Afg2b (AFG2 AAA ATPase homolog B) - Rat Genome Database

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Gene: Afg2b (AFG2 AAA ATPase homolog B) Mus musculus
Analyze
Symbol: Afg2b
Name: AFG2 AAA ATPase homolog B
RGD ID: 1623001
MGI Page MGI
Description: Predicted to enable preribosome binding activity. Predicted to be involved in ribosomal large subunit biogenesis. Predicted to act upstream of or within ribosome biogenesis. Predicted to be located in cytoplasm and spindle. Is expressed in placenta. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness. Orthologous to human AFG2B (AFG2 AAA ATPase homolog B).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ATPase family gene 2 protein homolog B; AV141009; C130039A10Rik; ribosome biogenesis protein SPATA5L1; Spata5l1; spermatogenesis associated 5-like 1; spermatogenesis-associated protein 5-like protein 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392122,461,112 - 122,474,933 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2122,461,120 - 122,474,750 (+)EnsemblGRCm39 Ensembl
GRCm382122,630,625 - 122,636,478 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2122,630,646 - 122,632,930 (+)EnsemblGRCm38mm10GRCm38
MGSCv372122,456,364 - 122,463,552 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362122,322,066 - 122,324,152 (+)NCBIMGSCv36mm8
Celera2123,797,050 - 123,816,636 (+)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.64NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
cytoskeleton  (IEA)
nucleus  (IEA)
spindle  (ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12520002   PMID:12671064   PMID:16141072   PMID:16141073   PMID:21779340  


Genomics

Comparative Map Data
Afg2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392122,461,112 - 122,474,933 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2122,461,120 - 122,474,750 (+)EnsemblGRCm39 Ensembl
GRCm382122,630,625 - 122,636,478 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2122,630,646 - 122,632,930 (+)EnsemblGRCm38mm10GRCm38
MGSCv372122,456,364 - 122,463,552 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362122,322,066 - 122,324,152 (+)NCBIMGSCv36mm8
Celera2123,797,050 - 123,816,636 (+)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.64NCBI
AFG2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381545,402,336 - 45,421,415 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1545,402,336 - 45,421,415 (+)EnsemblGRCh38hg38GRCh38
GRCh371545,694,534 - 45,713,613 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361543,481,878 - 43,500,905 (+)NCBINCBI36Build 36hg18NCBI36
Build 341543,481,877 - 43,500,903NCBI
Celera1522,585,940 - 22,605,033 (+)NCBICelera
Cytogenetic Map15q21.1NCBI
HuRef1522,518,626 - 22,537,724 (+)NCBIHuRef
CHM1_11545,813,504 - 45,832,601 (+)NCBICHM1_1
T2T-CHM13v2.01543,210,511 - 43,229,587 (+)NCBIT2T-CHM13v2.0
Afg2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83130,148,061 - 130,162,458 (+)NCBIGRCr8
mRatBN7.23109,694,739 - 109,708,356 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3109,694,757 - 109,707,757 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3113,591,129 - 113,604,153 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03122,186,654 - 122,199,678 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03119,847,036 - 119,860,061 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03114,747,410 - 114,760,409 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3114,747,410 - 114,760,409 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03121,285,518 - 121,298,517 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43109,584,705 - 109,597,704 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13109,490,333 - 109,503,047 (+)NCBI
Celera3108,572,672 - 108,585,655 (+)NCBICelera
Cytogenetic Map3q35NCBI
Afg2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554098,031,094 - 8,049,477 (-)NCBIChiLan1.0ChiLan1.0
AFG2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21634,642,922 - 34,661,998 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11538,819,606 - 38,838,683 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01524,350,226 - 24,369,308 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11542,680,949 - 42,700,008 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1542,681,127 - 42,699,801 (+)Ensemblpanpan1.1panPan2
AFG2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13011,767,166 - 11,788,402 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3011,767,064 - 11,788,398 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3011,758,341 - 11,779,550 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03011,904,377 - 11,925,634 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3011,904,275 - 11,925,631 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13011,825,502 - 11,846,719 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03011,932,005 - 11,953,258 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03012,052,285 - 12,073,489 (+)NCBIUU_Cfam_GSD_1.0
Afg2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864090,217,359 - 90,231,693 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364718,065,363 - 8,080,939 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364718,064,708 - 8,078,968 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AFG2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1126,313,402 - 126,335,475 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11126,314,573 - 126,335,193 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21140,888,564 - 140,909,181 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AFG2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12637,793,373 - 37,812,921 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2637,793,379 - 37,811,582 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048103,250,574 - 103,269,532 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Afg2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473113,901,347 - 13,917,051 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Afg2b
254 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:134
Count of miRNA genes:128
Interacting mature miRNAs:131
Transcripts:ENSMUST00000149090, ENSMUST00000152813
Prediction methods:Miranda, Rnahybrid
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302174Dssc2_mdextran sodium sulfate induced colitis QTL2 (mouse)Not determined224224632148700377Mouse
4141854T2dm2sa_mtype 2 diabetes mellitus 2 in SMXA RI mice (mouse)Not determined229307947148374934Mouse
1301344Lith1_mlithogenic gene 1 (mouse)Not determined245347635145312647Mouse
13824983Vclq1_mcurvilinear velocity QTL 1 (mouse)261830344136841920Mouse
5491197Mobq5_mmultigenic obesity QTL 5 (mouse)Not determined265269746162518926Mouse
11528549Sluc31_msusceptibility to lung cancer 31 (mouse)274524117129213005Mouse
4141155Plast2b_mplasma plant sterol 2b (mouse)Not determined284013198148522175Mouse
10412082Hylaq1_mHyperlocomotor activity related QTL 1 (mouse)Not determined284013198148667470Mouse
5491196Mobq6_mmultigenic obesity QTL 6 (mouse)Not determined285724269180896594Mouse
1301098Cd8mts3_mCD8 memory T cell subset 3 (mouse)Not determined291089974125090104Mouse
1301909Smdq2_msegregation of mitochondrial DNA QTL 2 (mouse)Not determined292778465126778607Mouse
27226761Feml18_mfemur length 18, 16 week (mouse)294230345154241920Mouse
11049569Lmr28d_mleishmaniasis resistance 28d (mouse)297123370131123532Mouse
11049568Lmr28c_mleishmaniasis resistance 28c (mouse)297123370131123532Mouse
12904935Edlmmq2_mextensor digitorum longus muscle mass QTL 2 (mouse)297210364131210364Mouse
12904954Gmmq2_mgastrocnemius muscle mass QTL 2 (mouse)297210364131210364Mouse
4141802Ignpq1_mIgA nephropathy QTL 1 (mouse)Not determined2100824060134824269Mouse
1302203Gvhd3_mgraft-versus host disease 3 (mouse)Not determined2100942930134943090Mouse
1301330Tbbmd2_mtotal body bone mineral density 2 (mouse)Not determined2100942930134943090Mouse
1302071Fembrs1_mfemur breaking strength 1 (mouse)Not determined2100942930134943090Mouse
27226788Feml13_mfemur length 13, 10 week (mouse)2102630345159941920Mouse
11041906Lmr28a_mleishmaniasis resistance 28a (mouse)2103095716129213005Mouse
11038702Ltpr2_mLeishmania tropica response 2 (mouse)2103095716167212356Mouse
1301825Pbrgcsf1_mperipheral blood stem cell response to granulocyte colony stimulating factor 1 (mouse)Not determined2106233580140233729Mouse
10043875Bw25_mbody weight QTL 25 (mouse)Not determined2107255676141255676Mouse
1301087Bbaa15_mB.burgdorferi-associated arthritis 15 (mouse)Not determined2110489658144489807Mouse
10045885Cplaq15_mcircadian period of locomotor activity 15 (mouse)Not determined2110916118154354667Mouse
1558990Skmw9_mskeletal muscle weight 9 (mouse)Not determined2111173704145173821Mouse
1300793Pcfm2_mperiosteal circumference and femur length 2 (mouse)Not determined2111173704145173821Mouse
1301905Lgth2_mbody length 2 (mouse)Not determined2111173704145173821Mouse
1301755Hrq1_mheart rate quantitative locus 1 (mouse)Not determined2111173704145173821Mouse
1301201Chab1_mcholesterol absorption 1 (mouse)Not determined2111551028145551163Mouse
1302033Nsv1_mNeuroadapted Sindbis viral RNA level 1 (mouse)Not determined2111623386145623526Mouse
1300798Actre3_mactivity response to ethanol 3 (mouse)Not determined2112024987128173821Mouse
1301415Actre4_mactivity response to ethanol 4 (mouse)Not determined2112024987128173821Mouse
11039520Ltpr2h_mLeishmania tropica response 2h (mouse)2112212746146213005Mouse
11038699Ltpr2b_mLeishmania tropica response 2b (mouse)2112212746146213005Mouse
11038700Ltpr2a_mLeishmania tropica response 2a (mouse)2112212746146213005Mouse
1301029T2dm3_mtype 2 diabetes mellitus 3 (mouse)Not determined2114288075132714157Mouse
11039521Ltpr2g_mLeishmania tropica response 2g (mouse)2115212857149212994Mouse
11038696Ltpr2f_mLeishmania tropica response 2f (mouse)2115212857149212994Mouse
13506762Tbvq2_mtrabecular bone volume QTL 2 (mouse)2115430481124741920Mouse
1301295Prdt1_mprion disease incubation time 1 (mouse)Not determined2116077623150077741Mouse
1558881Ses7_msalmonella enteritidis susceptibility 7 (mouse)Not determined2116306330150306474Mouse
1301618Bglu1_mblood glucose level 1 (mouse)Not determined2117942930174324863Mouse
12904007Cfq7_mconditioned fear QTL 7 (mouse)2118356772125048872Mouse
12910795Pwbwq5_mpost-weaning body weight QTL 5 (mouse)2118589253160611165Mouse
12910799Pwgrq2_mpre-weaning growth rate QTL 2 (mouse)2118589253160611165Mouse
12910812Pwgrq1_mpre-weaning growth rate QTL 1 (mouse)2118589253160611165Mouse
12910814Pwbwq1_mpre-weaning body weight QTL 1 (mouse)2118589253160611165Mouse
1300712El2_mepilepsy 2 (mouse)Not determined2122207146142532135Mouse

Markers in Region
AV141009  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2E5UniSTS
cM MapUN UniSTS
cM Map2 UniSTS
PMC153605P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm382122,631,674 - 122,632,067UniSTSGRCm38
MGSCv372122,457,410 - 122,457,803UniSTSGRCm37
Celera2123,798,090 - 123,798,483UniSTS
Cytogenetic Map2E5UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000152813
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl2122,630,646 - 122,632,930 (+)Ensembl
RefSeq Acc Id: ENSMUST00000239506   ⟹   ENSMUSP00000159384
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2122,461,120 - 122,474,750 (+)Ensembl
RefSeq Acc Id: ENSMUST00000239507
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2122,461,146 - 122,474,717 (+)Ensembl
RefSeq Acc Id: NM_001033256   ⟹   NP_001028428
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392122,461,112 - 122,474,933 (+)NCBI
GRCm382122,630,625 - 122,636,478 (+)NCBI
Celera2123,797,041 - 123,810,759 (+)ENTREZGENE
cM Map2 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_184860
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392122,461,112 - 122,474,933 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001028428 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0A7N9VSG0 (Get FASTA)   NCBI Sequence Viewer  
  BAE41185 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000159384
  ENSMUSP00000159384.2
Reference Protein Sequences
RefSeq Acc Id: NP_001028428   ⟸   NM_001033256
- UniProtKB: A0A7N9VSG0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000159384   ⟸   ENSMUST00000239506
Protein Domains
AAA+ ATPase

Promoters
RGD ID:6831708
Promoter ID:MM_KWN:31480
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000099458,   LINCRNA_608,   OTTMUST00000037228
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv362122,456,154 - 122,456,654 (+)MPROMDB
RGD ID:6878530
Promoter ID:EPDNEW_M2716
Type:initiation region
Name:Spata5l1_1
Description:Mus musculus spermatogenesis associated 5-like 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm382122,630,646 - 122,630,706EPDNEW
RGD ID:15092416
Promoter ID:EPDNEWNC_M316
Type:multiple initiation site
Name:Spata5l1_1
Description:spermatogenesis associated 5-like 1 [Source:MGISymbol;Acc:MGI:3036261]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm382122,630,646 - 122,630,706EPDNEWNC

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3036261 AgrOrtholog
Ensembl Genes ENSMUSG00000074876 Ensembl
  ENSMUSG00000118663 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000239506 ENTREZGENE
  ENSMUST00000239506.1 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.8.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/Swiss-Prot
  AAA_lid_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_AAA+_core UniProtKB/TrEMBL
  ATPase_AAA_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_AAA_CS UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:214616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:3036261 ENTREZGENE
NCBI Gene 214616 ENTREZGENE
PANTHER AAA-FAMILY ATPASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR VALOSIN-CONTAINING PROTEIN-LIKE UniProtKB/TrEMBL
  SPERMATOGENESIS-ASSOCIATED PROTEIN 5-LIKE PROTEIN 1 UniProtKB/Swiss-Prot
Pfam AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AAA_lid_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Afg2b PhenoGen
PROSITE AAA UniProtKB/Swiss-Prot
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A7N9VSG0 ENTREZGENE
  Q3TER3_MOUSE UniProtKB/TrEMBL
  SPA5L_MOUSE UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-04-24 Afg2b  AFG2 AAA ATPase homolog B  Spata5l1  spermatogenesis associated 5-like 1  Symbol and/or name updated 27372883 PROVISIONAL