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 localize to Cul3-RING ubiquitin ligase complex and cytoplasm. 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: PROVISIONAL
Also known as: giant axonal neuropathy; LOC307893
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21945,207,864 - 45,258,831 (+)NCBI
Rnor_6.0 Ensembl1949,695,579 - 49,741,965 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01949,692,790 - 49,746,178 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01960,480,642 - 60,533,157 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,263,532 - 47,310,683 (+)NCBIRGSC3.4rn4RGSC3.4
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-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

Additional References at PubMed
PMID:15983046   PMID:19424503  


Genomics

Comparative Map Data
Gan
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21945,207,864 - 45,258,831 (+)NCBI
Rnor_6.0 Ensembl1949,695,579 - 49,741,965 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01949,692,790 - 49,746,178 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01960,480,642 - 60,533,157 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,263,532 - 47,310,683 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl1681,314,966 - 81,380,198 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1681,314,944 - 81,390,809 (+)EnsemblGRCh38hg38GRCh38
GRCh381681,314,962 - 81,390,809 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371681,348,567 - 81,424,414 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361679,906,076 - 79,971,441 (+)NCBINCBI36hg18NCBI36
Build 341679,906,075 - 79,971,441NCBI
Celera1665,645,867 - 65,711,100 (+)NCBI
Cytogenetic Map16q23.2NCBI
HuRef1667,103,386 - 67,168,596 (+)NCBIHuRef
CHM1_11682,759,876 - 82,825,083 (+)NCBICHM1_1
Gan
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398117,884,720 - 117,932,573 (+)NCBIGRCm39mm39
GRCm39 Ensembl8117,884,874 - 117,942,736 (+)Ensembl
GRCm388117,157,981 - 117,205,834 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8117,158,135 - 117,215,997 (+)EnsemblGRCm38mm10GRCm38
MGSCv378119,682,035 - 119,729,086 (+)NCBIGRCm37mm9NCBIm37
MGSCv368120,044,112 - 120,091,163 (+)NCBImm8
Celera8121,377,818 - 121,424,875 (+)NCBICelera
Cytogenetic Map8E1NCBI
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
PanPan1.11681,347,221 - 81,410,363 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1681,347,215 - 81,410,363 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01661,919,004 - 61,994,811 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0570,823,382 - 70,884,349 (-)NCBI
UMICH_Zoey_3.1570,766,100 - 70,826,821 (-)NCBI
UNSW_CanFamBas_1.0570,601,294 - 70,662,010 (-)NCBI
UU_Cfam_GSD_1.0571,079,113 - 71,139,854 (-)NCBI
Gan
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934930,609,452 - 30,661,047 (-)NCBI
SpeTri2.0NW_00493647528,913,132 - 28,979,656 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GAN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl66,933,485 - 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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1566,754,752 - 66,820,933 (+)NCBI
ChlSab1.1 Ensembl566,754,893 - 66,816,761 (+)Ensembl
Gan
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247466,070,680 - 6,126,949 (-)NCBI

Position Markers
AU047749  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat

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.


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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1949,695,579 - 49,741,965 (+)Ensembl
RefSeq Acc Id: NM_001107434   ⟹   NP_001100904
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21945,207,864 - 45,254,107 (+)NCBI
Rnor_6.01949,695,579 - 49,741,965 (+)NCBI
Rnor_5.01960,480,642 - 60,533,157 (+)NCBI
RGSC_v3.41947,263,532 - 47,310,683 (+)RGD
Celera1944,479,857 - 44,526,017 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255685   ⟹   XP_006255747
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21945,207,869 - 45,258,831 (+)NCBI
Rnor_6.01949,692,790 - 49,746,178 (+)NCBI
Rnor_5.01960,480,642 - 60,533,157 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039097773   ⟹   XP_038953701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21945,238,804 - 45,258,831 (+)NCBI
RefSeq Acc Id: XM_039097774   ⟹   XP_038953702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21945,207,982 - 45,258,831 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100904 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255747 (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  
Reference Sequences
RefSeq Acc Id: NP_001100904   ⟸   NM_001107434
- UniProtKB: D3ZRI9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255747   ⟸   XM_006255685
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000016963   ⟸   ENSRNOT00000016963
RefSeq Acc Id: XP_038953702   ⟸   XM_039097774
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038953701   ⟸   XM_039097773
- Peptide Label: isoform X2
Protein Domains
BTB

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307766 AgrOrtholog
Ensembl Genes ENSRNOG00000012671 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016963 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016963 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 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
KEGG Report rno:307893 UniProtKB/TrEMBL
NCBI Gene 307893 ENTREZGENE
PANTHER 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
SMART BACK UniProtKB/TrEMBL
  BTB UniProtKB/TrEMBL
  Kelch UniProtKB/TrEMBL
Superfamily-SCOP BTB/POZ_fold UniProtKB/TrEMBL
  SSF117281 UniProtKB/TrEMBL
UniProt 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