Agfg1 (ArfGAP with FG repeats 1) - Rat Genome Database

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Gene: Agfg1 (ArfGAP with FG repeats 1) Rattus norvegicus
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Symbol: Agfg1
Name: ArfGAP with FG repeats 1
RGD ID: 1560041
Description: Predicted to enable DNA binding activity; GTPase activator activity; and metal ion binding activity. Predicted to be involved in acrosome assembly; intermediate filament organization; and spermatid nucleus differentiation. Predicted to be located in cell projection; intracellular membrane-bounded organelle; and neuronal cell body. Predicted to be active in cytoplasmic vesicle. Orthologous to human AGFG1 (ArfGAP with FG repeats 1); PARTICIPATES IN influenza A pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',5,5'-tetrabromobisphenol A; 4,4'-diaminodiphenylmethane.
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: VALIDATED
Previously known as: arf-GAP domain and FG repeat-containing protein 1; arf-GAP domain and FG repeats-containing protein 1; HIV-1 Rev-binding protein homolog; LOC363266; MGC116375; nucleoporin-like protein RIP; similar to HIV-1 Rev binding protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Agfg1-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8991,572,962 - 91,630,688 (+)NCBIGRCr8
mRatBN7.2984,124,845 - 84,182,615 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl984,125,120 - 84,178,128 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx992,555,084 - 92,612,806 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,683,552 - 97,741,275 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0996,066,495 - 96,124,218 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0988,607,508 - 88,663,486 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,607,508 - 88,662,224 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,354,885 - 88,410,590 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4982,162,480 - 82,216,301 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera981,565,840 - 81,618,403 (+)NCBICelera
Cytogenetic Map9q34NCBI
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

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:8889548   PMID:11711676   PMID:14724135   PMID:15340146   PMID:15489334   PMID:16421295   PMID:16765935  


Genomics

Comparative Map Data
Agfg1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8991,572,962 - 91,630,688 (+)NCBIGRCr8
mRatBN7.2984,124,845 - 84,182,615 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl984,125,120 - 84,178,128 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx992,555,084 - 92,612,806 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0997,683,552 - 97,741,275 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0996,066,495 - 96,124,218 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0988,607,508 - 88,663,486 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl988,607,508 - 88,662,224 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0988,354,885 - 88,410,590 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4982,162,480 - 82,216,301 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera981,565,840 - 81,618,403 (+)NCBICelera
Cytogenetic Map9q34NCBI
AGFG1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382227,472,156 - 227,561,217 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2227,472,152 - 227,561,217 (+)EnsemblGRCh38hg38GRCh38
GRCh372228,336,872 - 228,425,933 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362228,045,286 - 228,130,548 (+)NCBINCBI36Build 36hg18NCBI36
Build 342228,162,546 - 228,247,805NCBI
Celera2222,106,500 - 222,195,457 (+)NCBICelera
Cytogenetic Map2q36.3NCBI
HuRef2220,179,703 - 220,268,811 (+)NCBIHuRef
CHM1_12228,342,933 - 228,431,983 (+)NCBICHM1_1
T2T-CHM13v2.02227,954,843 - 228,043,867 (+)NCBIT2T-CHM13v2.0
Agfg1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39182,816,738 - 82,878,722 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl182,817,204 - 82,878,903 (+)EnsemblGRCm39 Ensembl
GRCm38182,839,017 - 82,901,001 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl182,839,483 - 82,901,182 (+)EnsemblGRCm38mm10GRCm38
MGSCv37182,836,058 - 82,892,850 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36182,718,507 - 82,775,299 (+)NCBIMGSCv36mm8
Celera182,905,296 - 82,962,088 (+)NCBICelera
Cytogenetic Map1C5NCBI
cM Map142.55NCBI
Agfg1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554537,069,806 - 7,109,703 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554537,066,509 - 7,127,878 (-)NCBIChiLan1.0ChiLan1.0
AGFG1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213130,085,868 - 130,174,679 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B130,100,809 - 130,189,649 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B114,711,697 - 114,800,680 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B233,542,190 - 233,611,623 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B233,542,185 - 233,604,897 (+)Ensemblpanpan1.1panPan2
AGFG1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12540,229,732 - 40,307,277 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2540,243,734 - 40,301,135 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2540,845,559 - 40,924,805 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02540,475,273 - 40,554,664 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2540,475,176 - 40,548,884 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12540,412,340 - 40,491,304 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02540,252,760 - 40,331,854 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02540,426,655 - 40,506,046 (+)NCBIUU_Cfam_GSD_1.0
Agfg1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303182,421,491 - 182,483,054 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365258,463,475 - 8,504,188 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365258,463,475 - 8,504,201 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AGFG1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15128,898,705 - 128,975,510 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115128,898,806 - 128,980,782 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215142,743,993 - 142,774,355 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AGFG1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110113,500,174 - 113,589,243 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10113,500,391 - 113,582,474 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604085,867,490 - 85,955,907 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Agfg1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248431,751,808 - 1,806,631 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248431,751,735 - 1,806,624 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Agfg1
485 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:175
Count of miRNA genes:109
Interacting mature miRNAs:146
Transcripts:ENSRNOT00000021309
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
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
12879506Pur33Proteinuria QTL 33urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 52 36 19 36 8 9 74 35 41 11 8
Low 1 5 5 5 2
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000021309   ⟹   ENSRNOP00000021309
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl984,125,120 - 84,178,128 (+)Ensembl
Rnor_6.0 Ensembl988,607,508 - 88,662,224 (+)Ensembl
RefSeq Acc Id: NM_001135596   ⟹   NP_001129068
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8991,572,962 - 91,630,688 (+)NCBI
mRatBN7.2984,124,845 - 84,182,615 (+)NCBI
Rnor_6.0988,607,508 - 88,663,486 (+)NCBI
Rnor_5.0988,354,885 - 88,410,590 (+)NCBI
RGSC_v3.4982,162,480 - 82,216,301 (+)RGD
Celera981,565,840 - 81,618,403 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001129068 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99202 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00055009614
  ENSRNOP00060009338
  ENSRNOP00065029466
GenBank Protein Q4KLH5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001129068   ⟸   NM_001135596
- UniProtKB: Q4KLH5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021309   ⟸   ENSRNOT00000021309
Protein Domains
Arf-GAP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4KLH5-F1-model_v2 AlphaFold Q4KLH5 1-561 view protein structure

Transcriptome

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

Promoters
RGD ID:13696803
Promoter ID:EPDNEW_R7326
Type:initiation region
Name:Agfg1_1
Description:ArfGAP with FG repeats 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0988,607,488 - 88,607,548EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560041 AgrOrtholog
BioCyc Gene G2FUF-26969 BioCyc
Ensembl Genes ENSRNOG00000015619 Ensembl
  ENSRNOG00055007270 UniProtKB/Swiss-Prot
  ENSRNOG00060007454 UniProtKB/Swiss-Prot
  ENSRNOG00065021491 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00055012116 UniProtKB/Swiss-Prot
  ENSRNOT00060012343 UniProtKB/Swiss-Prot
  ENSRNOT00065036599 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.220.150 UniProtKB/Swiss-Prot
  Longin domain UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7384071 IMAGE-MGC_LOAD
InterPro ARFGAP/RecO UniProtKB/Swiss-Prot
  ArfGAP_dom UniProtKB/Swiss-Prot
  ArfGAP_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:363266 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116375 IMAGE-MGC_LOAD
NCBI Gene 363266 ENTREZGENE
PANTHER ARF-GAP DOMAIN AND FG REPEAT-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot
  DRONGO, ISOFORM F UniProtKB/Swiss-Prot
Pfam ArfGap UniProtKB/Swiss-Prot
PhenoGen Agfg1 PhenoGen
PRINTS REVINTRACTNG UniProtKB/Swiss-Prot
PROSITE ARFGAP UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000015619 RatGTEx
  ENSRNOG00055007270 RatGTEx
  ENSRNOG00060007454 RatGTEx
  ENSRNOG00065021491 RatGTEx
SMART ArfGap UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57863 UniProtKB/Swiss-Prot
UniProt AGFG1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-01 Agfg1  ArfGAP with FG repeats 1  LOC363266  similar to HIV-1 Rev binding protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC363266  similar to HIV-1 Rev binding protein      Symbol and Name status set to provisional 70820 PROVISIONAL