Tmed4 (transmembrane p24 trafficking protein 4) - Rat Genome Database

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Gene: Tmed4 (transmembrane p24 trafficking protein 4) Rattus norvegicus
Analyze
Symbol: Tmed4
Name: transmembrane p24 trafficking protein 4
RGD ID: 1306319
Description: Predicted to be involved in several processes, including Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and positive regulation of canonical NF-kappaB signal transduction. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in several cellular components, including COPII-coated ER to Golgi transport vesicle; Golgi apparatus; and endoplasmic reticulum-Golgi intermediate compartment. Orthologous to human TMED4 (transmembrane p24 trafficking protein 4); INTERACTS WITH (+)-schisandrin B; 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC305502; RGD1306319; similar to RIKEN cDNA 1110014L17; transmembrane emp24 domain-containing protein 4; transmembrane emp24 protein transport domain containing 4
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
GRCr81485,338,980 - 85,343,577 (-)NCBIGRCr8
mRatBN7.21481,125,049 - 81,129,646 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1481,125,053 - 81,129,631 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1485,525,765 - 85,530,504 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01486,765,848 - 86,770,587 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01483,215,174 - 83,219,913 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01486,390,327 - 86,395,151 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,390,338 - 86,395,135 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01487,351,512 - 87,356,335 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41486,997,282 - 87,001,869 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11487,016,423 - 87,021,016 (-)NCBI
Celera1480,007,995 - 80,012,582 (-)NCBICelera
Cytogenetic Map14q21NCBI
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

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:12761501   PMID:23376485  


Genomics

Comparative Map Data
Tmed4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81485,338,980 - 85,343,577 (-)NCBIGRCr8
mRatBN7.21481,125,049 - 81,129,646 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1481,125,053 - 81,129,631 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1485,525,765 - 85,530,504 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01486,765,848 - 86,770,587 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01483,215,174 - 83,219,913 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01486,390,327 - 86,395,151 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,390,338 - 86,395,135 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01487,351,512 - 87,356,335 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41486,997,282 - 87,001,869 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11487,016,423 - 87,021,016 (-)NCBI
Celera1480,007,995 - 80,012,582 (-)NCBICelera
Cytogenetic Map14q21NCBI
TMED4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38744,577,894 - 44,582,231 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl744,576,392 - 44,582,287 (-)EnsemblGRCh38hg38GRCh38
GRCh37744,617,493 - 44,621,830 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36744,585,287 - 44,588,352 (-)NCBINCBI36Build 36hg18NCBI36
Build 34744,392,002 - 44,395,067NCBI
Celera744,717,606 - 44,720,671 (-)NCBICelera
Cytogenetic Map7p13NCBI
HuRef744,503,138 - 44,506,203 (-)NCBIHuRef
CHM1_1744,623,158 - 44,626,223 (-)NCBICHM1_1
T2T-CHM13v2.0744,737,656 - 44,741,987 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2744,658,279 - 44,661,344 (-)NCBI
Tmed4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,220,714 - 6,224,837 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,220,369 - 6,224,870 (-)EnsemblGRCm39 Ensembl
GRCm38116,270,714 - 6,274,837 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,270,369 - 6,274,870 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,170,717 - 6,174,840 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,170,717 - 6,174,840 (-)NCBIMGSCv36mm8
Celera116,752,660 - 6,756,791 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.94NCBI
Tmed4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554567,500,848 - 7,504,310 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554567,500,848 - 7,504,310 (+)NCBIChiLan1.0ChiLan1.0
TMED4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2649,487,406 - 49,494,805 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1797,811,961 - 97,819,543 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0745,289,666 - 45,297,030 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1745,358,692 - 45,366,036 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl745,361,693 - 45,366,395 (-)Ensemblpanpan1.1panPan2
TMED4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha162,355,451 - 2,357,820 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01614,503,747 - 14,506,117 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1614,503,778 - 14,516,659 (+)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.01614,135,234 - 14,137,604 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01614,115,849 - 14,118,219 (+)NCBIUU_Cfam_GSD_1.0
Tmed4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118100,265,967 - 100,270,922 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647819,477,698 - 19,482,706 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647819,477,698 - 19,482,656 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMED4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1850,699,470 - 50,702,705 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11850,698,819 - 50,702,333 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21855,602,126 - 55,605,640 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMED4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12114,095,120 - 14,099,415 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2114,095,538 - 14,098,321 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660628,431,190 - 8,440,353 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmed4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247407,558,717 - 7,562,517 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247407,549,549 - 7,562,517 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tmed4
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:440
Count of miRNA genes:197
Interacting mature miRNAs:231
Transcripts:ENSRNOT00000006802
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
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat

Markers in Region
RH137273  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21481,125,153 - 81,125,358 (+)MAPPERmRatBN7.2
Rnor_6.01486,390,432 - 86,390,636NCBIRnor6.0
Rnor_5.01487,351,617 - 87,351,821UniSTSRnor5.0
RGSC_v3.41486,997,376 - 86,997,580UniSTSRGSC3.4
Celera1480,008,089 - 80,008,293UniSTS
RH 3.4 Map14579.2UniSTS
Cytogenetic Map14q21UniSTS
AI409861  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21481,125,210 - 81,125,358 (+)MAPPERmRatBN7.2
Rnor_6.01486,390,489 - 86,390,636NCBIRnor6.0
Rnor_5.01487,351,674 - 87,351,821UniSTSRnor5.0
RGSC_v3.41486,997,433 - 86,997,580UniSTSRGSC3.4
Celera1480,008,146 - 80,008,293UniSTS
RH 3.4 Map14577.3UniSTS
Cytogenetic Map14q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000006802   ⟹   ENSRNOP00000006802
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1481,125,053 - 81,129,631 (-)Ensembl
Rnor_6.0 Ensembl1486,390,747 - 86,395,120 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000078572   ⟹   ENSRNOP00000074665
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1486,390,338 - 86,395,135 (-)Ensembl
RefSeq Acc Id: NM_001399064   ⟹   NP_001385993
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81485,338,980 - 85,343,577 (-)NCBI
mRatBN7.21481,125,049 - 81,129,646 (-)NCBI
RefSeq Acc Id: NM_001399065   ⟹   NP_001385994
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81485,338,980 - 85,343,577 (-)NCBI
mRatBN7.21481,125,049 - 81,129,646 (-)NCBI
Ensembl Acc Id: ENSRNOP00000006802   ⟸   ENSRNOT00000006802
Ensembl Acc Id: ENSRNOP00000074665   ⟸   ENSRNOT00000078572
RefSeq Acc Id: NP_001385993   ⟸   NM_001399064
- Peptide Label: isoform 1 precursor
- UniProtKB: A6IKS4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001385994   ⟸   NM_001399065
- Peptide Label: isoform 2 precursor
- UniProtKB: G3V6N2 (UniProtKB/TrEMBL)
Protein Domains
GOLD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6N2-F1-model_v2 AlphaFold G3V6N2 1-227 view protein structure

Transcriptome

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

Promoters
RGD ID:13699478
Promoter ID:EPDNEW_R9995
Type:multiple initiation site
Name:Tmed4_1
Description:transmembrane p24 trafficking protein 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_6.01486,395,133 - 86,395,193EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306319 AgrOrtholog
BioCyc Gene G2FUF-15099 BioCyc
Ensembl Genes ENSRNOG00000005016 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006802.6 UniProtKB/TrEMBL
InterPro GOLD UniProtKB/TrEMBL
  TMP21-related UniProtKB/TrEMBL
NCBI Gene 305502 ENTREZGENE
PANTHER PTHR22811 UniProtKB/TrEMBL
  TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam EMP24_GP25L UniProtKB/TrEMBL
PhenoGen Tmed4 PhenoGen
PROSITE GOLD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005016 RatGTEx
SMART EMP24_GP25L UniProtKB/TrEMBL
UniProt A6IKS4 ENTREZGENE, UniProtKB/TrEMBL
  B5DEM3_RAT UniProtKB/TrEMBL
  G3V6N2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-19 Tmed4  transmembrane p24 trafficking protein 4  Tmed4  transmembrane emp24 protein transport domain containing 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tmed4  transmembrane emp24 protein transport domain containing 4   Tmed4_predicted  transmembrane emp24 protein transport domain containing 4 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Tmed4_predicted  transmembrane emp24 protein transport domain containing 4 (predicted)  RGD1306319_predicted  similar to RIKEN cDNA 1110014L17 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1306319_predicted  similar to RIKEN cDNA 1110014L17 (predicted)  LOC305502_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC305502_predicted  similar to RIKEN cDNA 1110014L17 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL