Six6os1 (Six6 opposite strand transcript 1) - Rat Genome Database

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Gene: Six6os1 (Six6 opposite strand transcript 1) Rattus norvegicus
Analyze
Symbol: Six6os1
Name: Six6 opposite strand transcript 1
RGD ID: 1559456
Description: Predicted to be involved in meiosis I; oogenesis; and spermatogenesis. Predicted to be located in chromosome. Predicted to be active in central element. Human ortholog(s) of this gene implicated in primary ovarian insufficiency 18 and spermatogenic failure 52. Orthologous to human C14orf39 (chromosome 14 open reading frame 39); INTERACTS WITH bisphenol A; trichloroethene; 2-palmitoylglycerol (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC500673; RGD1559456; similar to RIKEN cDNA 4930447C04
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8697,314,829 - 97,351,069 (-)NCBIGRCr8
mRatBN7.2691,579,185 - 91,615,183 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl691,579,325 - 91,615,148 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0695,761,718 - 95,797,314 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,762,332 - 95,796,502 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06105,199,542 - 105,234,535 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,303,860 - 95,338,272 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera690,043,192 - 90,079,162 (-)NCBICelera
Cytogenetic Map6q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
central element  (IBA,ISO)
chromosome  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:27796301  


Genomics

Comparative Map Data
Six6os1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8697,314,829 - 97,351,069 (-)NCBIGRCr8
mRatBN7.2691,579,185 - 91,615,183 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl691,579,325 - 91,615,148 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0695,761,718 - 95,797,314 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,762,332 - 95,796,502 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06105,199,542 - 105,234,535 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,303,860 - 95,338,272 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera690,043,192 - 90,079,162 (-)NCBICelera
Cytogenetic Map6q24NCBI
C14orf39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381460,435,956 - 60,515,544 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1460,396,469 - 60,515,543 (-)EnsemblGRCh38hg38GRCh38
GRCh371460,902,674 - 60,952,781 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361459,972,428 - 60,022,502 (-)NCBINCBI36Build 36hg18NCBI36
Build 341459,972,427 - 60,022,502NCBI
Celera1440,952,829 - 41,002,917 (-)NCBICelera
Cytogenetic Map14q23.1NCBI
HuRef1441,066,304 - 41,116,353 (-)NCBIHuRef
CHM1_11460,841,920 - 60,891,999 (-)NCBICHM1_1
T2T-CHM13v2.01454,642,261 - 54,705,881 (-)NCBIT2T-CHM13v2.0
4930447C04Rik
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391272,926,967 - 72,964,742 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1272,927,883 - 72,987,548 (-)EnsemblGRCm39 Ensembl
GRCm381272,880,193 - 72,917,957 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1272,881,109 - 72,940,774 (-)EnsemblGRCm38mm10GRCm38
MGSCv371273,982,096 - 74,018,752 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361273,799,947 - 73,836,603 (-)NCBIMGSCv36mm8
Celera1273,997,662 - 74,034,381 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.3NCBI
CUNH14orf39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554669,157,944 - 9,195,226 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554669,158,022 - 9,194,088 (+)NCBIChiLan1.0ChiLan1.0
C15H14orf39
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21561,570,322 - 61,620,352 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11460,786,836 - 60,836,866 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01441,040,315 - 41,090,267 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11459,303,152 - 59,352,973 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,304,040 - 59,351,956 (-)Ensemblpanpan1.1panPan2
C8H14orf39
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1835,486,476 - 35,542,214 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl835,487,228 - 35,542,218 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha835,240,462 - 35,295,944 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0835,720,123 - 35,775,616 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl835,720,696 - 35,775,625 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1835,331,843 - 35,387,333 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0835,409,832 - 35,465,550 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0835,768,864 - 35,824,350 (-)NCBIUU_Cfam_GSD_1.0
CUNH14orf39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864069,496,271 - 69,531,605 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364954,660,641 - 4,694,402 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364954,660,616 - 4,695,338 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C1H14orf39
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1189,407,490 - 189,470,541 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,330,137 - 189,471,874 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,515,496 - 210,580,825 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CUNH14orf39
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,596,061 - 37,707,136 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2437,626,089 - 37,676,361 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605325,872,145 - 25,923,516 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
CUNH14orf39
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473440,656,132 - 40,702,148 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473440,656,054 - 40,701,404 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Six6os1
168 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:66
Interacting mature miRNAs:66
Transcripts:ENSRNOT00000041409
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)682523650110548006Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)689762877106752806Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
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
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
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
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
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
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
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
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

Markers in Region
RH142828  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2691,636,589 - 91,636,707 (+)MAPPERmRatBN7.2
Rnor_6.0695,818,771 - 95,818,888NCBIRnor6.0
Rnor_5.06105,255,971 - 105,256,088UniSTSRnor5.0
RGSC_v3.4695,360,568 - 95,360,685UniSTSRGSC3.4
Celera690,100,543 - 90,100,660UniSTS
RH 3.4 Map6660.2UniSTS
Cytogenetic Map6q24UniSTS
Six6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2691,634,736 - 91,636,425 (+)MAPPERmRatBN7.2
Rnor_6.0695,816,918 - 95,818,606NCBIRnor6.0
Rnor_5.06105,254,118 - 105,255,806UniSTSRnor5.0
RGSC_v3.4695,358,715 - 95,360,403UniSTSRGSC3.4
Celera690,098,690 - 90,100,378UniSTS
Cytogenetic Map6q24UniSTS


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

nervous system reproductive system respiratory system
High
Medium 8
Low 14
Below cutoff 1 7 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041409   ⟹   ENSRNOP00000045806
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl691,579,325 - 91,615,148 (-)Ensembl
Rnor_6.0 Ensembl695,762,332 - 95,796,502 (-)Ensembl
RefSeq Acc Id: XM_017594462   ⟹   XP_017449951
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8697,314,829 - 97,346,513 (-)NCBI
mRatBN7.2691,579,185 - 91,610,644 (-)NCBI
Rnor_6.0695,761,718 - 95,793,132 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039113252   ⟹   XP_038969180
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8697,314,829 - 97,351,052 (-)NCBI
mRatBN7.2691,579,186 - 91,615,183 (-)NCBI
RefSeq Acc Id: XM_039113253   ⟹   XP_038969181
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8697,314,829 - 97,351,052 (-)NCBI
mRatBN7.2691,579,186 - 91,615,183 (-)NCBI
RefSeq Acc Id: XM_063262668   ⟹   XP_063118738
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8697,314,829 - 97,351,069 (-)NCBI
RefSeq Acc Id: XM_063262669   ⟹   XP_063118739
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8697,314,829 - 97,351,052 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_017449951   ⟸   XM_017594462
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000045806   ⟸   ENSRNOT00000041409
RefSeq Acc Id: XP_038969181   ⟸   XM_039113253
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038969180   ⟸   XM_039113252
- Peptide Label: isoform X3
- UniProtKB: D4A1D9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063118738   ⟸   XM_063262668
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063118739   ⟸   XM_063262669
- Peptide Label: isoform X2
- UniProtKB: A6HC47 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A1D9-F1-model_v2 AlphaFold D4A1D9 1-576 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559456 AgrOrtholog
BioCyc Gene G2FUF-37127 BioCyc
Ensembl Genes ENSRNOG00000031655 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041409.5 UniProtKB/TrEMBL
InterPro SIX6OS1 UniProtKB/TrEMBL
NCBI Gene 500673 ENTREZGENE
PANTHER PROTEIN SIX6OS1 UniProtKB/TrEMBL
  PTHR35449 UniProtKB/TrEMBL
Pfam S6OS1 UniProtKB/TrEMBL
PhenoGen Six6os1 PhenoGen
RatGTEx ENSRNOG00000031655 RatGTEx
UniProt A6HC47 ENTREZGENE, UniProtKB/TrEMBL
  D4A1D9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Six6os1  Six6 opposite strand transcript 1  RGD1559456_predicted  similar to RIKEN cDNA 4930447C04 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559456_predicted  similar to RIKEN cDNA 4930447C04 (predicted)  LOC500673  similar to RIKEN cDNA 4930447C04  Symbol and Name status set to approved 1299863 APPROVED