Med4 (mediator complex subunit 4) - Rat Genome Database

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Gene: Med4 (mediator complex subunit 4) Rattus norvegicus
Analyze
Symbol: Med4
Name: mediator complex subunit 4
RGD ID: 1306671
Description: Predicted to enable nuclear thyroid hormone receptor binding activity and transcription coactivator activity. Predicted to be involved in positive regulation of transcription initiation by RNA polymerase II and transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of core mediator complex and mediator complex. Orthologous to human MED4 (mediator complex subunit 4); PARTICIPATES IN RNA polymerase II transcription pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC306030; mediator of RNA polymerase II transcription subunit 4; mediator of RNA polymerase II transcription, subunit 4 homolog; mediator of RNA polymerase II transcription, subunit 4 homolog (yeast); Vdrip; vitamin D receptor interacting protein
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
GRCr81555,106,079 - 55,116,354 (+)NCBIGRCr8
mRatBN7.21548,696,542 - 48,706,818 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1548,696,511 - 48,706,820 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1552,837,909 - 52,848,181 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01553,949,486 - 53,959,758 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01550,794,276 - 50,804,563 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01555,406,543 - 55,416,816 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1555,406,543 - 55,416,815 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01559,128,754 - 59,139,027 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41554,158,386 - 54,168,660 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11554,174,165 - 54,184,439 (+)NCBI
Celera1548,344,958 - 48,355,232 (+)NCBICelera
Cytogenetic Map15q11NCBI
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

Cellular Component
core mediator complex  (IBA,IEA,ISO)
mediator complex  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Gene dosage, expression, and ontology analysis identifies driver genes in the carcinogenesis and chemoradioresistance of cervical cancer. Lando M, etal., PLoS Genet. 2009 Nov;5(11):e1000719. doi: 10.1371/journal.pgen.1000719. Epub 2009 Nov 13.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. The Mediator complex and transcription regulation. Poss ZC, etal., Crit Rev Biochem Mol Biol. 2013 Nov-Dec;48(6):575-608. doi: 10.3109/10409238.2013.840259. Epub 2013 Oct 3.
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:10198638   PMID:10235267   PMID:10882111   PMID:11867769   PMID:12218053   PMID:12477932   PMID:14638676   PMID:15340084   PMID:19946888   PMID:20508642  


Genomics

Comparative Map Data
Med4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81555,106,079 - 55,116,354 (+)NCBIGRCr8
mRatBN7.21548,696,542 - 48,706,818 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1548,696,511 - 48,706,820 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1552,837,909 - 52,848,181 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01553,949,486 - 53,959,758 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01550,794,276 - 50,804,563 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01555,406,543 - 55,416,816 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1555,406,543 - 55,416,815 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01559,128,754 - 59,139,027 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41554,158,386 - 54,168,660 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11554,174,165 - 54,184,439 (+)NCBI
Celera1548,344,958 - 48,355,232 (+)NCBICelera
Cytogenetic Map15q11NCBI
MED4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381348,075,724 - 48,095,104 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1348,053,323 - 48,095,131 (-)EnsemblGRCh38hg38GRCh38
GRCh371348,649,860 - 48,669,240 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361347,548,093 - 47,567,241 (-)NCBINCBI36Build 36hg18NCBI36
Build 341347,548,092 - 47,567,241NCBI
Celera1329,704,843 - 29,723,982 (-)NCBICelera
Cytogenetic Map13q14.2NCBI
HuRef1329,441,920 - 29,461,323 (-)NCBIHuRef
CHM1_11348,617,590 - 48,636,992 (-)NCBICHM1_1
T2T-CHM13v2.01347,296,104 - 47,315,464 (-)NCBIT2T-CHM13v2.0
Med4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391473,747,489 - 73,755,985 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1473,747,465 - 73,756,289 (+)EnsemblGRCm39 Ensembl
GRCm381473,510,049 - 73,518,545 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1473,510,025 - 73,518,849 (+)EnsemblGRCm38mm10GRCm38
MGSCv371473,909,856 - 73,918,352 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361472,244,204 - 72,252,700 (+)NCBIMGSCv36mm8
Celera1471,030,090 - 71,038,619 (+)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1439.05NCBI
Med4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554311,794,115 - 1,812,889 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554311,794,863 - 1,812,641 (-)NCBIChiLan1.0ChiLan1.0
MED4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21449,501,810 - 49,549,339 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11348,153,026 - 48,200,552 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01329,227,620 - 29,247,082 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11347,929,918 - 47,948,836 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1347,929,918 - 47,948,836 (-)Ensemblpanpan1.1panPan2
MED4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1223,396,276 - 3,411,037 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl223,396,267 - 3,410,608 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha223,382,963 - 3,439,510 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0223,468,131 - 3,524,954 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl223,509,920 - 3,524,949 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1223,253,448 - 3,309,631 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0223,316,446 - 3,372,886 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0223,321,556 - 3,377,754 (+)NCBIUU_Cfam_GSD_1.0
Med4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945157,913,380 - 157,930,626 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365651,396,088 - 1,415,248 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365651,397,434 - 1,414,674 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MED4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1119,551,863 - 19,566,926 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11119,551,858 - 19,566,915 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21120,010,002 - 20,019,435 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MED4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1325,990,203 - 26,009,472 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl325,990,159 - 26,009,438 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605717,900,930 - 17,920,167 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Med4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247486,770,231 - 6,790,385 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Med4
66 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:322
Count of miRNA genes:217
Interacting mature miRNAs:256
Transcripts:ENSRNOT00000023195
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154028990149308583Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat

Markers in Region
RH134687  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21548,706,506 - 48,706,693 (+)MAPPERmRatBN7.2
Rnor_6.01555,416,505 - 55,416,691NCBIRnor6.0
Rnor_5.01559,138,716 - 59,138,902UniSTSRnor5.0
RGSC_v3.41554,168,349 - 54,168,535UniSTSRGSC3.4
Celera1548,354,921 - 48,355,107UniSTS
Cytogenetic Map15p11UniSTS


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 55 41 19 41 2 5 74 32 41 11 2
Low 8 2 6 6 3 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023195   ⟹   ENSRNOP00000023195
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1548,696,511 - 48,706,820 (+)Ensembl
Rnor_6.0 Ensembl1555,406,543 - 55,416,815 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113571   ⟹   ENSRNOP00000077263
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1548,696,529 - 48,706,673 (+)Ensembl
RefSeq Acc Id: NM_001024256   ⟹   NP_001019427
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81555,106,079 - 55,116,354 (+)NCBI
mRatBN7.21548,696,542 - 48,706,818 (+)NCBI
Rnor_6.01555,406,543 - 55,416,816 (+)NCBI
Rnor_5.01559,128,754 - 59,139,027 (+)NCBI
RGSC_v3.41554,158,386 - 54,168,660 (+)RGD
Celera1548,344,958 - 48,355,232 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001019427 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH93402 (Get FASTA)   NCBI Sequence Viewer  
  EDM02270 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000023195
  ENSRNOP00000023195.5
  ENSRNOP00000077263.1
GenBank Protein Q561Q8 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001019427   ⟸   NM_001024256
- UniProtKB: Q561Q8 (UniProtKB/Swiss-Prot),   A0A8L2QD52 (UniProtKB/TrEMBL),   A6HTQ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023195   ⟸   ENSRNOT00000023195
RefSeq Acc Id: ENSRNOP00000077263   ⟸   ENSRNOT00000113571

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q561Q8-F1-model_v2 AlphaFold Q561Q8 1-270 view protein structure

Transcriptome

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

Promoters
RGD ID:13699824
Promoter ID:EPDNEW_R10348
Type:multiple initiation site
Name:Med4_1
Description:mediator complex subunit 4
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_6.01555,406,528 - 55,406,588EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306671 AgrOrtholog
BioCyc Gene G2FUF-13162 BioCyc
Ensembl Genes ENSRNOG00000017170 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023195 ENTREZGENE
  ENSRNOT00000023195.6 UniProtKB/TrEMBL
  ENSRNOT00000113571.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7389622 IMAGE-MGC_LOAD
InterPro Mediator_Med4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:306030 UniProtKB/Swiss-Prot
MGC_CLONE MGC:112765 IMAGE-MGC_LOAD
NCBI Gene 306030 ENTREZGENE
PANTHER MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13208 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Med4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Med4 PhenoGen
RatGTEx ENSRNOG00000017170 RatGTEx
UniProt A0A8I5Y634_RAT UniProtKB/TrEMBL
  A0A8L2QD52 ENTREZGENE, UniProtKB/TrEMBL
  A6HTQ7 ENTREZGENE, UniProtKB/TrEMBL
  MED4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Med4  mediator complex subunit 4  Med4  mediator of RNA polymerase II transcription, subunit 4 homolog (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Med4  mediator of RNA polymerase II transcription, subunit 4 homolog (yeast)  Vdrip  vitamin D receptor interacting protein  Symbol and Name updated 1299863 APPROVED
2005-12-06 Vdrip  vitamin D receptor interacting protein  Vdrip_predicted  vitamin D receptor interacting protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Vdrip_predicted  vitamin D receptor interacting protein (predicted)      Symbol and Name status set to approved 70820 APPROVED