Res. 2007 Sep;10(3):281-92.
6. Mammalian autophagy: core molecular machinery and signaling regulation. Yang Z and Klionsky DJ, Curr Opin Cell Biol. 2010 Apr;22(2):124-31. Epub 2009 Dec 23.
Additional References at PubMed
PMID:15755735  


Genomics

Comparative Map Data
Atg9b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8411,678,548 - 11,686,097 (+)NCBIGRCr8
mRatBN7.2410,784,934 - 10,793,832 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl410,786,114 - 10,793,651 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx415,932,374 - 15,939,036 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0411,752,565 - 11,759,227 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0410,104,349 - 10,111,011 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.047,314,369 - 7,322,095 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,314,369 - 7,321,029 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,325,733 - 7,332,623 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,151,128 - 6,157,788 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera46,400,691 - 6,407,351 (+)NCBICelera
Cytogenetic Map4q11NCBI
ATG9B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387151,012,209 - 151,024,499 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7151,012,209 - 151,024,499 (-)EnsemblGRCh38hg38GRCh38
GRCh377150,709,297 - 150,721,586 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367150,340,233 - 150,352,519 (-)NCBINCBI36Build 36hg18NCBI36
Build 347150,146,953 - 150,159,234NCBI
Celera7145,266,630 - 145,278,919 (-)NCBICelera
Cytogenetic Map7q36.1NCBI
HuRef7144,521,635 - 144,533,925 (-)NCBIHuRef
CHM1_17150,717,703 - 150,729,992 (-)NCBICHM1_1
T2T-CHM13v2.07152,185,332 - 152,201,351 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27150,038,886 - 150,051,176 (-)NCBI
Atg9b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39524,589,179 - 24,597,141 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl524,589,179 - 24,597,141 (-)EnsemblGRCm39 Ensembl
GRCm38524,384,181 - 24,392,143 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl524,384,181 - 24,392,143 (-)EnsemblGRCm38mm10GRCm38
MGSCv37523,889,999 - 23,897,961 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36523,894,246 - 23,902,208 (-)NCBIMGSCv36mm8
Celera521,333,933 - 21,341,895 (-)NCBICelera
Cytogenetic Map5A3NCBI
cM Map511.49NCBI
Atg9b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554915,458,398 - 5,465,551 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554915,458,152 - 5,467,260 (-)NCBIChiLan1.0ChiLan1.0
ATG9B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26187,435,449 - 187,449,421 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1739,445,713 - 39,459,688 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07142,600,894 - 142,614,336 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17154,752,882 - 154,764,744 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7154,756,535 - 154,764,744 (-)Ensemblpanpan1.1panPan2
ATG9B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11615,072,436 - 15,082,867 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1615,072,312 - 15,080,397 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1615,680,763 - 15,688,684 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01616,794,726 - 16,802,656 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1616,795,686 - 16,802,641 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11615,167,172 - 15,175,100 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01615,748,627 - 15,756,553 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01615,799,326 - 15,807,261 (-)NCBIUU_Cfam_GSD_1.0
Atg9b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244051186,447,684 - 6,459,777 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365276,446,667 - 6,453,511 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365276,445,824 - 6,453,582 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATG9B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl186,200,639 - 6,208,286 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1186,200,246 - 6,208,988 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2186,570,334 - 6,579,023 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATG9B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121119,197,387 - 119,209,578 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21119,198,125 - 119,206,599 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607215,164,824 - 15,177,822 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Atg9b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248005,591,297 - 5,598,739 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248005,589,366 - 5,600,253 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Atg9b
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:42
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000029724
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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat


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
7 4 44 78 44 51 24 15 24 6 136 71 66 30 55 27

Sequence


Ensembl Acc Id: ENSRNOT00000029724   ⟹   ENSRNOP00000033321
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl410,786,114 - 10,793,651 (+)Ensembl
Rnor_6.0 Ensembl47,314,369 - 7,321,029 (+)Ensembl
RefSeq Acc Id: NM_001191968   ⟹   NP_001178897
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8411,678,548 - 11,685,209 (+)NCBI
mRatBN7.2410,786,114 - 10,792,775 (+)NCBI
Rnor_6.047,314,369 - 7,321,029 (+)NCBI
Rnor_5.047,325,733 - 7,332,623 (+)NCBI
Celera46,400,691 - 6,407,351 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235960   ⟹   XP_006236022
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8411,678,548 - 11,686,097 (+)NCBI
mRatBN7.2410,784,934 - 10,793,832 (+)NCBI
Rnor_6.047,314,369 - 7,322,095 (+)NCBI
Rnor_5.047,325,733 - 7,332,623 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178897 (Get FASTA)   NCBI Sequence Viewer  
  XP_006236022 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99376 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033321.3
RefSeq Acc Id: NP_001178897   ⟸   NM_001191968
- UniProtKB: D4ABD5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236022   ⟸   XM_006235960
- Peptide Label: isoform X1
- UniProtKB: D4ABD5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000033321   ⟸   ENSRNOT00000029724

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ABD5-F1-model_v2 AlphaFold D4ABD5 1-924 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:1560887 AgrOrtholog
BioCyc Gene G2FUF-46039 BioCyc
Ensembl Genes ENSRNOG00000023449 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029724.4 UniProtKB/TrEMBL
InterPro Autophagy-rel_prot_9 UniProtKB/TrEMBL
KEGG Report rno:499973 UniProtKB/TrEMBL
NCBI Gene 499973 ENTREZGENE
PANTHER APG9 UniProtKB/TrEMBL
  AUTOPHAGY-RELATED PROTEIN 9B UniProtKB/TrEMBL
Pfam APG9 UniProtKB/TrEMBL
PhenoGen Atg9b PhenoGen
RatGTEx ENSRNOG00000023449 RatGTEx
UniProt D4ABD5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-06-07 Atg9b  autophagy related 9B  Atg9b  ATG9 autophagy related 9 homolog B (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Atg9b  ATG9 autophagy related 9 homolog B (S. cerevisiae)  RGD1560887_predicted  similar to autophagy 9-like 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560887_predicted  similar to autophagy 9-like 2 (predicted)  LOC499973  similar to autophagy 9-like 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499973  similar to autophagy 9-like 2      Symbol and Name status set to provisional 70820 PROVISIONAL