Six4 (SIX homeobox 4) - Rat Genome Database

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Gene: Six4 (SIX homeobox 4) Rattus norvegicus
Analyze
Symbol: Six4
Name: SIX homeobox 4
RGD ID: 1306726
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including positive regulation of morphogenesis of an epithelium; regulation of transcription, DNA-templated; and striated muscle cell differentiation. Predicted to act upstream of or within several processes, including embryonic organ morphogenesis; myoblast migration; and thymus development. Predicted to be located in cytoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human SIX4 (SIX homeobox 4); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeobox protein SIX4; LOC299138; sine oculis-related homeobox 4 homolog; sine oculis-related homeobox 4 homolog (Drosophila)
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
mRatBN7.2691,802,328 - 91,816,062 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl691,802,329 - 91,815,992 (-)Ensembl
Rnor_6.0695,984,868 - 95,999,709 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,984,868 - 95,998,529 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06105,420,180 - 105,433,894 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,526,293 - 95,539,953 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1695,533,549 - 95,543,176 (-)NCBI
Celera690,265,300 - 90,278,960 (-)NCBICelera
Cytogenetic Map6q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (ISO)
embryonic cranial skeleton morphogenesis  (ISO)
embryonic skeletal system morphogenesis  (ISO)
fungiform papilla morphogenesis  (ISO)
generation of neurons  (ISO)
inner ear morphogenesis  (ISO)
male gonad development  (ISO)
male sex determination  (ISO)
male sex differentiation  (ISO)
metanephric mesenchyme development  (ISO)
myoblast migration  (ISO)
myotome development  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of neuron apoptotic process  (ISO)
negative regulation of satellite cell differentiation  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
olfactory placode formation  (ISO)
pharyngeal system development  (ISO)
positive regulation of branching involved in ureteric bud morphogenesis  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of ureteric bud formation  (ISO)
protein localization to nucleus  (ISO)
regulation of branch elongation involved in ureteric bud branching  (ISO)
regulation of epithelial cell proliferation  (ISO)
regulation of gene expression  (ISO)
regulation of protein localization  (ISO)
regulation of synaptic assembly at neuromuscular junction  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (ISO)
sarcomere organization  (ISO)
skeletal muscle fiber differentiation  (ISO)
skeletal muscle tissue development  (ISO)
thymus development  (ISO)
tongue development  (ISO)
trigeminal ganglion development  (ISO)

Cellular Component

References

Additional References at PubMed
PMID:8814301   PMID:9826681   PMID:9990334   PMID:10490620   PMID:14966291   PMID:15788460   PMID:15955062   PMID:16530750   PMID:16938278   PMID:17300925   PMID:17592144   PMID:19027001  
PMID:19962975   PMID:20515681   PMID:20696153   PMID:21884692   PMID:21978088   PMID:23987514  


Genomics

Comparative Map Data
Six4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2691,802,328 - 91,816,062 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl691,802,329 - 91,815,992 (-)Ensembl
Rnor_6.0695,984,868 - 95,999,709 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,984,868 - 95,998,529 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06105,420,180 - 105,433,894 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,526,293 - 95,539,953 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1695,533,549 - 95,543,176 (-)NCBI
Celera690,265,300 - 90,278,960 (-)NCBICelera
Cytogenetic Map6q24NCBI
SIX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381460,709,539 - 60,724,351 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1460,709,539 - 60,724,351 (-)EnsemblGRCh38hg38GRCh38
GRCh371461,176,257 - 61,191,069 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361460,246,009 - 60,260,545 (-)NCBINCBI36hg18NCBI36
Build 341460,249,877 - 60,260,482NCBI
Celera1441,226,507 - 41,241,110 (-)NCBI
Cytogenetic Map14q23.1NCBI
HuRef1441,338,950 - 41,376,872 (-)NCBIHuRef
CHM1_11461,115,577 - 61,130,176 (-)NCBICHM1_1
Six4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391273,146,383 - 73,160,805 (-)NCBIGRCm39mm39
GRCm39 Ensembl1273,146,383 - 73,160,230 (-)Ensembl
GRCm381273,099,609 - 73,114,031 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,099,609 - 73,113,456 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,201,246 - 74,214,232 (-)NCBIGRCm37mm9NCBIm37
MGSCv361274,019,097 - 74,032,083 (-)NCBImm8
Celera1274,211,796 - 74,224,743 (-)NCBICelera
Cytogenetic Map12C3NCBI
Six4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554668,902,517 - 8,915,723 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554668,902,728 - 8,915,685 (+)NCBIChiLan1.0ChiLan1.0
SIX4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11459,580,587 - 59,592,654 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,580,587 - 59,594,014 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01441,316,169 - 41,332,160 (-)NCBIMhudiblu_PPA_v0panPan3
SIX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1835,735,893 - 35,748,976 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl835,737,058 - 35,748,893 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha835,489,928 - 35,502,823 (-)NCBI
ROS_Cfam_1.0835,969,183 - 35,982,082 (-)NCBI
ROS_Cfam_1.0 Ensembl835,970,354 - 35,982,196 (-)Ensembl
UMICH_Zoey_3.1835,581,305 - 35,594,193 (-)NCBI
UNSW_CanFamBas_1.0835,658,978 - 35,671,679 (-)NCBI
UU_Cfam_GSD_1.0836,020,222 - 36,033,117 (-)NCBI
Six4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864069,291,248 - 69,302,270 (+)NCBI
SpeTri2.0NW_0049364954,887,718 - 4,900,198 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1189,670,390 - 189,682,783 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,670,390 - 189,682,378 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,780,397 - 210,792,387 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SIX4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,899,463 - 37,911,875 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2437,900,909 - 37,911,612 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605326,152,002 - 26,164,077 (-)NCBIVero_WHO_p1.0
Six4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473440,397,276 - 40,409,951 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH129748  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2691,802,403 - 91,802,570 (+)MAPPERmRatBN7.2
Rnor_6.0695,984,943 - 95,985,109NCBIRnor6.0
Rnor_5.06105,420,255 - 105,420,421UniSTSRnor5.0
RGSC_v3.4695,526,368 - 95,526,534UniSTSRGSC3.4
Celera690,265,375 - 90,265,541UniSTS
RH 3.4 Map6660.2UniSTS
Cytogenetic Map6q24UniSTS
D50417  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2691,811,705 - 91,811,865 (+)MAPPERmRatBN7.2
Rnor_6.0695,994,242 - 95,994,401NCBIRnor6.0
Rnor_5.06105,429,554 - 105,429,713UniSTSRnor5.0
RGSC_v3.4695,535,667 - 95,535,826UniSTSRGSC3.4
Celera690,274,674 - 90,274,833UniSTS
Cytogenetic Map6q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
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
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
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
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)681132889104393926Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)681132889104393926Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)682523650110548006Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)683190345106747639Rat
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
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)689762877106752806Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:550
Count of miRNA genes:269
Interacting mature miRNAs:367
Transcripts:ENSRNOT00000050138
Prediction methods:Miranda, 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 8 9 4 4 13 8
Low 43 22 6 13 6 2 50 31 18 11
Below cutoff 3 18 18 5 18 20 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050138   ⟹   ENSRNOP00000050667
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl691,802,329 - 91,815,992 (-)Ensembl
Rnor_6.0 Ensembl695,984,868 - 95,998,529 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117601   ⟹   ENSRNOP00000089936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl691,802,329 - 91,815,992 (-)Ensembl
RefSeq Acc Id: NM_001106739   ⟹   NP_001100209
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,802,329 - 91,815,992 (-)NCBI
Rnor_6.0695,984,868 - 95,998,529 (-)NCBI
Rnor_5.06105,420,180 - 105,433,894 (-)NCBI
RGSC_v3.4695,526,293 - 95,539,953 (-)RGD
Celera690,265,300 - 90,278,960 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240207   ⟹   XP_006240269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,802,328 - 91,815,837 (-)NCBI
Rnor_6.0695,984,868 - 95,998,351 (-)NCBI
Rnor_5.06105,420,180 - 105,433,894 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240208   ⟹   XP_006240270
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,802,328 - 91,816,062 (-)NCBI
Rnor_6.0695,984,868 - 95,999,709 (-)NCBI
Rnor_5.06105,420,180 - 105,433,894 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039111999   ⟹   XP_038967927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,806,791 - 91,815,837 (-)NCBI
RefSeq Acc Id: XM_039112000   ⟹   XP_038967928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,802,328 - 91,814,652 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100209   ⟸   NM_001106739
- UniProtKB: D3ZAJ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240270   ⟸   XM_006240208
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006240269   ⟸   XM_006240207
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000050667   ⟸   ENSRNOT00000050138
RefSeq Acc Id: XP_038967928   ⟸   XM_039112000
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038967927   ⟸   XM_039111999
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000089936   ⟸   ENSRNOT00000117601
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAJ7-F1-model_v2 AlphaFold D3ZAJ7 1-705 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 95994602 95994603 G A snv LEW/Crl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306726 AgrOrtholog
BioCyc Gene G2FUF-37118 BioCyc
Ensembl Genes ENSRNOG00000007250 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000050667 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000089936 ENTREZGENE
Ensembl Transcript ENSRNOT00000050138 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000117601 ENTREZGENE
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
KEGG Report rno:299138 UniProtKB/TrEMBL
NCBI Gene 299138 ENTREZGENE
Pfam Homeobox UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
PhenoGen Six4 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt D3ZAJ7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Six4  SIX homeobox 4  Six4  sine oculis-related homeobox 4 homolog (Drosophila)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Six4  sine oculis-related homeobox 4 homolog (Drosophila)   Six4_predicted  sine oculis-related homeobox 4 homolog (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Six4_predicted  sine oculis-related homeobox 4 homolog (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED