Fam172a (family with sequence similarity 172, member A) - Rat Genome Database

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Gene: Fam172a (family with sequence similarity 172, member A) Rattus norvegicus
Analyze
Symbol: Fam172a
Name: family with sequence similarity 172, member A
RGD ID: 1305526
Description: Predicted to contribute to siRNA binding activity. Predicted to be involved in heterochromatin assembly by small RNA; neural crest cell development; and regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in endoplasmic reticulum. Predicted to be active in nucleus. Orthologous to human FAM172A (family with sequence similarity 172 member A); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cotranscriptional regulator FAM172A; hypothetical protein LOC294606; LOC294606; RGD1305526; similar to Sperm 1 POU-domain transcription factor (SPRM-1) ; uncharacterized protein LOC294606
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.227,553,873 - 8,018,183 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl27,553,891 - 8,018,162 (+)Ensembl
Rnor_6.024,942,795 - 5,547,744 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl24,942,775 - 5,545,144 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.024,923,715 - 5,531,001 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.425,266,234 - 5,742,306 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.125,283,425 - 5,766,266 (+)NCBI
Celera24,004,369 - 4,466,879 (+)NCBICelera
Cytogenetic Map2q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
endoplasmic reticulum  (ISO)
nucleus  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:7902581   PMID:29311329  


Genomics

Comparative Map Data
Fam172a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.227,553,873 - 8,018,183 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl27,553,891 - 8,018,162 (+)Ensembl
Rnor_6.024,942,795 - 5,547,744 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl24,942,775 - 5,545,144 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.024,923,715 - 5,531,001 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.425,266,234 - 5,742,306 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.125,283,425 - 5,766,266 (+)NCBI
Celera24,004,369 - 4,466,879 (+)NCBICelera
Cytogenetic Map2q11NCBI
FAM172A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl593,617,725 - 94,111,699 (-)EnsemblGRCh38hg38GRCh38
GRCh38593,615,130 - 94,111,699 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37592,953,431 - 93,447,404 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36592,979,531 - 93,436,221 (-)NCBINCBI36hg18NCBI36
Celera588,812,827 - 89,307,611 (-)NCBI
Cytogenetic Map5q15NCBI
HuRef588,126,382 - 88,620,383 (-)NCBIHuRef
CHM1_1592,386,140 - 92,880,378 (-)NCBICHM1_1
Fam172a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391377,856,799 - 78,314,359 (+)NCBIGRCm39mm39
GRCm39 Ensembl1377,850,152 - 78,314,354 (+)Ensembl
GRCm381377,708,677 - 78,166,240 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1377,702,033 - 78,166,235 (+)EnsemblGRCm38mm10GRCm38
MGSCv371377,847,951 - 78,305,501 (+)NCBIGRCm37mm9NCBIm37
MGSCv361378,172,232 - 78,629,787 (+)NCBImm8
Celera1380,000,607 - 80,449,739 (+)NCBICelera
Cytogenetic Map13C1NCBI
Fam172a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541818,245,947 - 18,589,185 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541818,213,824 - 18,624,082 (+)NCBIChiLan1.0ChiLan1.0
FAM172A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1521,394,235 - 21,886,210 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl521,431,125 - 21,761,210 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0521,256,767 - 21,749,797 (+)NCBIMhudiblu_PPA_v0panPan3
FAM172A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1315,281,442 - 15,695,303 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl315,281,448 - 15,694,715 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha316,618,008 - 17,043,554 (+)NCBI
ROS_Cfam_1.0315,165,482 - 15,591,272 (+)NCBI
ROS_Cfam_1.0 Ensembl315,165,479 - 15,579,768 (+)Ensembl
UMICH_Zoey_3.1315,121,740 - 15,547,400 (+)NCBI
UNSW_CanFamBas_1.0315,121,094 - 15,533,650 (+)NCBI
UU_Cfam_GSD_1.0315,326,251 - 15,751,883 (+)NCBI
Fam172a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213170,852,074 - 171,299,071 (+)NCBI
SpeTri2.0NW_0049365239,037,516 - 9,485,257 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FAM172A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2100,477,775 - 100,893,580 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12100,477,770 - 100,893,594 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22104,270,706 - 104,541,750 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FAM172A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1487,499,061 - 87,978,159 (-)NCBIChlSab1.1chlSab2
ChlSab1.1487,499,061 - 87,978,159 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604936,694,485 - 37,141,391 (-)NCBIVero_WHO_p1.0
Fam172a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474312,513,337 - 12,935,578 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D2Mit29  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.227,887,772 - 7,888,014 (+)MAPPERmRatBN7.2
Rnor_6.025,417,336 - 5,417,577NCBIRnor6.0
Rnor_5.025,396,621 - 5,396,862UniSTSRnor5.0
RGSC_v3.425,601,529 - 5,601,770UniSTSRGSC3.4
RGSC_v3.425,601,528 - 5,601,770RGDRGSC3.4
RGSC_v3.125,627,976 - 5,628,373RGD
Celera24,338,310 - 4,338,555UniSTS
Cytogenetic Map2q11UniSTS
PMC123630P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.227,907,992 - 7,908,642 (+)MAPPERmRatBN7.2
Rnor_6.025,437,556 - 5,438,205NCBIRnor6.0
Rnor_5.025,416,841 - 5,417,490UniSTSRnor5.0
RGSC_v3.425,621,749 - 5,622,398UniSTSRGSC3.4
Celera24,358,532 - 4,359,181UniSTS
Cytogenetic Map2q11UniSTS
BI299099  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.227,729,665 - 7,729,842 (+)MAPPERmRatBN7.2
Rnor_6.025,260,146 - 5,260,322NCBIRnor6.0
Rnor_6.025,118,556 - 5,118,732NCBIRnor6.0
Rnor_5.025,239,107 - 5,239,283UniSTSRnor5.0
Rnor_5.025,097,517 - 5,097,693UniSTSRnor5.0
RGSC_v3.425,441,988 - 5,442,164UniSTSRGSC3.4
Celera24,179,945 - 4,180,121UniSTS
Cytogenetic Map2q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
731166Mamtr2Mammary tumor resistance QTL 20.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777212654247Rat
61368Mcs1Mammary carcinoma susceptibility QTL 14.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777223319447Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:363
Count of miRNA genes:230
Interacting mature miRNAs:262
Transcripts:ENSRNOT00000041541
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 8 36 20 19 20 3 3 74 31 36 11 3
Low 35 21 21 21 5 8 4 5 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106401 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006231726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101898 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC099302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC118290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000041541   ⟹   ENSRNOP00000051391
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,554,003 - 7,904,952 (+)Ensembl
Rnor_6.0 Ensembl24,989,295 - 5,545,140 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093155
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl24,942,818 - 5,111,076 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093535
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl24,942,840 - 4,975,875 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093548   ⟹   ENSRNOP00000076094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,553,892 - 7,904,525 (+)Ensembl
Rnor_6.0 Ensembl24,942,775 - 5,418,063 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093741   ⟹   ENSRNOP00000076112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,553,891 - 8,018,162 (+)Ensembl
Rnor_6.0 Ensembl24,942,798 - 5,545,144 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094560   ⟹   ENSRNOP00000093689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,553,892 - 8,018,162 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095380   ⟹   ENSRNOP00000089372
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,553,892 - 8,018,162 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099388   ⟹   ENSRNOP00000077745
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,553,891 - 8,018,162 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103663   ⟹   ENSRNOP00000082005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,553,892 - 8,018,162 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114522   ⟹   ENSRNOP00000093437
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl27,600,443 - 8,018,162 (+)Ensembl
RefSeq Acc Id: NM_001106401   ⟹   NP_001099871
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,891 - 8,018,180 (+)NCBI
Rnor_6.024,942,802 - 5,547,744 (+)NCBI
Rnor_5.024,923,715 - 5,531,001 (+)NCBI
RGSC_v3.425,266,234 - 5,742,306 (+)RGD
Celera24,004,369 - 4,466,879 (+)RGD
Sequence:
RefSeq Acc Id: XM_008760625   ⟹   XP_008758847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,876 - 7,904,813 (+)NCBI
Rnor_6.024,942,796 - 5,111,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760626   ⟹   XP_008758848
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,875 - 8,018,183 (+)NCBI
Rnor_6.024,942,795 - 5,111,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039101891   ⟹   XP_038957819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101892   ⟹   XP_038957820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101893   ⟹   XP_038957821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101894   ⟹   XP_038957822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,875 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101895   ⟹   XP_038957823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101896   ⟹   XP_038957824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,875 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101897   ⟹   XP_038957825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101898   ⟹   XP_038957826
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101899   ⟹   XP_038957827
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101900   ⟹   XP_038957828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,875 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101901   ⟹   XP_038957829
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 7,974,796 (+)NCBI
RefSeq Acc Id: XM_039101902   ⟹   XP_038957830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,873 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101903   ⟹   XP_038957831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,876 - 8,018,183 (+)NCBI
RefSeq Acc Id: XM_039101904   ⟹   XP_038957832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 7,904,813 (+)NCBI
RefSeq Acc Id: XM_039101905   ⟹   XP_038957833
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,874 - 7,939,216 (+)NCBI
RefSeq Acc Id: XM_039101906   ⟹   XP_038957834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.227,553,873 - 8,018,183 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099871   ⟸   NM_001106401
- UniProtKB: D3ZYE5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008758848   ⟸   XM_008760626
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_008758847   ⟸   XM_008760625
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: ENSRNOP00000051391   ⟸   ENSRNOT00000041541
RefSeq Acc Id: ENSRNOP00000076094   ⟸   ENSRNOT00000093548
RefSeq Acc Id: ENSRNOP00000076112   ⟸   ENSRNOT00000093741
RefSeq Acc Id: XP_038957830   ⟸   XM_039101902
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038957834   ⟸   XM_039101906
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038957819   ⟸   XM_039101891
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957827   ⟸   XM_039101899
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038957823   ⟸   XM_039101895
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038957820   ⟸   XM_039101892
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957825   ⟸   XM_039101897
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957821   ⟸   XM_039101893
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957826   ⟸   XM_039101898
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957829   ⟸   XM_039101901
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038957833   ⟸   XM_039101905
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038957832   ⟸   XM_039101904
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038957828   ⟸   XM_039101900
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038957822   ⟸   XM_039101894
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038957824   ⟸   XM_039101896
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038957831   ⟸   XM_039101903
- Peptide Label: isoform X9
RefSeq Acc Id: ENSRNOP00000077745   ⟸   ENSRNOT00000099388
RefSeq Acc Id: ENSRNOP00000089372   ⟸   ENSRNOT00000095380
RefSeq Acc Id: ENSRNOP00000093437   ⟸   ENSRNOT00000114522
RefSeq Acc Id: ENSRNOP00000082005   ⟸   ENSRNOT00000103663
RefSeq Acc Id: ENSRNOP00000093689   ⟸   ENSRNOT00000094560
Protein Domains
Arb2

Transcriptome

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

Promoters
RGD ID:13691042
Promoter ID:EPDNEW_R1566
Type:initiation region
Name:Fam172a_1
Description:family with sequence similarity 172, member A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1567  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.024,942,803 - 4,942,863EPDNEW
RGD ID:13691057
Promoter ID:EPDNEW_R1567
Type:multiple initiation site
Name:Fam172a_2
Description:family with sequence similarity 172, member A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1566  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.024,942,912 - 4,942,972EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
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/EurMcwi (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)
ACI/EurMcwi (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
ACI/N (2020)
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Sequenced By: MCW
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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/SsN (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
BUF/N (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/Stm (2020)
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Sequenced By: MCW
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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Sequenced By: MCW
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
GH/OmrMcwi (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)
GK/FarMcwi (2019)
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Sequenced By: MCW
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
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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
LE/Stm (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
LEW/Crl (2019)
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Sequenced By: MCW
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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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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Sequenced By: MCW
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/MavRrrc (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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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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Sequenced By: MCW
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/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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
MWF/Hsd (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
SBH/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: 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)
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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)
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)
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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/OlalpcvMcwi (2019)
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Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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/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 (2019)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 4989266 4989267 T C snv BUF/N (2020), Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305526 AgrOrtholog
Ensembl Genes ENSRNOG00000013844 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051391 UniProtKB/TrEMBL
  ENSRNOP00000076094 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000076112 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000089372 ENTREZGENE
  ENSRNOP00000093689 ENTREZGENE
Ensembl Transcript ENSRNOT00000041541 UniProtKB/TrEMBL
  ENSRNOT00000093548 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000093741 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000094560 ENTREZGENE
  ENSRNOT00000095380 ENTREZGENE
InterPro AB_hydrolase UniProtKB/TrEMBL
  Arb2_domain UniProtKB/TrEMBL
  FAM172A UniProtKB/TrEMBL
KEGG Report rno:294606 UniProtKB/TrEMBL
NCBI Gene 294606 ENTREZGENE
PANTHER PTHR21357:SF3 UniProtKB/TrEMBL
Pfam Arb2 UniProtKB/TrEMBL
PhenoGen Fam172a PhenoGen
Superfamily-SCOP SSF53474 UniProtKB/TrEMBL
UniProt A0A1W2Q607_RAT UniProtKB/TrEMBL
  D3ZYE5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Fam172a  family with sequence similarity 172, member A  RGD1305526  similar to Sperm 1 POU-domain transcription factor (SPRM-1)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1305526  similar to Sperm 1 POU-domain transcription factor (SPRM-1)   RGD1305526_predicted  similar to Sperm 1 POU-domain transcription factor (SPRM-1) (predicted)  'predicted' is removed 2292626 APPROVED
2008-01-09 RGD1305526_predicted  similar to Sperm 1 POU-domain transcription factor (SPRM-1) (predicted)  LOC682045  similar to CG10038-PB, isoform B  Data Merged 1643240 APPROVED
2006-11-19 LOC682045  similar to CG10038-PB, isoform B      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1305526_predicted  similar to Sperm 1 POU-domain transcription factor (SPRM-1) (predicted)  LOC294606_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC294606_predicted  similar to Sperm 1 POU-domain transcription factor (SPRM-1) (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL