Gan (gigaxonin) - Rat Genome Database

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Gene: Gan (gigaxonin) Rattus norvegicus
Analyze
Symbol: Gan
Name: gigaxonin
RGD ID: 1307766
Description: Predicted to be involved in protein ubiquitination. Predicted to be located in cytoplasm. Predicted to be part of Cul3-RING ubiquitin ligase complex. Human ortholog(s) of this gene implicated in giant axonal neuropathy 1. Orthologous to human GAN (gigaxonin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: giant axonal neuropathy; LOC307893
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
GRCr81962,116,600 - 62,173,879 (+)NCBIGRCr8
mRatBN7.21945,207,783 - 45,265,066 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,207,184 - 45,254,107 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1952,017,893 - 52,064,198 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01952,670,909 - 52,717,223 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01954,915,137 - 54,961,451 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01949,692,790 - 49,746,178 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1949,695,579 - 49,741,965 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01960,480,642 - 60,533,157 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,263,532 - 47,310,683 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11947,268,492 - 47,315,557 (+)NCBI
Celera1944,479,857 - 44,526,017 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15983046   PMID:19424503  


Genomics

Comparative Map Data
Gan
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81962,116,600 - 62,173,879 (+)NCBIGRCr8
mRatBN7.21945,207,783 - 45,265,066 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,207,184 - 45,254,107 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1952,017,893 - 52,064,198 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01952,670,909 - 52,717,223 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01954,915,137 - 54,961,451 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01949,692,790 - 49,746,178 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1949,695,579 - 49,741,965 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01960,480,642 - 60,533,157 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,263,532 - 47,310,683 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11947,268,492 - 47,315,557 (+)NCBI
Celera1944,479,857 - 44,526,017 (+)NCBICelera
Cytogenetic Map19q12NCBI
GAN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381681,314,962 - 81,390,809 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1681,314,944 - 81,390,809 (+)EnsemblGRCh38hg38GRCh38
GRCh371681,348,567 - 81,424,414 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361679,906,076 - 79,971,441 (+)NCBINCBI36Build 36hg18NCBI36
Build 341679,906,075 - 79,971,441NCBI
Celera1665,645,867 - 65,711,100 (+)NCBICelera
Cytogenetic Map16q23.2NCBI
HuRef1667,103,386 - 67,168,596 (+)NCBIHuRef
CHM1_11682,759,876 - 82,825,083 (+)NCBICHM1_1
T2T-CHM13v2.01687,375,728 - 87,451,557 (+)NCBIT2T-CHM13v2.0
Gan
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398117,884,720 - 117,932,573 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8117,884,874 - 117,942,736 (+)EnsemblGRCm39 Ensembl
GRCm388117,157,981 - 117,205,834 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8117,158,135 - 117,215,997 (+)EnsemblGRCm38mm10GRCm38
MGSCv378119,682,035 - 119,729,086 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368120,044,112 - 120,091,163 (+)NCBIMGSCv36mm8
Celera8121,377,818 - 121,424,875 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map863.71NCBI
Gan
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555224,035,672 - 4,090,630 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555224,035,672 - 4,096,845 (+)NCBIChiLan1.0ChiLan1.0
GAN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21891,056,924 - 91,140,629 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11696,976,406 - 97,060,039 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01661,919,004 - 61,994,811 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11681,347,221 - 81,410,363 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1681,347,215 - 81,410,363 (+)Ensemblpanpan1.1panPan2
GAN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1570,518,667 - 70,579,398 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl570,530,396 - 70,579,567 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha570,488,907 - 70,528,607 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0570,823,382 - 70,884,349 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl570,827,374 - 70,884,517 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1570,766,100 - 70,826,821 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0570,601,294 - 70,662,010 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0571,079,113 - 71,139,854 (-)NCBIUU_Cfam_GSD_1.0
Gan
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934930,609,452 - 30,661,047 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647528,945,908 - 28,967,653 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647528,913,132 - 28,979,656 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GAN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl66,933,503 - 6,989,653 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.166,921,446 - 6,989,670 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.267,466,847 - 7,524,943 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GAN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1566,754,752 - 66,820,933 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl566,754,893 - 66,816,761 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660479,017,449 - 9,081,670 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gan
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247466,081,033 - 6,126,858 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247466,070,680 - 6,126,949 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gan
361 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:501
Count of miRNA genes:261
Interacting mature miRNAs:332
Transcripts:ENSRNOT00000016963
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat

Markers in Region
AU047749  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21945,219,809 - 45,220,021 (+)MAPPERmRatBN7.2
Rnor_6.01949,707,511 - 49,707,722NCBIRnor6.0
Rnor_5.01960,494,570 - 60,494,781UniSTSRnor5.0
RGSC_v3.41947,275,479 - 47,275,690UniSTSRGSC3.4
Celera1944,491,791 - 44,492,002UniSTS
Cytogenetic Map19q12UniSTS
BQ193745  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21945,205,999 - 45,206,175 (+)MAPPERmRatBN7.2
Rnor_6.01949,693,715 - 49,693,890NCBIRnor6.0
Rnor_5.01960,480,774 - 60,480,949UniSTSRnor5.0
RGSC_v3.41947,261,668 - 47,261,843UniSTSRGSC3.4
Celera1944,477,993 - 44,478,168UniSTS
RH 3.4 Map19631.7UniSTS
Cytogenetic Map19q12UniSTS


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 12 1 6 1 31 1 6 2
Low 3 42 45 40 13 40 8 10 43 34 34 9 8
Below cutoff 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016963   ⟹   ENSRNOP00000016963
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1945,207,184 - 45,254,107 (+)Ensembl
Rnor_6.0 Ensembl1949,695,579 - 49,741,965 (+)Ensembl
RefSeq Acc Id: NM_001414939   ⟹   NP_001401868
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81962,116,600 - 62,173,879 (+)NCBI
mRatBN7.21945,207,783 - 45,265,066 (+)NCBI
RefSeq Acc Id: XM_039097773   ⟹   XP_038953701
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81962,147,610 - 62,173,879 (+)NCBI
mRatBN7.21945,238,804 - 45,258,831 (+)NCBI
RefSeq Acc Id: XM_039097774   ⟹   XP_038953702
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81962,116,797 - 62,173,879 (+)NCBI
mRatBN7.21945,207,982 - 45,258,831 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001401868 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953701 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953702 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92649 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016963
  ENSRNOP00000016963.6
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000016963   ⟸   ENSRNOT00000016963
RefSeq Acc Id: XP_038953702   ⟸   XM_039097774
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953701   ⟸   XM_039097773
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001401868   ⟸   NM_001414939
- UniProtKB: D3ZRI9 (UniProtKB/TrEMBL)
Protein Domains
BTB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRI9-F1-model_v2 AlphaFold D3ZRI9 1-603 view protein structure

Transcriptome

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

Promoters
RGD ID:13701171
Promoter ID:EPDNEW_R11694
Type:single initiation site
Name:Gan_1
Description:gigaxonin
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_6.01949,695,498 - 49,695,558EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307766 AgrOrtholog
BioCyc Gene G2FUF-5554 BioCyc
Ensembl Genes ENSRNOG00000012671 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016963 ENTREZGENE
  ENSRNOT00000016963.6 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.420 UniProtKB/TrEMBL
  2.120.10.80 UniProtKB/TrEMBL
InterPro BACK UniProtKB/TrEMBL
  BTB/POZ-like UniProtKB/TrEMBL
  BTB/POZ_fold UniProtKB/TrEMBL
  Kelch-like_gigaxonin UniProtKB/TrEMBL
  Kelch-typ_b-propeller UniProtKB/TrEMBL
  Kelch_1 UniProtKB/TrEMBL
  KLHL16 UniProtKB/TrEMBL
  KLHL16_BTB_POZ UniProtKB/TrEMBL
KEGG Report rno:307893 UniProtKB/TrEMBL
NCBI Gene 307893 ENTREZGENE
PANTHER KELCH PROTEIN UniProtKB/TrEMBL
  PTHR24412:SF232 UniProtKB/TrEMBL
Pfam BACK UniProtKB/TrEMBL
  BTB UniProtKB/TrEMBL
  Kelch_1 UniProtKB/TrEMBL
PhenoGen Gan PhenoGen
PIRSF Kelch-like_protein_gigaxonin UniProtKB/TrEMBL
PROSITE BTB UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012671 RatGTEx
SMART BACK UniProtKB/TrEMBL
  BTB UniProtKB/TrEMBL
  Kelch UniProtKB/TrEMBL
Superfamily-SCOP BTB/POZ_fold UniProtKB/TrEMBL
  SSF117281 UniProtKB/TrEMBL
UniProt A6IZH1_RAT UniProtKB/TrEMBL
  D3ZRI9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-17 Gan  gigaxonin  Gan  giant axonal neuropathy   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Gan  giant axonal neuropathy   Gan_predicted  giant axonal neuropathy (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Gan_predicted  giant axonal neuropathy (predicted)      Symbol and Name status set to approved 70820 APPROVED