Glis2 (GLIS family zinc finger 2) - Rat Genome Database

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Gene: Glis2 (GLIS family zinc finger 2) Rattus norvegicus
Analyze
Symbol: Glis2
Name: GLIS family zinc finger 2
RGD ID: 1309177
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 central nervous system development; negative regulation of smoothened signaling pathway; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including hematopoietic stem cell homeostasis; positive regulation of protein localization to nucleus; and regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm; non-motile cilium; and nuclear speck. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in nephronophthisis 7. Orthologous to human GLIS2 (GLIS family zinc finger 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC302946; zinc finger protein GLIS2
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
GRCr81011,457,594 - 11,484,948 (-)NCBIGRCr8
mRatBN7.21010,951,157 - 10,978,524 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1010,951,371 - 10,971,578 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1015,660,062 - 15,680,211 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01015,148,880 - 15,169,029 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01010,818,026 - 10,838,187 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01011,154,459 - 11,177,063 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,154,658 - 11,174,861 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0109,919,818 - 9,940,224 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41011,080,702 - 11,100,905 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11011,082,230 - 11,102,224 (-)NCBI
Celera109,913,630 - 9,933,828 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11262234   PMID:11741991   PMID:17344476   PMID:17618285   PMID:18227149   PMID:18298960   PMID:21127075   PMID:21816948   PMID:25370802  


Genomics

Comparative Map Data
Glis2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81011,457,594 - 11,484,948 (-)NCBIGRCr8
mRatBN7.21010,951,157 - 10,978,524 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1010,951,371 - 10,971,578 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1015,660,062 - 15,680,211 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01015,148,880 - 15,169,029 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01010,818,026 - 10,838,187 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01011,154,459 - 11,177,063 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,154,658 - 11,174,861 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0109,919,818 - 9,940,224 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41011,080,702 - 11,100,905 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11011,082,230 - 11,102,224 (-)NCBI
Celera109,913,630 - 9,933,828 (-)NCBICelera
Cytogenetic Map10q12NCBI
GLIS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38164,314,761 - 4,339,595 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl164,314,761 - 4,339,597 (+)EnsemblGRCh38hg38GRCh38
GRCh37164,364,762 - 4,389,596 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36164,322,226 - 4,329,599 (+)NCBINCBI36Build 36hg18NCBI36
Build 34164,322,225 - 4,327,803NCBI
Celera164,589,173 - 4,596,546 (+)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef164,349,132 - 4,356,464 (+)NCBIHuRef
CHM1_1164,382,161 - 4,389,534 (+)NCBICHM1_1
T2T-CHM13v2.0164,342,063 - 4,366,887 (+)NCBIT2T-CHM13v2.0
Glis2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39164,412,217 - 4,443,076 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl164,412,577 - 4,442,788 (+)EnsemblGRCm39 Ensembl
GRCm38164,594,320 - 4,625,141 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl164,594,713 - 4,624,924 (+)EnsemblGRCm38mm10GRCm38
MGSCv37164,594,713 - 4,615,957 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36164,509,941 - 4,531,181 (+)NCBIMGSCv36mm8
Celera165,224,178 - 5,245,422 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map162.45NCBI
Glis2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544213,097,636 - 13,105,210 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544213,097,636 - 13,113,514 (-)NCBIChiLan1.0ChiLan1.0
GLIS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2184,838,920 - 4,862,398 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1168,623,258 - 8,646,814 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0163,234,549 - 3,257,994 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1164,418,525 - 4,425,633 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl164,418,524 - 4,425,631 (+)Ensemblpanpan1.1panPan2
GLIS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1637,048,380 - 37,069,740 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl637,048,367 - 37,088,880 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha638,376,682 - 38,397,969 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0637,252,704 - 37,274,023 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl637,252,691 - 37,259,075 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1637,046,934 - 37,068,217 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0636,940,101 - 36,961,380 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0637,341,402 - 37,362,697 (-)NCBIUU_Cfam_GSD_1.0
Glis2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344106,539,539 - 106,548,046 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936694163,501 - 167,659 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936694161,419 - 168,012 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GLIS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl337,998,078 - 38,009,024 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1337,998,072 - 38,018,726 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2339,051,838 - 39,072,357 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GLIS2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.153,996,333 - 4,019,499 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl53,996,372 - 4,019,542 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606826,672,065 - 26,695,145 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Glis2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248242,098,384 - 2,127,733 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248242,106,261 - 2,127,740 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Glis2
117 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:379
Count of miRNA genes:214
Interacting mature miRNAs:245
Transcripts:ENSRNOT00000006680
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
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat

Markers in Region
BI288960  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21010,973,321 - 10,973,480 (+)MAPPERmRatBN7.2
Rnor_6.01011,176,615 - 11,176,773NCBIRnor6.0
Rnor_5.0109,941,645 - 9,941,803UniSTSRnor5.0
RGSC_v3.41011,103,179 - 11,103,337UniSTSRGSC3.4
Celera109,935,426 - 9,935,584UniSTS
Cytogenetic Map10q12UniSTS


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 34 6 6 1 6 61 35 33 11
Low 3 9 51 35 18 35 8 11 13 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006680   ⟹   ENSRNOP00000006680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1010,951,371 - 10,971,578 (-)Ensembl
Rnor_6.0 Ensembl1011,154,658 - 11,174,861 (-)Ensembl
RefSeq Acc Id: NM_001106978   ⟹   NP_001100448
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81011,457,792 - 11,477,995 (-)NCBI
mRatBN7.21010,951,371 - 10,971,578 (-)NCBI
Rnor_6.01011,154,658 - 11,174,861 (-)NCBI
Rnor_5.0109,919,818 - 9,940,224 (-)NCBI
RGSC_v3.41011,080,702 - 11,100,905 (-)RGD
Celera109,913,630 - 9,933,828 (-)RGD
Sequence:
RefSeq Acc Id: XM_039085846   ⟹   XP_038941774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81011,457,594 - 11,484,948 (-)NCBI
mRatBN7.21010,951,157 - 10,978,524 (-)NCBI
RefSeq Acc Id: XM_039085847   ⟹   XP_038941775
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81011,457,594 - 11,484,948 (-)NCBI
mRatBN7.21010,951,157 - 10,973,507 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100448 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941774 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941775 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96297 (Get FASTA)   NCBI Sequence Viewer  
  EDL96298 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006680
  ENSRNOP00000006680.5
Reference Protein Sequences
RefSeq Acc Id: NP_001100448   ⟸   NM_001106978
- UniProtKB: A6K4S5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006680   ⟸   ENSRNOT00000006680
RefSeq Acc Id: XP_038941774   ⟸   XM_039085846
- Peptide Label: isoform X1
- UniProtKB: D3ZIA9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038941775   ⟸   XM_039085847
- Peptide Label: isoform X1
- UniProtKB: D3ZIA9 (UniProtKB/TrEMBL)
Protein Domains
C2H2-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZIA9-F1-model_v2 AlphaFold D3ZIA9 1-521 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:1309177 AgrOrtholog
BioCyc Gene G2FUF-26031 BioCyc
Ensembl Genes ENSRNOG00000004766 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006680.6 UniProtKB/TrEMBL
Gene3D-CATH Classic Zinc Finger UniProtKB/TrEMBL
InterPro GLI-like UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:302946 UniProtKB/TrEMBL
NCBI Gene 302946 ENTREZGENE
PANTHER C2H2-TYPE DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  TRANSCRIPTIONAL ACTIVATOR CUBITUS INTERRUPTUS UniProtKB/TrEMBL
Pfam zf-C2H2 UniProtKB/TrEMBL
PhenoGen Glis2 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004766 RatGTEx
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A6K4S5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZIA9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Glis2  GLIS family zinc finger 2   Glis2_predicted  GLIS family zinc finger 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Glis2_predicted  GLIS family zinc finger 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED