Ttc8 (tetratricopeptide repeat domain 8) - Rat Genome Database

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Gene: Ttc8 (tetratricopeptide repeat domain 8) Rattus norvegicus
Analyze
Symbol: Ttc8
Name: tetratricopeptide repeat domain 8
RGD ID: 1307769
Description: Predicted to enable RNA polymerase II-specific DNA-binding transcription factor binding activity. Predicted to be involved in establishment of anatomical structure orientation and non-motile cilium assembly. Predicted to act upstream of or within several processes, including morphogenesis of a polarized epithelium; negative regulation of GTPase activity; and nervous system development. Predicted to be located in centrosome; membrane; and photoreceptor connecting cilium. Predicted to be part of BBSome. Predicted to be active in ciliary basal body and non-motile cilium. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome; Bardet-Biedl syndrome 8; and retinitis pigmentosa 51. Orthologous to human TTC8 (tetratricopeptide repeat domain 8); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cobalt dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC299246; tetratricopeptide repeat protein 8
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
mRatBN7.26118,198,186 - 118,252,422 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6118,198,201 - 118,252,418 (+)Ensembl
Rnor_6.06122,920,308 - 122,974,525 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6122,920,317 - 122,974,522 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06132,140,808 - 132,207,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46123,117,534 - 123,171,840 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16123,121,373 - 123,174,881 (+)NCBI
Celera6115,755,975 - 115,810,232 (+)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:12477932   PMID:17379567   PMID:17574030   PMID:20080638   PMID:21646512   PMID:22072986   PMID:22139371   PMID:22302990   PMID:22479622   PMID:22500027   PMID:23716571   PMID:24550735  
PMID:25243405   PMID:25605782   PMID:27684375  


Genomics

Comparative Map Data
Ttc8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26118,198,186 - 118,252,422 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6118,198,201 - 118,252,418 (+)Ensembl
Rnor_6.06122,920,308 - 122,974,525 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6122,920,317 - 122,974,522 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06132,140,808 - 132,207,306 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46123,117,534 - 123,171,840 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16123,121,373 - 123,174,881 (+)NCBI
Celera6115,755,975 - 115,810,232 (+)NCBICelera
Cytogenetic Map6q32NCBI
TTC8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1488,824,153 - 88,881,078 (+)EnsemblGRCh38hg38GRCh38
GRCh381488,824,153 - 88,881,079 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371489,290,497 - 89,347,423 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361488,360,731 - 88,414,088 (+)NCBINCBI36hg18NCBI36
Build 341488,360,730 - 88,414,087NCBI
Celera1469,339,325 - 69,392,681 (+)NCBI
Cytogenetic Map14q31.3NCBI
HuRef1469,465,840 - 69,519,171 (+)NCBIHuRef
CHM1_11489,228,786 - 89,282,145 (+)NCBICHM1_1
Ttc8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391298,886,796 - 98,949,509 (+)NCBIGRCm39mm39
GRCm39 Ensembl1298,886,833 - 98,949,497 (+)Ensembl
GRCm381298,920,537 - 98,983,250 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1298,920,574 - 98,983,238 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712100,158,784 - 100,221,448 (+)NCBIGRCm37mm9NCBIm37
MGSCv361299,321,639 - 99,384,288 (+)NCBImm8
Celera12100,146,253 - 100,210,179 (+)NCBICelera
Cytogenetic Map12ENCBI
Ttc8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543811,409,982 - 11,466,523 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543811,410,196 - 11,466,044 (+)NCBIChiLan1.0ChiLan1.0
TTC8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11488,802,812 - 88,857,055 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1488,802,812 - 88,857,055 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01469,446,355 - 69,502,351 (+)NCBIMhudiblu_PPA_v0panPan3
TTC8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1860,061,670 - 60,115,464 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl860,061,732 - 60,115,075 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha859,641,066 - 59,693,906 (+)NCBI
ROS_Cfam_1.0860,332,658 - 60,386,187 (+)NCBI
UMICH_Zoey_3.1860,013,742 - 60,066,541 (+)NCBI
UNSW_CanFamBas_1.0860,063,485 - 60,116,262 (+)NCBI
UU_Cfam_GSD_1.0860,391,356 - 60,444,177 (+)NCBI
Ttc8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864015,762,381 - 15,810,727 (-)NCBI
SpeTri2.0NW_00493648816,258,247 - 16,306,077 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TTC8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7110,731,668 - 110,784,855 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17110,731,729 - 110,783,999 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27117,222,186 - 117,274,088 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TTC8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12466,483,808 - 66,539,717 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2466,483,864 - 66,539,142 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605353,829,890 - 53,884,739 (+)NCBIVero_WHO_p1.0
Ttc8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473413,437,234 - 13,497,269 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6116506292130245370Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:11
Count of miRNA genes:11
Interacting mature miRNAs:11
Transcripts:ENSRNOT00000068595
Prediction methods:Miranda, Rnahybrid
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 4 11 4 4 67 23 37
Low 3 39 46 37 19 37 8 10 7 12 4 11 8
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC117104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC161880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218326 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218342 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218344 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218345 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX218361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000068595   ⟹   ENSRNOP00000060304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,198,201 - 118,252,415 (+)Ensembl
Rnor_6.0 Ensembl6122,920,317 - 122,974,522 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082856   ⟹   ENSRNOP00000068618
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,198,211 - 118,252,418 (+)Ensembl
Rnor_6.0 Ensembl6122,920,339 - 122,974,519 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094428   ⟹   ENSRNOP00000085100
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,198,255 - 118,252,270 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094918   ⟹   ENSRNOP00000096518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,198,201 - 118,217,368 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097062   ⟹   ENSRNOP00000093561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,214,467 - 118,252,270 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102593   ⟹   ENSRNOP00000083411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,199,380 - 118,252,270 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107635   ⟹   ENSRNOP00000085312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,198,201 - 118,232,325 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114010   ⟹   ENSRNOP00000097577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,212,002 - 118,252,418 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114433   ⟹   ENSRNOP00000088851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,198,255 - 118,252,270 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118948   ⟹   ENSRNOP00000077009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6118,198,211 - 118,252,418 (+)Ensembl
RefSeq Acc Id: NM_001106752   ⟹   NP_001100222
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,198,201 - 118,252,415 (+)NCBI
Rnor_6.06122,920,317 - 122,974,522 (+)NCBI
Rnor_5.06132,140,808 - 132,207,306 (+)NCBI
RGSC_v3.46123,117,534 - 123,171,840 (+)RGD
Celera6115,755,975 - 115,810,232 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240422   ⟹   XP_006240484
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,198,195 - 118,252,422 (+)NCBI
Rnor_6.06122,920,308 - 122,974,525 (+)NCBI
Rnor_5.06132,140,808 - 132,207,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006240423   ⟹   XP_006240485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,198,197 - 118,252,419 (+)NCBI
Rnor_6.06122,920,308 - 122,974,525 (+)NCBI
Rnor_5.06132,140,808 - 132,207,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008764762   ⟹   XP_008762984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,214,468 - 118,252,422 (+)NCBI
Rnor_6.06122,936,495 - 122,974,525 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039112065   ⟹   XP_038967993
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,198,186 - 118,232,479 (+)NCBI
RefSeq Acc Id: XM_039112066   ⟹   XP_038967994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,198,191 - 118,232,479 (+)NCBI
RefSeq Acc Id: XM_039112067   ⟹   XP_038967995
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,214,472 - 118,252,422 (+)NCBI
RefSeq Acc Id: XM_039112068   ⟹   XP_038967996
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,198,190 - 118,232,479 (+)NCBI
RefSeq Acc Id: XM_039112069   ⟹   XP_038967997
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26118,198,194 - 118,232,478 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100222 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240484 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240485 (Get FASTA)   NCBI Sequence Viewer  
  XP_008762984 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967993 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967994 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967995 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967996 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967997 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61880 (Get FASTA)   NCBI Sequence Viewer  
  AQA28051 (Get FASTA)   NCBI Sequence Viewer  
  AQA28052 (Get FASTA)   NCBI Sequence Viewer  
  AQA28053 (Get FASTA)   NCBI Sequence Viewer  
  AQA28054 (Get FASTA)   NCBI Sequence Viewer  
  AQA28055 (Get FASTA)   NCBI Sequence Viewer  
  AQA28056 (Get FASTA)   NCBI Sequence Viewer  
  AQA28057 (Get FASTA)   NCBI Sequence Viewer  
  AQA28058 (Get FASTA)   NCBI Sequence Viewer  
  AQA28059 (Get FASTA)   NCBI Sequence Viewer  
  AQA28060 (Get FASTA)   NCBI Sequence Viewer  
  AQA28061 (Get FASTA)   NCBI Sequence Viewer  
  AQA28062 (Get FASTA)   NCBI Sequence Viewer  
  AQA28063 (Get FASTA)   NCBI Sequence Viewer  
  AQA28064 (Get FASTA)   NCBI Sequence Viewer  
  AQA28065 (Get FASTA)   NCBI Sequence Viewer  
  AQA28066 (Get FASTA)   NCBI Sequence Viewer  
  AQA28067 (Get FASTA)   NCBI Sequence Viewer  
  AQA28068 (Get FASTA)   NCBI Sequence Viewer  
  AQA28069 (Get FASTA)   NCBI Sequence Viewer  
  AQA28070 (Get FASTA)   NCBI Sequence Viewer  
  AQA28071 (Get FASTA)   NCBI Sequence Viewer  
  AQA28072 (Get FASTA)   NCBI Sequence Viewer  
  AQA28073 (Get FASTA)   NCBI Sequence Viewer  
  AQA28074 (Get FASTA)   NCBI Sequence Viewer  
  AQA28075 (Get FASTA)   NCBI Sequence Viewer  
  AQA28076 (Get FASTA)   NCBI Sequence Viewer  
  AQA28077 (Get FASTA)   NCBI Sequence Viewer  
  AQA28078 (Get FASTA)   NCBI Sequence Viewer  
  AQA28079 (Get FASTA)   NCBI Sequence Viewer  
  AQA28080 (Get FASTA)   NCBI Sequence Viewer  
  AQA28081 (Get FASTA)   NCBI Sequence Viewer  
  AQA28082 (Get FASTA)   NCBI Sequence Viewer  
  AQA28083 (Get FASTA)   NCBI Sequence Viewer  
  AQA28084 (Get FASTA)   NCBI Sequence Viewer  
  AQA28085 (Get FASTA)   NCBI Sequence Viewer  
  AQA28086 (Get FASTA)   NCBI Sequence Viewer  
  AQA28087 (Get FASTA)   NCBI Sequence Viewer  
  AQA28088 (Get FASTA)   NCBI Sequence Viewer  
  AQA28089 (Get FASTA)   NCBI Sequence Viewer  
  AQA28090 (Get FASTA)   NCBI Sequence Viewer  
  AQA28091 (Get FASTA)   NCBI Sequence Viewer  
  AQA28092 (Get FASTA)   NCBI Sequence Viewer  
  EDL81698 (Get FASTA)   NCBI Sequence Viewer  
  EDL81699 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100222   ⟸   NM_001106752
- UniProtKB: D3ZND5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240484   ⟸   XM_006240422
- Peptide Label: isoform X1
- UniProtKB: A0A1P8YVD0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240485   ⟸   XM_006240423
- Peptide Label: isoform X2
- UniProtKB: B1WBT5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008762984   ⟸   XM_008764762
- Peptide Label: isoform X3
- UniProtKB: A0A1P8YVH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068618   ⟸   ENSRNOT00000082856
RefSeq Acc Id: ENSRNOP00000060304   ⟸   ENSRNOT00000068595
RefSeq Acc Id: XP_038967993   ⟸   XM_039112065
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038967996   ⟸   XM_039112068
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038967994   ⟸   XM_039112066
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038967997   ⟸   XM_039112069
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038967995   ⟸   XM_039112067
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000093561   ⟸   ENSRNOT00000097062
RefSeq Acc Id: ENSRNOP00000083411   ⟸   ENSRNOT00000102593
RefSeq Acc Id: ENSRNOP00000077009   ⟸   ENSRNOT00000118948
RefSeq Acc Id: ENSRNOP00000096518   ⟸   ENSRNOT00000094918
RefSeq Acc Id: ENSRNOP00000088851   ⟸   ENSRNOT00000114433
RefSeq Acc Id: ENSRNOP00000085100   ⟸   ENSRNOT00000094428
RefSeq Acc Id: ENSRNOP00000097577   ⟸   ENSRNOT00000114010
RefSeq Acc Id: ENSRNOP00000085312   ⟸   ENSRNOT00000107635
Protein Domains
TPR_REGION

Transcriptome

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

Promoters
RGD ID:13694773
Promoter ID:EPDNEW_R5296
Type:initiation region
Name:Ttc8_1
Description:tetratricopeptide repeat domain 8
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06122,920,327 - 122,920,387EPDNEW

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)
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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
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)
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
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)
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
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)
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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
MNS/Gib (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
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)
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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
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)
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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
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 (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)
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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 (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
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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307769 AgrOrtholog
Ensembl Genes ENSRNOG00000004542 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060304 UniProtKB/TrEMBL
  ENSRNOP00000068618 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068595 UniProtKB/TrEMBL
  ENSRNOT00000082856 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7126409 IMAGE-MGC_LOAD
InterPro BBS8 UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
KEGG Report rno:299246 UniProtKB/TrEMBL
MGC_CLONE MGC:187444 IMAGE-MGC_LOAD
NCBI Gene 299246 ENTREZGENE
PANTHER PTHR44177 UniProtKB/TrEMBL
Pfam TPR_7 UniProtKB/TrEMBL
  TPR_8 UniProtKB/TrEMBL
PhenoGen Ttc8 PhenoGen
PROSITE TPR UniProtKB/TrEMBL
SMART TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A1P8YVD0 ENTREZGENE, UniProtKB/TrEMBL
  A0A1P8YVD2_RAT UniProtKB/TrEMBL
  A0A1P8YVD4_RAT UniProtKB/TrEMBL
  A0A1P8YVD6_RAT UniProtKB/TrEMBL
  A0A1P8YVD7_RAT UniProtKB/TrEMBL
  A0A1P8YVD8_RAT UniProtKB/TrEMBL
  A0A1P8YVE2_RAT UniProtKB/TrEMBL
  A0A1P8YVE4_RAT UniProtKB/TrEMBL
  A0A1P8YVE5_RAT UniProtKB/TrEMBL
  A0A1P8YVF2_RAT UniProtKB/TrEMBL
  A0A1P8YVF5_RAT UniProtKB/TrEMBL
  A0A1P8YVF7_RAT UniProtKB/TrEMBL
  A0A1P8YVF8_RAT UniProtKB/TrEMBL
  A0A1P8YVF9_RAT UniProtKB/TrEMBL
  A0A1P8YVG2_RAT UniProtKB/TrEMBL
  A0A1P8YVG3_RAT UniProtKB/TrEMBL
  A0A1P8YVG4_RAT UniProtKB/TrEMBL
  A0A1P8YVG5_RAT UniProtKB/TrEMBL
  A0A1P8YVG6_RAT UniProtKB/TrEMBL
  A0A1P8YVG7_RAT UniProtKB/TrEMBL
  A0A1P8YVG8_RAT UniProtKB/TrEMBL
  A0A1P8YVG9_RAT UniProtKB/TrEMBL
  A0A1P8YVH6 ENTREZGENE, UniProtKB/TrEMBL
  A0A1P8YVH7_RAT UniProtKB/TrEMBL
  B1WBT5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZND5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ttc8  tetratricopeptide repeat domain 8   Ttc8_predicted  tetratricopeptide repeat domain 8 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ttc8_predicted  tetratricopeptide repeat domain 8 (predicted)      Symbol and Name status set to approved 70820 APPROVED