Fam117b (family with sequence similarity 117, member B) - Rat Genome Database
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Gene: Fam117b (family with sequence similarity 117, member B) Rattus norvegicus
Analyze
Symbol: Fam117b
Name: family with sequence similarity 117, member B
RGD ID: 1307676
Description: Orthologous to human FAM117B (family with sequence similarity 117 member B); INTERACTS WITH 2,3,4,7,8-Pentachlorodibenzofuran; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Als2cr13; amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13; amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13 (human); LOC363236
Orthologs:
Homo sapiens (human) : FAM117B (family with sequence similarity 117 member B)  HGNC  Alliance
Mus musculus (house mouse) : Fam117b (family with sequence similarity 117, member B)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Fam117b (family with sequence similarity 117 member B)
Pan paniscus (bonobo/pygmy chimpanzee) : FAM117B (family with sequence similarity 117 member B)
Canis lupus familiaris (dog) : FAM117B (family with sequence similarity 117 member B)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Fam117b (family with sequence similarity 117 member B)
Sus scrofa (pig) : FAM117B (family with sequence similarity 117 member B)
Chlorocebus sabaeus (African green monkey) : FAM117B (family with sequence similarity 117 member B)
Heterocephalus glaber (naked mole-rat) : Fam117b (family with sequence similarity 117 member B)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0966,716,969 - 66,784,487 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl966,716,969 - 66,784,487 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0966,520,071 - 66,596,356 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4958,476,287 - 58,544,228 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1958,622,696 - 58,688,285 (+)NCBI
Celera958,775,417 - 58,842,774 (+)NCBICelera
Cytogenetic Map9q31NCBI
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

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21873635  


Genomics

Comparative Map Data
Fam117b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0966,716,969 - 66,784,487 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl966,716,969 - 66,784,487 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0966,520,071 - 66,596,356 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4958,476,287 - 58,544,228 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1958,622,696 - 58,688,285 (+)NCBI
Celera958,775,417 - 58,842,774 (+)NCBICelera
Cytogenetic Map9q31NCBI
FAM117B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2202,634,969 - 202,769,757 (+)EnsemblGRCh38hg38GRCh38
GRCh382202,634,969 - 202,769,757 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372203,499,901 - 203,634,480 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362203,208,456 - 203,342,725 (+)NCBINCBI36hg18NCBI36
Celera2197,252,014 - 197,387,230 (+)NCBI
Cytogenetic Map2q33.2NCBI
HuRef2195,346,934 - 195,481,383 (+)NCBIHuRef
CHM1_12203,506,619 - 203,641,107 (+)NCBICHM1_1
Fam117b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39159,952,165 - 60,024,507 (+)NCBI
GRCm38159,913,006 - 59,985,348 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl159,913,006 - 59,985,346 (+)EnsemblGRCm38mm10GRCm38
MGSCv37159,969,850 - 60,042,190 (+)NCBIGRCm37mm9NCBIm37
MGSCv36159,857,552 - 59,929,893 (+)NCBImm8
Celera160,428,884 - 60,500,816 (+)NCBICelera
Cytogenetic Map1C2NCBI
Fam117b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495545712,107,141 - 12,180,614 (-)NCBIChiLan1.0ChiLan1.0
FAM117B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B208,043,335 - 208,177,158 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B208,042,146 - 208,173,180 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B89,896,400 - 90,030,724 (+)NCBIMhudiblu_PPA_v0panPan3
FAM117B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3711,583,684 - 11,661,903 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13711,583,542 - 11,668,488 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Fam117b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367261,753,318 - 1,846,977 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FAM117B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15106,183,055 - 106,296,893 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115106,183,217 - 106,284,318 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215117,639,859 - 117,740,819 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FAM117B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11088,370,979 - 88,513,138 (+)NCBI
Fam117b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476513,661,928 - 13,782,962 (-)NCBI

Position Markers
D9Rat16  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0966,757,444 - 66,757,620NCBIRnor6.0
Rnor_5.0966,570,118 - 66,570,294UniSTSRnor5.0
RGSC_v3.4958,516,719 - 58,516,896RGDRGSC3.4
RGSC_v3.4958,516,720 - 58,516,896UniSTSRGSC3.4
RGSC_v3.1958,663,702 - 58,663,878RGD
Celera958,815,886 - 58,816,062UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9495.2UniSTS
RH 3.4 Map9495.2RGD
RH 2.0 Map9574.9RGD
SHRSP x BN Map942.2298RGD
RH133076  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0966,784,710 - 66,784,920NCBIRnor6.0
Rnor_5.0966,596,579 - 66,596,789UniSTSRnor5.0
RGSC_v3.4958,544,451 - 58,544,661UniSTSRGSC3.4
Celera958,842,997 - 58,843,207UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9515.3UniSTS
BE107857  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0966,766,179 - 66,766,371NCBIRnor6.0
Rnor_5.0966,578,074 - 66,578,266UniSTSRnor5.0
RGSC_v3.4958,525,452 - 58,525,644UniSTSRGSC3.4
Celera958,824,453 - 58,824,645UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9495.8UniSTS
RH137964  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0966,773,127 - 66,773,334NCBIRnor6.0
Rnor_5.0966,585,022 - 66,585,229UniSTSRnor5.0
RGSC_v3.4958,532,400 - 58,532,607UniSTSRGSC3.4
Celera958,831,401 - 58,831,608UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9514.9UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92748603666757620Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1598849Memor17Memory QTL 172.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)95488504176677636Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1578659Tspe1Trichinella spiralis expulsion QTL 14.8parasite quantity (VT:0010441)logarithm of the intestinal adult Trichinella spiralis count (CMO:0002024)96675744471010122Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:967
Count of miRNA genes:344
Interacting mature miRNAs:458
Transcripts:ENSRNOT00000031261
Prediction methods:Microtar, Miranda
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 3 14 32 16 19 16 74 35 37 11
Low 29 25 25 25 8 11 4 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031261   ⟹   ENSRNOP00000029910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl966,716,969 - 66,784,487 (+)Ensembl
RefSeq Acc Id: NM_001108797   ⟹   NP_001102267
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0966,716,969 - 66,784,487 (+)NCBI
Rnor_5.0966,520,071 - 66,596,356 (+)NCBI
RGSC_v3.4958,476,287 - 58,544,228 (+)RGD
Celera958,775,417 - 58,842,774 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102267 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL98943 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102267   ⟸   NM_001108797
- UniProtKB: F1M8D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000029910   ⟸   ENSRNOT00000031261

Transcriptome

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


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)
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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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/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
SHRSP/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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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/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:1307676 AgrOrtholog
Ensembl Genes ENSRNOG00000022066 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000029910 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031261 ENTREZGENE, UniProtKB/TrEMBL
InterPro FAM117B UniProtKB/TrEMBL
  Glcci1/FAM117 UniProtKB/TrEMBL
KEGG Report rno:363236 UniProtKB/TrEMBL
NCBI Gene 363236 ENTREZGENE
PANTHER PTHR14972 UniProtKB/TrEMBL
  PTHR14972:SF6 UniProtKB/TrEMBL
Pfam FAM117 UniProtKB/TrEMBL
PhenoGen Fam117b PhenoGen
UniGene Rn.8070 ENTREZGENE
UniProt F1M8D5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Fam117b  family with sequence similarity 117, member B  Als2cr13  amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-15 Als2cr13  amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13 (human)  Als2cr13  amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Als2cr13  amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13  Als2cr13_predicted  amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Als2cr13_predicted  amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13 (predicted)      Symbol and Name status set to approved 70820 APPROVED