Fhl1 (four and a half LIM domains 1) - Rat Genome Database

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Gene: Fhl1 (four and a half LIM domains 1) Rattus norvegicus
Analyze
Symbol: Fhl1
Name: four and a half LIM domains 1
RGD ID: 2615
Description: Predicted to enable transmembrane transporter binding activity. Predicted to be involved in several processes, including negative regulation of mitotic cell cycle phase transition; regulation of membrane depolarization; and regulation of potassium ion transport. Predicted to be located in cytosol; nucleus; and plasma membrane. Human ortholog(s) of this gene implicated in Uruguay faciocardiomusculoskeletal syndrome; X-linked Emery-Dreifuss muscular dystrophy 6; reducing body myopathy 1A; and reducing body myopathy 1B. Orthologous to human FHL1 (four and a half LIM domains 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: FHL-1; four and a half LIM domains 1 (skeletal muscle LIM-protein 1); four and a half LIM domains protein 1; skeletal muscle LIM-protein 1; SLIM1
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
mRatBN7.2X134,555,399 - 134,614,930 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX134,555,479 - 134,614,928 (+)Ensembl
Rnor_6.0X159,112,516 - 159,172,528 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX159,112,880 - 159,172,524 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X141,315,765 - 141,329,278 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X141,389,200 - 141,401,948 (+)NCBI
CeleraX142,605,050 - 142,663,917 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
25-hydroxycholesterol  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (EXP)
acrylamide  (EXP)
actinomycin D  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP,ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
brefeldin A  (EXP)
caffeine  (EXP)
cannabidiol  (ISO)
capecitabine  (ISO)
carbofuran  (EXP)
carbon nanotube  (ISO)
chloroform  (EXP)
chloropicrin  (ISO)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cumene  (ISO)
Cuprizon  (EXP)
cycloheximide  (EXP)
cyclophosphamide  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibenzo[a,l]pyrene  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxifluridine  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
etoposide  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP)
isoprenaline  (EXP,ISO)
ivermectin  (ISO)
lead nitrate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
metaproterenol  (EXP)
methapyrilene  (EXP)
methoxyacetic acid  (EXP)
methylmercury chloride  (EXP)
milrinone  (EXP)
mitomycin C  (ISO)
mitoxantrone  (EXP)
Monobutylphthalate  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
orciprenaline  (EXP)
oxaliplatin  (EXP,ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
quercetin  (EXP)
raloxifene  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP)
sodium fluoride  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (EXP,ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
trichloroethene  (EXP)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO)
cytosol  (ISO)
nucleus  (ISO)
plasma membrane  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:17161435   PMID:18281375   PMID:18756007   PMID:20149813   PMID:21126853   PMID:21423176   PMID:21702045   PMID:23628900   PMID:24265776   PMID:25931508   PMID:25975448  
PMID:26316108  


Genomics

Comparative Map Data
Fhl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X134,555,399 - 134,614,930 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX134,555,479 - 134,614,928 (+)Ensembl
Rnor_6.0X159,112,516 - 159,172,528 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX159,112,880 - 159,172,524 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X141,315,765 - 141,329,278 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X141,389,200 - 141,401,948 (+)NCBI
CeleraX142,605,050 - 142,663,917 (+)NCBICelera
Cytogenetic MapXq37NCBI
FHL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX136,146,702 - 136,211,359 (+)EnsemblGRCh38hg38GRCh38
GRCh38X136,146,702 - 136,211,359 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X135,228,861 - 135,293,518 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X135,057,346 - 135,121,176 (+)NCBINCBI36hg18NCBI36
Build 34X134,955,199 - 135,019,028NCBI
CeleraX135,591,521 - 135,656,168 (+)NCBI
Cytogenetic MapXq26.3NCBI
HuRefX124,502,588 - 124,565,831 (+)NCBIHuRef
CHM1_1X135,139,444 - 135,204,087 (+)NCBICHM1_1
Fhl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X55,776,569 - 55,838,706 (+)NCBIGRCm39mm39
GRCm39 EnsemblX55,777,147 - 55,838,706 (+)Ensembl
GRCm38X56,731,209 - 56,793,346 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX56,731,787 - 56,793,346 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X53,984,964 - 54,046,523 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X53,078,598 - 53,140,127 (+)NCBImm8
CeleraX43,224,152 - 43,274,965 (+)NCBICelera
Cytogenetic MapXA6NCBI
Fhl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554898,888,779 - 8,901,970 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554898,888,845 - 8,944,778 (-)NCBIChiLan1.0ChiLan1.0
FHL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X135,538,152 - 135,602,375 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX135,559,321 - 135,602,375 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X125,270,340 - 125,334,961 (+)NCBIMhudiblu_PPA_v0panPan3
FHL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X106,542,450 - 106,604,494 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX106,590,988 - 106,604,029 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX92,361,797 - 92,424,954 (+)NCBI
ROS_Cfam_1.0X108,518,918 - 108,582,088 (+)NCBI
ROS_Cfam_1.0 EnsemblX108,518,948 - 108,582,088 (+)Ensembl
UMICH_Zoey_3.1X105,662,634 - 105,725,800 (+)NCBI
UNSW_CanFamBas_1.0X107,839,961 - 107,904,929 (+)NCBI
UU_Cfam_GSD_1.0X107,494,648 - 107,557,811 (+)NCBI
Fhl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X104,530,356 - 104,588,870 (+)NCBI
SpeTri2.0NW_00493651311,025,753 - 11,064,312 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FHL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX111,310,684 - 111,367,904 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X111,309,989 - 111,367,900 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X127,231,947 - 127,289,864 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig CytomapXq23-q24NCBI
FHL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X111,160,389 - 111,226,713 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX111,211,911 - 111,226,841 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606548,829,354 - 48,897,371 (+)NCBIVero_WHO_p1.0
Fhl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480810,924,606 - 10,984,422 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
AI556806  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X134,614,703 - 134,614,892 (+)MAPPERmRatBN7.2
Rnor_6.0X159,172,302 - 159,172,490NCBIRnor6.0
Rnor_5.0X153,802,934 - 153,803,122UniSTSRnor5.0
RGSC_v3.4X141,329,057 - 141,329,245UniSTSRGSC3.4
CeleraX142,663,691 - 142,663,879UniSTS
RH 3.4 MapX952.91UniSTS
Cytogenetic MapXq36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:946
Count of miRNA genes:295
Interacting mature miRNAs:391
Transcripts:ENSRNOT00000001169, ENSRNOT00000043820
Prediction methods:Microtar, Miranda, Pita, Pita,Targetscan, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 3 3 1 3
Medium 3 43 29 18 14 18 5 8 74 35 38 10 5
Low 28 23 5 23 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001033926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_145669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF134773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY115564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC061782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB702630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK477468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK840296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM042472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ119120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217594 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001169   ⟹   ENSRNOP00000001169
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX134,601,136 - 134,614,920 (+)Ensembl
Rnor_6.0 EnsemblX159,158,194 - 159,172,518 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000043820   ⟹   ENSRNOP00000049677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX134,555,479 - 134,614,755 (+)Ensembl
Rnor_6.0 EnsemblX159,158,194 - 159,172,518 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083502   ⟹   ENSRNOP00000072490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX134,601,137 - 134,614,924 (+)Ensembl
Rnor_6.0 EnsemblX159,158,195 - 159,172,524 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084594   ⟹   ENSRNOP00000074052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX134,555,694 - 134,614,926 (+)Ensembl
Rnor_6.0 EnsemblX159,112,880 - 159,172,518 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087274   ⟹   ENSRNOP00000074817
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX134,608,976 - 134,614,924 (+)Ensembl
Rnor_6.0 EnsemblX159,165,169 - 159,172,518 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110431   ⟹   ENSRNOP00000088085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX134,601,030 - 134,614,928 (+)Ensembl
RefSeq Acc Id: NM_001033926   ⟹   NP_001029098
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,601,136 - 134,614,930 (+)NCBI
Rnor_6.0X159,158,194 - 159,172,528 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
RGSC_v3.4X141,315,765 - 141,329,278 (+)RGD
CeleraX142,650,349 - 142,663,917 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271199   ⟹   NP_001258128
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,816 - 134,614,930 (+)NCBI
Rnor_6.0X159,112,880 - 159,172,528 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
CeleraX142,605,050 - 142,663,917 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271200   ⟹   NP_001258129
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,608,112 - 134,614,930 (+)NCBI
Rnor_6.0X159,165,169 - 159,172,528 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
CeleraX142,657,325 - 142,663,917 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271201   ⟹   NP_001258130
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,608,112 - 134,614,930 (+)NCBI
Rnor_6.0X159,165,169 - 159,172,528 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
CeleraX142,657,325 - 142,663,917 (+)NCBI
Sequence:
RefSeq Acc Id: NM_145669   ⟹   NP_663702
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,601,136 - 134,614,930 (+)NCBI
Rnor_6.0X159,158,194 - 159,172,528 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
RGSC_v3.4X141,315,765 - 141,329,278 (+)RGD
CeleraX142,650,349 - 142,663,917 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257671   ⟹   XP_006257733
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,601,085 - 134,614,928 (+)NCBI
Rnor_6.0X159,157,945 - 159,172,526 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257672   ⟹   XP_006257734
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,399 - 134,614,928 (+)NCBI
Rnor_6.0X159,112,516 - 159,172,526 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257673   ⟹   XP_006257735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,705 - 134,614,928 (+)NCBI
Rnor_6.0X159,112,792 - 159,172,526 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257674   ⟹   XP_006257736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,500 - 134,614,928 (+)NCBI
Rnor_6.0X159,112,516 - 159,172,526 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257675   ⟹   XP_006257737
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,608,022 - 134,614,928 (+)NCBI
Rnor_6.0X159,165,080 - 159,172,526 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257676   ⟹   XP_006257738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,436 - 134,614,928 (+)NCBI
Rnor_6.0X159,112,516 - 159,172,526 (+)NCBI
Rnor_5.0X153,743,208 - 153,803,160 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099493   ⟹   XP_038955421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,399 - 134,614,928 (+)NCBI
RefSeq Acc Id: XM_039099494   ⟹   XP_038955422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,483 - 134,614,928 (+)NCBI
RefSeq Acc Id: XM_039099495   ⟹   XP_038955423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,399 - 134,614,928 (+)NCBI
RefSeq Acc Id: XM_039099496   ⟹   XP_038955424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,555,420 - 134,614,928 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_663702   ⟸   NM_145669
- Peptide Label: isoform 2
- UniProtKB: Q6P792 (UniProtKB/TrEMBL),   Q8K3G3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001029098   ⟸   NM_001033926
- Peptide Label: isoform 1
- UniProtKB: Q6P792 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258128   ⟸   NM_001271199
- Peptide Label: isoform 3
- UniProtKB: Q9WUH4 (UniProtKB/Swiss-Prot),   Q6P792 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258129   ⟸   NM_001271200
- Peptide Label: isoform 3
- UniProtKB: Q9WUH4 (UniProtKB/Swiss-Prot),   Q6P792 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258130   ⟸   NM_001271201
- Peptide Label: isoform 4
- UniProtKB: Q6P792 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257738   ⟸   XM_006257676
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006257736   ⟸   XM_006257674
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006257734   ⟸   XM_006257672
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006257735   ⟸   XM_006257673
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006257733   ⟸   XM_006257671
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K338 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257737   ⟸   XM_006257675
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000049677   ⟸   ENSRNOT00000043820
RefSeq Acc Id: ENSRNOP00000074052   ⟸   ENSRNOT00000084594
RefSeq Acc Id: ENSRNOP00000074817   ⟸   ENSRNOT00000087274
RefSeq Acc Id: ENSRNOP00000072490   ⟸   ENSRNOT00000083502
RefSeq Acc Id: ENSRNOP00000001169   ⟸   ENSRNOT00000001169
RefSeq Acc Id: XP_038955421   ⟸   XM_039099493
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955423   ⟸   XM_039099495
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955424   ⟸   XM_039099496
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955422   ⟸   XM_039099494
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000088085   ⟸   ENSRNOT00000110431
Protein Domains
LIM zinc-binding

Transcriptome

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

Promoters
RGD ID:13702068
Promoter ID:EPDNEW_R12592
Type:initiation region
Name:Fhl1_2
Description:four and a half LIM domains 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12594  EPDNEW_R12593  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X159,112,812 - 159,112,872EPDNEW
RGD ID:13702076
Promoter ID:EPDNEW_R12593
Type:multiple initiation site
Name:Fhl1_1
Description:four and a half LIM domains 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12592  EPDNEW_R12594  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X159,158,220 - 159,158,280EPDNEW
RGD ID:13702070
Promoter ID:EPDNEW_R12594
Type:multiple initiation site
Name:Fhl1_3
Description:four and a half LIM domains 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12592  EPDNEW_R12593  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X159,165,184 - 159,165,244EPDNEW

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)
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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)
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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
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)
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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
LN/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
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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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:2615 AgrOrtholog
Ensembl Genes ENSRNOG00000000875 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001169 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000049677 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072490 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074052 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000074817 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000088085 ENTREZGENE
Ensembl Transcript ENSRNOT00000001169 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000043820 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000083502 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084594 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000087274 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000110431 ENTREZGENE
IMAGE_CLONE IMAGE:5623247 IMAGE-MGC_LOAD
InterPro Fhl1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25177 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:72291 IMAGE-MGC_LOAD
NCBI Gene 25177 ENTREZGENE
PANTHER PTHR47029 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Fhl1 PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K338 ENTREZGENE, UniProtKB/TrEMBL
  FHL1_RAT UniProtKB/Swiss-Prot
  Q6P792 ENTREZGENE, UniProtKB/TrEMBL
  Q8K3G3 ENTREZGENE, UniProtKB/TrEMBL
  Q9WUH4 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-11-06 Fhl1  four and a half LIM domains 1    Four and a half LIM domains 1 (skeletal muscle LIM-protein 1)  Name updated 625702 APPROVED
2002-06-10 Fhl1  Four and a half LIM domains 1 (skeletal muscle LIM-protein 1)      Symbol and Name status set to approved 70586 APPROVED