Surf6 (surfeit 6) - Rat Genome Database

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Gene: Surf6 (surfeit 6) Rattus norvegicus
Analyze
Symbol: Surf6
Name: surfeit 6
RGD ID: 1307382
Description: Predicted to enable DNA binding activity and RNA binding activity. Predicted to be involved in ribosomal large subunit biogenesis and ribosomal small subunit biogenesis. Predicted to act upstream of or within ribosome biogenesis. Predicted to be located in chromosome; granular component; and nucleoplasm. Predicted to be active in nucleolus. Orthologous to human SURF6 (surfeit 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC108352178; LOC311823; MGC109125; Surf6_predicted; surfeit gene 6; surfeit gene 6 (predicted); surfeit locus protein 6; surfeit locus protein 6-like
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
GRCr8330,619,525 - 30,630,388 (-)NCBIGRCr8
mRatBN7.2310,221,450 - 10,232,306 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,221,452 - 10,232,251 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx313,281,440 - 13,292,254 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,866,841 - 21,877,655 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,122,142 - 20,132,956 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,441,404 - 5,452,156 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,441,409 - 5,452,156 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0310,803,314 - 10,814,066 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.435,790,323 - 5,801,072 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.135,790,623 - 5,801,372 (-)NCBI
Celera35,019,513 - 5,030,262 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8639267   PMID:9548374   PMID:12477932   PMID:16855206   PMID:22658674   PMID:22681889  


Genomics

Comparative Map Data
Surf6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8330,619,525 - 30,630,388 (-)NCBIGRCr8
mRatBN7.2310,221,450 - 10,232,306 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,221,452 - 10,232,251 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx313,281,440 - 13,292,254 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,866,841 - 21,877,655 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,122,142 - 20,132,956 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,441,404 - 5,452,156 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,441,409 - 5,452,156 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0310,803,314 - 10,814,066 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.435,790,323 - 5,801,072 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.135,790,623 - 5,801,372 (-)NCBI
Celera35,019,513 - 5,030,262 (-)NCBICelera
Cytogenetic Map3p13NCBI
SURF6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389133,328,776 - 133,336,188 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9133,328,776 - 133,336,188 (-)EnsemblGRCh38hg38GRCh38
GRCh379136,195,612 - 136,203,025 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369135,187,373 - 135,192,868 (-)NCBINCBI36Build 36hg18NCBI36
Build 349133,227,106 - 133,232,598NCBI
Celera9106,748,057 - 106,753,551 (-)NCBICelera
Cytogenetic Map9q34.2NCBI
HuRef9105,697,497 - 105,702,999 (-)NCBIHuRef
CHM1_19136,347,741 - 136,353,244 (-)NCBICHM1_1
T2T-CHM13v2.09145,542,703 - 145,550,115 (-)NCBIT2T-CHM13v2.0
Surf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,780,430 - 26,792,899 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl226,778,640 - 26,792,891 (-)EnsemblGRCm39 Ensembl
GRCm38226,890,418 - 26,902,887 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,888,628 - 26,902,879 (-)EnsemblGRCm38mm10GRCm38
MGSCv37226,746,292 - 26,758,333 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36226,712,781 - 26,724,829 (-)NCBIMGSCv36mm8
Celera226,600,515 - 26,612,557 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.08NCBI
Surf6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555132,692,806 - 2,696,481 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555132,691,648 - 2,696,018 (-)NCBIChiLan1.0ChiLan1.0
SURF6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2116,016,970 - 6,024,335 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan196,019,310 - 6,026,671 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09104,453,832 - 104,459,589 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19133,064,755 - 133,070,302 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9133,064,755 - 133,070,302 (-)Ensemblpanpan1.1panPan2
SURF6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,769,338 - 49,774,136 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha949,050,875 - 49,055,669 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0950,643,360 - 50,648,222 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,642,893 - 50,648,773 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,405,912 - 49,410,703 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,747,372 - 49,752,154 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,825,278 - 49,830,139 (-)NCBIUU_Cfam_GSD_1.0
Surf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,827,029 - 199,831,820 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366693,542,644 - 3,548,762 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366693,543,250 - 3,548,756 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SURF6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,949,247 - 272,955,197 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11272,949,236 - 272,955,674 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SURF6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1124,803,231 - 4,804,973 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666058181,666 - 187,771 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Surf6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247601,797,740 - 1,804,231 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247601,799,764 - 1,804,194 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Surf6
41 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:769
Count of miRNA genes:300
Interacting mature miRNAs:400
Transcripts:ENSRNOT00000006699
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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat

Markers in Region
AW212655  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2310,234,035 - 10,234,169 (+)MAPPERmRatBN7.2
Rnor_6.034,862,035 - 4,862,168NCBIRnor6.0
Rnor_6.035,453,960 - 5,454,093NCBIRnor6.0
Rnor_5.0310,217,232 - 10,217,365UniSTSRnor5.0
Rnor_5.0310,815,870 - 10,816,003UniSTSRnor5.0
RGSC_v3.435,802,876 - 5,803,009UniSTSRGSC3.4
Celera35,032,066 - 5,032,199UniSTS
Cytogenetic Map3p12UniSTS
RH133460  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2310,232,601 - 10,232,800 (+)MAPPERmRatBN7.2
Rnor_6.035,452,526 - 5,452,724NCBIRnor6.0
Rnor_6.034,860,602 - 4,860,800NCBIRnor6.0
Rnor_5.0310,215,799 - 10,215,997UniSTSRnor5.0
Rnor_5.0310,814,436 - 10,814,634UniSTSRnor5.0
RGSC_v3.435,801,442 - 5,801,640UniSTSRGSC3.4
Celera35,030,632 - 5,030,830UniSTS
Cytogenetic Map3p12UniSTS
BF396659  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21031,174,589 - 31,174,867 (+)MAPPERmRatBN7.2
mRatBN7.2310,221,573 - 10,221,794 (+)MAPPERmRatBN7.2
Rnor_6.035,441,528 - 5,441,748NCBIRnor6.0
Rnor_6.01031,869,745 - 31,870,022NCBIRnor6.0
Rnor_5.01031,691,075 - 31,691,352UniSTSRnor5.0
Rnor_5.0310,803,438 - 10,803,658UniSTSRnor5.0
RGSC_v3.435,790,444 - 5,790,664UniSTSRGSC3.4
RGSC_v3.41031,880,905 - 31,881,182UniSTSRGSC3.4
Celera1030,619,422 - 30,619,699UniSTS
Celera35,019,634 - 5,019,854UniSTS
RH 3.4 Map321.9UniSTS
Cytogenetic Map3p12UniSTS
RH141946  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2310,221,589 - 10,221,794 (+)MAPPERmRatBN7.2
mRatBN7.21031,174,657 - 31,174,867 (+)MAPPERmRatBN7.2
Rnor_6.01031,869,813 - 31,870,022NCBIRnor6.0
Rnor_6.035,441,544 - 5,441,748NCBIRnor6.0
Rnor_5.01031,691,143 - 31,691,352UniSTSRnor5.0
Rnor_5.0310,803,454 - 10,803,658UniSTSRnor5.0
RGSC_v3.435,790,460 - 5,790,664UniSTSRGSC3.4
RGSC_v3.41031,880,973 - 31,881,182UniSTSRGSC3.4
Celera1030,619,490 - 30,619,699UniSTS
Celera35,019,650 - 5,019,854UniSTS
RH 3.4 Map321.9UniSTS
Cytogenetic Map3p12UniSTS


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 35 47 32 19 32 1 3 74 35 40 11 1
Low 8 10 9 9 7 8 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006699   ⟹   ENSRNOP00000006699
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl310,221,452 - 10,232,251 (-)Ensembl
Rnor_6.0 Ensembl35,441,409 - 5,452,156 (-)Ensembl
RefSeq Acc Id: NM_001015014   ⟹   NP_001015014
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,619,528 - 30,630,307 (-)NCBI
mRatBN7.2310,221,453 - 10,232,232 (-)NCBI
Rnor_6.035,441,407 - 5,452,156 (-)NCBI
Rnor_5.0310,803,314 - 10,814,066 (-)NCBI
RGSC_v3.435,790,323 - 5,801,072 (-)RGD
Celera35,019,513 - 5,030,262 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233784   ⟹   XP_006233846
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,619,525 - 30,630,388 (-)NCBI
mRatBN7.2310,221,450 - 10,232,306 (-)NCBI
Rnor_6.035,441,404 - 5,452,017 (-)NCBI
Rnor_5.0310,803,314 - 10,814,066 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001015014 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233846 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91270 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006699
  ENSRNOP00000006699.4
Reference Protein Sequences
RefSeq Acc Id: NP_001015014   ⟸   NM_001015014
- UniProtKB: Q5BJZ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233846   ⟸   XM_006233784
- Peptide Label: isoform X1
- UniProtKB: F7F149 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006699   ⟸   ENSRNOT00000006699
Protein Domains
Ribosomal RNA-processing protein 14/surfeit locus

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BJZ4-F1-model_v2 AlphaFold Q5BJZ4 1-354 view protein structure

Transcriptome

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

Promoters
RGD ID:13691915
Promoter ID:EPDNEW_R2440
Type:initiation region
Name:Surf6_1
Description:surfeit 6
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_6.035,452,197 - 5,452,257EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307382 AgrOrtholog
BioCyc Gene G2FUF-50331 BioCyc
Ensembl Genes ENSRNOG00000005031 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006699.5 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7381547 IMAGE-MGC_LOAD
InterPro Rrp14/SURF6_C UniProtKB/TrEMBL
  Surf6 UniProtKB/TrEMBL
KEGG Report rno:303076 UniProtKB/TrEMBL
MGC_CLONE MGC:109125 IMAGE-MGC_LOAD
NCBI Gene Surf6 ENTREZGENE
PANTHER Surf6 UniProtKB/TrEMBL
  SURFEIT LOCUS PROTEIN 6 UniProtKB/TrEMBL
Pfam SURF6 UniProtKB/TrEMBL
PhenoGen Surf6 PhenoGen
RatGTEx ENSRNOG00000005031 RatGTEx
UniProt F7F149 ENTREZGENE, UniProtKB/TrEMBL
  Q5BJZ4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Surf6  surfeit 6  LOC108352178  surfeit locus protein 6-like  Data merged from RGD:11365920 737654 PROVISIONAL
2016-08-02 LOC108352178  surfeit locus protein 6-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-10-23 Surf6  surfeit 6  Surf6  surfeit gene 6   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Surf6  surfeit gene 6   Surf6_predicted  surfeit gene 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Surf6_predicted  surfeit gene 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED