Tmed9 (transmembrane p24 trafficking protein 9) - Rat Genome Database

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Gene: Tmed9 (transmembrane p24 trafficking protein 9) Rattus norvegicus
Analyze
Symbol: Tmed9
Name: transmembrane p24 trafficking protein 9
RGD ID: 1307627
Description: Predicted to enable cargo receptor activity and syntaxin binding activity. Predicted to be involved in several processes, including Golgi organization; Golgi vesicle transport; and intracellular protein transport. Predicted to be located in synaptic vesicle. 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 TMED9 (transmembrane p24 trafficking protein 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: gp25L2-like; LOC361207; MGC95048; p24 family protein alpha-2; p24alpha2; RGD1307627; similar to gp25L2 protein; transmembrane emp24 domain-containing protein 9; transmembrane emp24 protein transport domain containing 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
GRCr8179,034,797 - 9,039,311 (-)NCBIGRCr8
mRatBN7.2179,029,646 - 9,034,160 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl179,029,646 - 9,034,176 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx179,044,730 - 9,049,243 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01710,574,585 - 10,579,092 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0179,041,119 - 9,045,632 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0179,560,735 - 9,565,249 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl179,560,761 - 9,565,249 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01711,668,160 - 11,672,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,070,667 - 15,075,182 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11715,070,672 - 15,075,182 (-)NCBI
Celera179,111,260 - 9,115,773 (-)NCBICelera
Cytogenetic Map17p14NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Golgi matrix proteins interact with p24 cargo receptors and aid their efficient retention in the Golgi apparatus. Barr FA, etal., J Cell Biol. 2001 Dec 10;155(6):885-91. Epub 2001 Dec 10.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9472029   PMID:12237308   PMID:12477932   PMID:18287528   PMID:18504258   PMID:20458337   PMID:21545355   PMID:25438880  


Genomics

Comparative Map Data
Tmed9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8179,034,797 - 9,039,311 (-)NCBIGRCr8
mRatBN7.2179,029,646 - 9,034,160 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl179,029,646 - 9,034,176 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx179,044,730 - 9,049,243 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01710,574,585 - 10,579,092 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0179,041,119 - 9,045,632 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0179,560,735 - 9,565,249 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl179,560,761 - 9,565,249 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01711,668,160 - 11,672,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,070,667 - 15,075,182 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11715,070,672 - 15,075,182 (-)NCBI
Celera179,111,260 - 9,115,773 (-)NCBICelera
Cytogenetic Map17p14NCBI
TMED9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385177,592,203 - 177,597,242 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5177,592,203 - 177,597,242 (+)EnsemblGRCh38hg38GRCh38
GRCh375177,019,204 - 177,024,243 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365176,951,819 - 176,955,714 (+)NCBINCBI36Build 36hg18NCBI36
Build 345176,951,818 - 176,955,703NCBI
Celera5171,479,350 - 171,483,233 (-)NCBICelera
Cytogenetic Map5q35.3NCBI
HuRef5171,938,890 - 171,942,773 (+)NCBIHuRef
CHM1_15176,451,599 - 176,455,493 (+)NCBICHM1_1
T2T-CHM13v2.05178,134,482 - 178,139,521 (+)NCBIT2T-CHM13v2.0
Tmed9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391355,740,948 - 55,745,510 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1355,721,545 - 55,745,510 (+)EnsemblGRCm39 Ensembl
GRCm381355,593,135 - 55,597,697 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1355,573,732 - 55,597,697 (+)EnsemblGRCm38mm10GRCm38
MGSCv371355,694,496 - 55,699,058 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361355,602,765 - 55,607,310 (+)NCBIMGSCv36mm8
Celera1356,647,217 - 56,651,779 (+)NCBICelera
Cytogenetic Map13B1NCBI
cM Map1330.06NCBI
Tmed9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540829,829,503 - 29,834,408 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540829,830,125 - 29,834,408 (+)NCBIChiLan1.0ChiLan1.0
TMED9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24172,680,400 - 172,684,406 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15170,819,941 - 170,823,947 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05172,897,814 - 172,901,789 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15179,957,842 - 179,961,840 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5179,957,842 - 179,963,279 (+)Ensemblpanpan1.1panPan2
TMED9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1113,510,302 - 3,513,489 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl113,510,724 - 3,513,462 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha113,652,960 - 3,656,150 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0113,486,022 - 3,489,212 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl113,458,636 - 3,489,190 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1113,453,527 - 3,456,715 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0113,532,215 - 3,535,405 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0113,776,163 - 3,779,353 (-)NCBIUU_Cfam_GSD_1.0
TMED9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl280,364,769 - 80,368,589 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1280,364,532 - 80,368,434 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2281,918,845 - 81,922,750 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMED9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12379,609,832 - 79,613,960 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2379,609,826 - 79,614,084 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607510,802,769 - 10,806,907 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmed9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473312,455,790 - 12,464,521 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473312,459,484 - 12,463,596 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tmed9
19 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:78
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000036140
Prediction methods: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
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1581553Pur14Proteinuria QTL 145.30.0001urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat

Markers in Region
RH137175  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2179,030,507 - 9,030,727 (+)MAPPERmRatBN7.2
Rnor_6.0179,561,597 - 9,561,816NCBIRnor6.0
Rnor_5.01711,669,022 - 11,669,241UniSTSRnor5.0
RGSC_v3.41715,071,529 - 15,071,748UniSTSRGSC3.4
Celera179,112,122 - 9,112,341UniSTS
RH 3.4 Map1775.8UniSTS
Cytogenetic Map17p14UniSTS


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000036140   ⟹   ENSRNOP00000030668
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,029,646 - 9,034,176 (-)Ensembl
Rnor_6.0 Ensembl179,560,761 - 9,565,249 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109911   ⟹   ENSRNOP00000083476
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,029,651 - 9,034,163 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111563   ⟹   ENSRNOP00000089772
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,030,317 - 9,034,172 (-)Ensembl
RefSeq Acc Id: NM_001009703   ⟹   NP_001009703
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8179,034,797 - 9,039,311 (-)NCBI
mRatBN7.2179,029,646 - 9,034,160 (-)NCBI
Rnor_6.0179,560,735 - 9,565,249 (-)NCBI
Rnor_5.01711,668,160 - 11,672,674 (-)NCBI
RGSC_v3.41715,070,667 - 15,075,182 (-)RGD
Celera179,111,260 - 9,115,773 (-)RGD
Sequence:
RefSeq Acc Id: NP_001009703   ⟸   NM_001009703
- Peptide Label: precursor
- UniProtKB: Q5I0E7 (UniProtKB/Swiss-Prot),   A0A8L2UKN3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030668   ⟸   ENSRNOT00000036140
RefSeq Acc Id: ENSRNOP00000089772   ⟸   ENSRNOT00000111563
RefSeq Acc Id: ENSRNOP00000083476   ⟸   ENSRNOT00000109911
Protein Domains
GOLD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5I0E7-F1-model_v2 AlphaFold Q5I0E7 1-235 view protein structure

Transcriptome

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

Promoters
RGD ID:13700298
Promoter ID:EPDNEW_R10822
Type:multiple initiation site
Name:Tmed9_1
Description:transmembrane p24 trafficking protein 9
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_6.0179,565,257 - 9,565,317EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307627 AgrOrtholog
BioCyc Gene G2FUF-10216 BioCyc
Ensembl Genes ENSRNOG00000021882 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055015170 UniProtKB/Swiss-Prot
  ENSRNOG00060021751 UniProtKB/Swiss-Prot
  ENSRNOG00065021846 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000036140.7 UniProtKB/TrEMBL
  ENSRNOT00000109911 ENTREZGENE
  ENSRNOT00000109911.1 UniProtKB/Swiss-Prot
  ENSRNOT00000111563.1 UniProtKB/TrEMBL
  ENSRNOT00055025962 UniProtKB/Swiss-Prot
  ENSRNOT00060037738 UniProtKB/Swiss-Prot
  ENSRNOT00065037165 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7123664 IMAGE-MGC_LOAD
InterPro Emp24-like UniProtKB/TrEMBL
  GOLD_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TMP21-related UniProtKB/Swiss-Prot
KEGG Report rno:361207 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95048 IMAGE-MGC_LOAD
NCBI Gene 361207 ENTREZGENE
PANTHER PTHR22811 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EMP24_GP25L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tmed9 PhenoGen
PROSITE GOLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021882 RatGTEx
  ENSRNOG00055015170 RatGTEx
  ENSRNOG00060021751 RatGTEx
  ENSRNOG00065021846 RatGTEx
SMART EMP24_GP25L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AAI6_RAT UniProtKB/TrEMBL
  A0A8L2UKN3 ENTREZGENE, UniProtKB/TrEMBL
  A6KAQ7_RAT UniProtKB/TrEMBL
  Q5I0E7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-19 Tmed9  transmembrane p24 trafficking protein 9  Tmed9  transmembrane emp24 protein transport domain containing 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Tmed9  transmembrane emp24 protein transport domain containing 9  RGD1307627  similar to gp25L2 protein  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1307627  similar to gp25L2 protein  RGD1307627_predicted  similar to gp25L2 protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307627_predicted  similar to gp25L2 protein (predicted)  LOC361207_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361207_predicted  similar to gp25L2 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL