Fermt2 (FERM domain containing kindlin 2) - Rat Genome Database
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Gene: Fermt2 (FERM domain containing kindlin 2) Rattus norvegicus
Analyze
Symbol: Fermt2
Name: FERM domain containing kindlin 2
RGD ID: 1311799
Description: Predicted to have actin filament binding activity; integrin binding activity; and phosphatidylinositol-3,4,5-trisphosphate binding activity. Predicted to be involved in several processes, including cell surface receptor signaling pathway; focal adhesion assembly; and integrin activation. Predicted to colocalize with stress fiber. Orthologous to human FERMT2 (fermitin family member 2); PARTICIPATES IN integrin mediated signaling pathway; INTERACTS WITH 1,3-dinitrobenzene; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: fermitin family homolog 2; fermitin family homolog 2 (Drosophila); fermitin family member 2; LOC289992; pleckstrin homology domain containing, family C (with FERM domain) member 1; Plekhc1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21518,682,927 - 18,751,959 (-)NCBI
Rnor_6.0 Ensembl1519,807,808 - 19,876,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01519,807,806 - 19,876,557 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01523,771,816 - 23,840,554 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41521,358,411 - 21,427,264 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11521,358,412 - 21,427,264 (-)NCBI
Celera1519,110,289 - 19,178,605 (-)NCBICelera
Cytogenetic Map15p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17beta-estradiol  (ISO)
2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
acrolein  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
daidzein  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fipronil  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
glafenine  (EXP)
leflunomide  (ISO)
levonorgestrel  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
phytoestrogen  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
rimonabant  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP)
sodium fluoride  (ISO)
staurosporine  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
testosterone undecanoate  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adherens junction maintenance  (IEA,ISO)
cell adhesion  (ISO)
cell-matrix adhesion  (IBA,ISO)
focal adhesion assembly  (ISO)
integrin activation  (ISO)
integrin-mediated signaling pathway  (ISO)
limb development  (IEA,ISO)
negative regulation of cell death  (IEA,ISO)
negative regulation of fat cell differentiation  (IEA,ISO)
negative regulation of vascular permeability  (IEA,ISO)
positive regulation of cell migration  (ISO)
positive regulation of epithelial to mesenchymal transition  (IEA,ISO)
positive regulation of ERK1 and ERK2 cascade  (IEA,ISO)
positive regulation of focal adhesion assembly  (IEA,ISO)
positive regulation of GTPase activity  (IEA,ISO)
positive regulation of integrin activation  (IEA,ISO)
positive regulation of mesenchymal stem cell proliferation  (IEA,ISO)
positive regulation of myosin light chain kinase activity  (IEA,ISO)
positive regulation of osteoblast differentiation  (IEA,ISO)
positive regulation of protein kinase B signaling  (IEA,ISO)
positive regulation of protein localization to nucleus  (IEA,ISO)
positive regulation of stress fiber assembly  (IEA,ISO)
positive regulation of substrate adhesion-dependent cell spreading  (IEA,ISO)
positive regulation of wound healing, spreading of epidermal cells  (IEA,ISO)
protein localization to cell junction  (IEA,ISO)
protein localization to membrane  (ISO)
regulation of cell morphogenesis  (ISO)
substrate adhesion-dependent cell spreading  (ISO)
transforming growth factor beta receptor signaling pathway  (ISO)
Wnt signaling pathway  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:16876785   PMID:18483218   PMID:21325030   PMID:21423176   PMID:22030399   PMID:22699938   PMID:26143257   PMID:26676966   PMID:29162887  


Genomics

Comparative Map Data
Fermt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21518,682,927 - 18,751,959 (-)NCBI
Rnor_6.0 Ensembl1519,807,808 - 19,876,408 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01519,807,806 - 19,876,557 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01523,771,816 - 23,840,554 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41521,358,411 - 21,427,264 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11521,358,412 - 21,427,264 (-)NCBI
Celera1519,110,289 - 19,178,605 (-)NCBICelera
Cytogenetic Map15p14NCBI
FERMT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1452,857,268 - 52,952,435 (-)EnsemblGRCh38hg38GRCh38
GRCh381452,857,271 - 52,951,050 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371453,323,991 - 53,417,768 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh371453,323,989 - 53,417,856 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361452,393,743 - 52,487,460 (-)NCBINCBI36hg18NCBI36
Build 341452,393,742 - 52,487,460NCBI
Celera1433,373,704 - 33,467,553 (-)NCBI
Cytogenetic Map14q22.1NCBI
HuRef1433,486,674 - 33,581,054 (-)NCBIHuRef
CHM1_11453,262,863 - 53,356,715 (-)NCBICHM1_1
Fermt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391445,696,249 - 45,767,767 (-)NCBIGRCm39mm39
GRCm381445,458,792 - 45,530,310 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1445,458,795 - 45,530,118 (-)EnsemblGRCm38mm10GRCm38
MGSCv371446,078,467 - 46,149,740 (-)NCBIGRCm37mm9NCBIm37
MGSCv361444,380,669 - 44,451,942 (-)NCBImm8
Celera1441,642,480 - 41,713,283 (-)NCBICelera
Cytogenetic Map14C1NCBI
Fermt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540910,285,793 - 10,327,468 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540910,285,780 - 10,327,286 (+)NCBIChiLan1.0ChiLan1.0
FERMT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11451,737,188 - 51,830,109 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1451,737,188 - 51,829,766 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01433,453,983 - 33,547,721 (-)NCBIMhudiblu_PPA_v0panPan3
FERMT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl829,084,531 - 29,133,391 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1829,083,538 - 29,135,915 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Fermt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366971,927,817 - 2,008,268 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FERMT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1182,519,681 - 182,606,869 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11182,519,681 - 182,606,890 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21202,790,224 - 202,816,460 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FERMT2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12429,954,706 - 30,053,012 (-)NCBI
Fermt2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473116,168,179 - 16,247,747 (+)NCBI

Position Markers
AA960555  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01519,807,938 - 19,808,034NCBIRnor6.0
Rnor_5.01523,771,948 - 23,772,044UniSTSRnor5.0
RGSC_v3.41521,358,543 - 21,358,639UniSTSRGSC3.4
Celera1519,110,421 - 19,110,517UniSTS
Cytogenetic Map15p14UniSTS
RH134534  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01519,807,915 - 19,808,125NCBIRnor6.0
Rnor_5.01523,771,925 - 23,772,135UniSTSRnor5.0
RGSC_v3.41521,358,520 - 21,358,730UniSTSRGSC3.4
Celera1519,110,398 - 19,110,608UniSTS
RH 3.4 Map15149.4UniSTS
Cytogenetic Map15p14UniSTS
AI179101  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01519,808,872 - 19,808,966NCBIRnor6.0
Rnor_5.01523,772,882 - 23,772,976UniSTSRnor5.0
RGSC_v3.41521,359,477 - 21,359,571UniSTSRGSC3.4
Celera1519,111,355 - 19,111,449UniSTS
RH 3.4 Map15156.3UniSTS
Cytogenetic Map15p14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15130597196Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15232787726288802Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15232787726288802Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151582824233657761Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:659
Count of miRNA genes:280
Interacting mature miRNAs:351
Transcripts:ENSRNOT00000012400
Prediction methods:Microtar, Miranda, 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
Medium 3 43 57 41 19 41 8 11 74 35 38 11 8
Low 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012400   ⟹   ENSRNOP00000012400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1519,807,808 - 19,876,389 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086368   ⟹   ENSRNOP00000069828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1519,807,815 - 19,876,408 (-)Ensembl
RefSeq Acc Id: NM_001011915   ⟹   NP_001011915
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,778 (-)NCBI
Rnor_6.01519,807,806 - 19,876,389 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
RGSC_v3.41521,358,411 - 21,427,264 (-)RGD
Celera1519,110,289 - 19,178,605 (-)RGD
Sequence:
RefSeq Acc Id: XM_006251755   ⟹   XP_006251817
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,838 (-)NCBI
Rnor_6.01519,807,806 - 19,876,414 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251756   ⟹   XP_006251818
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,959 (-)NCBI
Rnor_6.01519,807,806 - 19,876,557 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251757   ⟹   XP_006251819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,838 (-)NCBI
Rnor_6.01519,807,806 - 19,876,414 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251758   ⟹   XP_006251820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,837 (-)NCBI
Rnor_6.01519,807,806 - 19,876,414 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251759   ⟹   XP_006251821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,837 (-)NCBI
Rnor_6.01519,807,806 - 19,876,414 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251760   ⟹   XP_006251822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,837 (-)NCBI
Rnor_6.01519,807,806 - 19,876,414 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251761   ⟹   XP_006251823
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01519,807,806 - 19,853,245 (-)NCBI
Rnor_5.01523,771,816 - 23,840,554 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093097   ⟹   XP_038949025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21518,682,927 - 18,751,956 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001011915   ⟸   NM_001011915
- UniProtKB: Q5XI19 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251818   ⟸   XM_006251756
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006251822   ⟸   XM_006251760
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006251820   ⟸   XM_006251758
- Peptide Label: isoform X3
- UniProtKB: A0A0G2JWC7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251821   ⟸   XM_006251759
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006251819   ⟸   XM_006251757
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006251817   ⟸   XM_006251755
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006251823   ⟸   XM_006251761
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000012400   ⟸   ENSRNOT00000012400
RefSeq Acc Id: ENSRNOP00000069828   ⟸   ENSRNOT00000086368
RefSeq Acc Id: XP_038949025   ⟸   XM_039093097
- Peptide Label: isoform X6
Protein Domains
PH

Transcriptome

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

Promoters
RGD ID:13699598
Promoter ID:EPDNEW_R10122
Type:initiation region
Name:Fermt2_1
Description:fermitin family member 2
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_6.01519,876,369 - 19,876,429EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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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 (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)
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
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
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/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
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 (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
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
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
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
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
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 (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
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
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311799 AgrOrtholog
Ensembl Genes ENSRNOG00000009102 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012400 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069828 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012400 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000086368 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7129898 IMAGE-MGC_LOAD
InterPro Band_41_domain UniProtKB/TrEMBL
  FERM_2 UniProtKB/TrEMBL
  FERM_central UniProtKB/TrEMBL
  Kindlin/fermitin UniProtKB/TrEMBL
  Kindlin_2_N UniProtKB/TrEMBL
  PH_Kindlin/fermitin UniProtKB/TrEMBL
  PH_like_dom UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
KEGG Report rno:289992 UniProtKB/TrEMBL
MGC_CLONE MGC:95154 IMAGE-MGC_LOAD
NCBI Gene 289992 ENTREZGENE
PANTHER PTHR16160 UniProtKB/TrEMBL
Pfam FERM_M UniProtKB/TrEMBL
  Kindlin_2_N UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
PhenoGen Fermt2 PhenoGen
PROSITE PH_DOMAIN UniProtKB/TrEMBL
SMART B41 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP FERM_3-hlx UniProtKB/TrEMBL
UniProt A0A0G2JWC7 ENTREZGENE, UniProtKB/TrEMBL
  Q5XI19 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-02-18 Fermt2  FERM domain containing kindlin 2  Fermt2  fermitin family member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Fermt2  fermitin family member 2  Fermt2  fermitin family homolog 2 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-25 Fermt2  fermitin family homolog 2 (Drosophila)  Plekhc1  pleckstrin homology domain containing, family C (with FERM domain) member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Plekhc1  pleckstrin homology domain containing, family C (with FERM domain) member 1  Plekhc1_predicted  pleckstrin homology domain containing, family C (with FERM domain) member 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Plekhc1_predicted  pleckstrin homology domain containing, family C (with FERM domain) member 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED