C5h1orf87 (similar to human chromosome 1 open reading frame 87) - Rat Genome Database

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Gene: C5h1orf87 (similar to human chromosome 1 open reading frame 87) Rattus norvegicus
Analyze
Symbol: C5h1orf87
Name: similar to human chromosome 1 open reading frame 87
RGD ID: 1560146
Description: Orthologous to human C1orf87 (chromosome 1 open reading frame 87); INTERACTS WITH bisphenol A; aflatoxin B1 (ortholog); benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC500505; LOC500505; RGD1560146; similar to hypothetical protein MGC34837; uncharacterized protein C1orf87 homolog; uncharacterized protein LOC500505
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25111,342,381 - 111,411,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5111,342,387 - 111,411,590 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5113,911,108 - 113,978,340 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.05115,636,487 - 115,703,719 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.05115,699,002 - 115,766,230 (-)NCBIRnor_WKY
Rnor_6.05115,320,125 - 115,388,963 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5115,320,134 - 115,387,413 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05119,265,950 - 119,334,741 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45116,864,803 - 116,932,065 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5109,932,808 - 109,999,594 (-)NCBICelera
Cytogenetic Map5q33NCBI
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
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

Genomics

Comparative Map Data
C5h1orf87
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25111,342,381 - 111,411,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5111,342,387 - 111,411,590 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5113,911,108 - 113,978,340 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.05115,636,487 - 115,703,719 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.05115,699,002 - 115,766,230 (-)NCBIRnor_WKY
Rnor_6.05115,320,125 - 115,388,963 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5115,320,134 - 115,387,413 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05119,265,950 - 119,334,741 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45116,864,803 - 116,932,065 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5109,932,808 - 109,999,594 (-)NCBICelera
Cytogenetic Map5q33NCBI
C1orf87
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38159,990,394 - 60,073,770 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl159,987,269 - 60,073,770 (-)EnsemblGRCh38hg38GRCh38
GRCh37160,456,066 - 60,539,442 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36160,228,654 - 60,312,014 (-)NCBINCBI36Build 36hg18NCBI36
Celera158,744,771 - 58,828,195 (-)NCBICelera
Cytogenetic Map1p32.1NCBI
HuRef158,567,323 - 58,650,789 (-)NCBIHuRef
CHM1_1160,571,545 - 60,654,892 (-)NCBICHM1_1
T2T-CHM13v2.0159,868,848 - 59,952,337 (-)NCBIT2T-CHM13v2.0
Gm12695
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39496,611,818 - 96,675,067 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl496,611,884 - 96,673,423 (-)EnsemblGRCm39 Ensembl
GRCm38496,723,581 - 96,786,830 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl496,723,647 - 96,785,186 (-)EnsemblGRCm38mm10GRCm38
MGSCv37496,390,578 - 96,451,851 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36496,215,905 - 96,277,178 (-)NCBIMGSCv36mm8
Celera495,093,115 - 95,154,670 (-)NCBICelera
Cytogenetic Map4C5NCBI
CUNH1orf87
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542328,893,115 - 28,989,576 (+)NCBIChiLan1.0ChiLan1.0
C1H1orf87
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1160,953,430 - 61,035,260 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl160,953,381 - 61,035,275 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0159,248,281 - 59,330,506 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
C5H1orf87
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1549,815,138 - 49,893,632 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl549,814,666 - 49,894,745 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha549,882,064 - 49,960,541 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0549,994,691 - 50,073,621 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl549,994,716 - 50,074,721 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1549,946,608 - 50,025,100 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0549,892,009 - 49,970,489 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0550,174,507 - 50,253,011 (+)NCBIUU_Cfam_GSD_1.0
CUNH1orf87
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505873,464,919 - 73,611,134 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365221,872,484 - 1,950,348 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C6H1orf87
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6152,174,440 - 152,256,958 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16152,174,431 - 152,256,697 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26139,663,734 - 139,782,164 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CUNH1orf87
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12072,931,512 - 73,014,342 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2072,931,898 - 73,014,318 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603344,375,052 - 44,458,082 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Position Markers
D4Mit154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25111,410,443 - 111,410,587 (+)MAPPERmRatBN7.2
Rnor_6.05115,387,872 - 115,388,015NCBIRnor6.0
Rnor_5.05119,333,690 - 119,333,833UniSTSRnor5.0
RGSC_v3.45116,932,560 - 116,932,703UniSTSRGSC3.4
Celera5110,000,089 - 110,000,232UniSTS
Cytogenetic Map5q33UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)590067849128034027Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)590067849128034027Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1582212Livw2Liver weight QTL 23.50.0004liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)599016066119085810Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
7394708Emca11Estrogen-induced mammary cancer QTL 11mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)599753548113061097Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:90
Interacting mature miRNAs:96
Transcripts:ENSRNOT00000036030
Prediction methods:Microtar, 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

circulatory system endocrine system hemolymphoid system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 5
Low 4 5 11
Below cutoff 7 2 3 4 4 40 2 14 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036030   ⟹   ENSRNOP00000030210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5111,342,387 - 111,411,590 (-)Ensembl
Rnor_6.0 Ensembl5115,320,489 - 115,387,377 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077492   ⟹   ENSRNOP00000075653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5111,342,387 - 111,411,590 (-)Ensembl
Rnor_6.0 Ensembl5115,320,134 - 115,387,413 (-)Ensembl
RefSeq Acc Id: NM_001134625   ⟹   NP_001128097
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25111,342,893 - 111,409,949 (-)NCBI
Rnor_6.05115,320,489 - 115,387,377 (-)NCBI
Rnor_5.05119,265,950 - 119,334,741 (-)NCBI
RGSC_v3.45116,864,803 - 116,932,065 (-)RGD
Celera5109,932,808 - 109,999,594 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238420   ⟹   XP_006238482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25111,342,381 - 111,411,576 (-)NCBI
Rnor_6.05115,320,125 - 115,388,963 (-)NCBI
Rnor_5.05119,265,950 - 119,334,741 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593577   ⟹   XP_017449066
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25111,342,381 - 111,411,576 (-)NCBI
Rnor_6.05115,320,500 - 115,388,963 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001128097 (Get FASTA)   NCBI Sequence Viewer  
  NP_001398792 (Get FASTA)   NCBI Sequence Viewer  
  XP_006238482 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449066 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97786 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001128097   ⟸   NM_001134625
- Sequence:
RefSeq Acc Id: XP_006238482   ⟸   XM_006238420
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KB50 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449066   ⟸   XM_017593577
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000030210   ⟸   ENSRNOT00000036030
RefSeq Acc Id: ENSRNOP00000075653   ⟸   ENSRNOT00000077492

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KB50-F1-model_v2 AlphaFold A0A0G2KB50 1-537 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 115350510 115350511 A G snv CDR, CDS, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), GK/Ox (RGD), LE/Stm (RGD), LEW/NCrlBR (RGD), LN/MavRrrc (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), GK/FarMcwi (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WN/N (2020), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW), LEW/Crl (RGD), LH/MavRrrc (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), WAG/Rij (RGD), HXB10/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), HXB31/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEW/Crl (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), MWF/Hsd (2019), SR/JrHsd (2020)
5 115354976 115354977 T A snv FHH/EurMcwi (MCW), M520/NRrrcMcwi (2019), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), FHH/EurMcwi (RGD), GK/Ox (RGD), LE/Stm (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/Stm (2019), FHH/EurMcwi (2019), GK/FarMcwi (2019), LE/Stm (2019), M520/N (2020), CDS, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), F344/NCrl (RGD), FHL/EurMcwi (RGD), F344/N (2020), FXLE16/Stm (2020), FXLE18/Stm (2020), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LEXF10A/StmMcwi (2020), SBN/Ygl (MCW)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 119296328 119296329 A G snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), WN/N (KNAW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), MNS/Gib (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 116895282 116895283 A G snv ACI/EurMcwi (MCW), F344/NHsd (ICAHN), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), MR/N (KNAW), WKY/N (KNAW), WN/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), LE/Stm (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), DA/BklArbNsi (ICAHN), FHH/EurMcwi (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 111373044 111373045 A G snv ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), HXB31/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MR/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WN/N (2020)
5 111377544 111377545 T A snv ACI/EurMcwi (2019), M520/N (2020), BUF/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), GK/FarMcwi (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), ACI/N (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560146 AgrOrtholog
BioCyc Gene G2FUF-40621 BioCyc
Ensembl Genes ENSRNOG00000026169 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030210.4 UniProtKB/TrEMBL
  ENSRNOP00000075653 ENTREZGENE
  ENSRNOP00000075653.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036030.5 UniProtKB/TrEMBL
  ENSRNOT00000077492 ENTREZGENE
  ENSRNOT00000077492.2 UniProtKB/TrEMBL
InterPro DUF5580 UniProtKB/TrEMBL
  EF-hand-like_dom UniProtKB/TrEMBL
KEGG Report rno:500505 UniProtKB/TrEMBL
NCBI Gene 500505 ENTREZGENE
PANTHER PTHR34830 UniProtKB/TrEMBL
Pfam DUF5580 UniProtKB/TrEMBL
PhenoGen C5h1orf87 PhenoGen
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniProt A0A0G2KB50 ENTREZGENE, UniProtKB/TrEMBL
  D4A8S3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-28 C5h1orf87  similar to human chromosome 1 open reading frame 87  RGD1560146  similar to hypothetical protein MGC34837  Name and Symbol changed 629549 APPROVED
2008-04-30 RGD1560146  similar to hypothetical protein MGC34837   RGD1560146_predicted  similar to hypothetical protein MGC34837 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560146_predicted  similar to hypothetical protein MGC34837 (predicted)  LOC500505  similar to hypothetical protein MGC34837  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500505  similar to hypothetical protein MGC34837      Symbol and Name status set to provisional 70820 PROVISIONAL