Tmem59l (transmembrane protein 59-like) - Rat Genome Database

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Gene: Tmem59l (transmembrane protein 59-like) Rattus norvegicus
Analyze
Symbol: Tmem59l
Name: transmembrane protein 59-like
RGD ID: 1305557
Description: Predicted to be involved in branching involved in ureteric bud morphogenesis. Predicted to be located in Golgi membrane. Orthologous to human TMEM59L (transmembrane protein 59 like); INTERACTS WITH 1-naphthyl isothiocyanate; 6-propyl-2-thiouracil; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: brain-specific membrane-anchored protein; C19orf4; LOC306349; RGD1305557; similar to Brain specific membrane-anchored protein precursor
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
GRCr81618,975,217 - 18,979,354 (+)NCBIGRCr8
mRatBN7.21618,941,370 - 18,945,381 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,941,567 - 18,945,381 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,983,445 - 18,987,168 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01620,116,252 - 20,119,975 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01619,036,407 - 19,040,130 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01620,691,956 - 20,695,701 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,691,978 - 20,695,701 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01620,547,447 - 20,551,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41619,448,403 - 19,452,133 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11619,448,409 - 19,452,106 (+)NCBI
Celera1619,133,030 - 19,136,753 (+)NCBICelera
Cytogenetic Map16p14NCBI
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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:22871113   PMID:27324899  


Genomics

Comparative Map Data
Tmem59l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81618,975,217 - 18,979,354 (+)NCBIGRCr8
mRatBN7.21618,941,370 - 18,945,381 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1618,941,567 - 18,945,381 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1618,983,445 - 18,987,168 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01620,116,252 - 20,119,975 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01619,036,407 - 19,040,130 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01620,691,956 - 20,695,701 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1620,691,978 - 20,695,701 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01620,547,447 - 20,551,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41619,448,403 - 19,452,133 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11619,448,409 - 19,452,106 (+)NCBI
Celera1619,133,030 - 19,136,753 (+)NCBICelera
Cytogenetic Map16p14NCBI
TMEM59L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381918,612,870 - 18,621,039 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1918,607,430 - 18,621,039 (+)EnsemblGRCh38hg38GRCh38
GRCh371918,723,680 - 18,731,849 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361918,584,682 - 18,592,849 (+)NCBINCBI36Build 36hg18NCBI36
Build 341918,584,711 - 18,592,822NCBI
Celera1918,625,877 - 18,634,029 (+)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1918,286,195 - 18,294,347 (+)NCBIHuRef
CHM1_11918,723,794 - 18,731,960 (+)NCBICHM1_1
T2T-CHM13v2.01918,747,943 - 18,756,107 (+)NCBIT2T-CHM13v2.0
Tmem59l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39870,936,505 - 70,939,998 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl870,936,517 - 70,940,008 (-)EnsemblGRCm39 Ensembl
GRCm38870,483,855 - 70,487,348 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl870,483,867 - 70,487,358 (-)EnsemblGRCm38mm10GRCm38
MGSCv37873,007,766 - 73,011,257 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36873,412,856 - 73,416,347 (-)NCBIMGSCv36mm8
Celera873,040,279 - 73,043,770 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.15NCBI
Tmem59l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555242,981,909 - 2,988,080 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555242,983,699 - 2,988,080 (-)NCBIChiLan1.0ChiLan1.0
TMEM59L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22023,466,005 - 23,479,748 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11922,478,891 - 22,488,150 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01918,089,605 - 18,097,943 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11919,059,627 - 19,068,171 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1919,059,660 - 19,067,669 (+)Ensemblpanpan1.1panPan2
TMEM59L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12044,450,164 - 44,455,983 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2044,450,349 - 44,455,933 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2044,364,940 - 44,370,757 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02044,936,442 - 44,942,263 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2044,795,504 - 44,942,267 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12044,173,818 - 44,179,635 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02044,583,774 - 44,589,594 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02044,859,226 - 44,865,046 (-)NCBIUU_Cfam_GSD_1.0
Tmem59l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118203,130,553 - 203,136,185 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365962,679,227 - 2,685,492 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365962,679,689 - 2,685,323 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM59L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl259,210,792 - 59,223,202 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1259,211,404 - 59,223,017 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2258,965,371 - 58,970,420 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM59L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1617,080,955 - 17,093,524 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl617,080,093 - 17,093,574 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660742,247,652 - 2,255,760 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem59l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249081,766,758 - 1,772,260 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249081,767,673 - 1,772,145 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tmem59l
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:288
Count of miRNA genes:178
Interacting mature miRNAs:193
Transcripts:ENSRNOT00000038139
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
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat

Markers in Region
RH133321  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21618,945,073 - 18,945,286 (+)MAPPERmRatBN7.2
Rnor_6.01620,695,394 - 20,695,606NCBIRnor6.0
Rnor_5.01620,550,873 - 20,551,085UniSTSRnor5.0
RGSC_v3.41619,451,826 - 19,452,038UniSTSRGSC3.4
Celera1619,136,446 - 19,136,658UniSTS
Cytogenetic Map16p14UniSTS


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 7 29 112 63 63 32 18 32 6 148 67 93 34 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000038139   ⟹   ENSRNOP00000029378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,941,658 - 18,945,381 (+)Ensembl
Rnor_6.0 Ensembl1620,691,978 - 20,695,701 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000082319   ⟹   ENSRNOP00000075600
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1618,941,567 - 18,945,381 (+)Ensembl
Rnor_6.0 Ensembl1620,692,032 - 20,695,676 (+)Ensembl
RefSeq Acc Id: NM_001271055   ⟹   NP_001257984
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,975,631 - 18,979,354 (+)NCBI
mRatBN7.21618,941,658 - 18,945,381 (+)NCBI
Rnor_6.01620,691,978 - 20,695,701 (+)NCBI
Rnor_5.01620,547,447 - 20,551,180 (+)NCBI
Celera1619,133,030 - 19,136,753 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252897   ⟹   XP_006252959
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81618,975,217 - 18,979,329 (+)NCBI
mRatBN7.21618,941,370 - 18,945,361 (+)NCBI
Rnor_6.01620,691,956 - 20,695,686 (+)NCBI
Rnor_5.01620,547,447 - 20,551,180 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001257984 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252959 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH89056 (Get FASTA)   NCBI Sequence Viewer  
  EDL90687 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000029378.5
  ENSRNOP00000075600.1
GenBank Protein Q5HZE8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001257984   ⟸   NM_001271055
- Peptide Label: precursor
- UniProtKB: Q5HZE8 (UniProtKB/Swiss-Prot),   A0A0H2UHT4 (UniProtKB/TrEMBL),   A6KA50 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252959   ⟸   XM_006252897
- Peptide Label: isoform X1
- UniProtKB: Q5HZE8 (UniProtKB/Swiss-Prot),   A0A0G2KB04 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075600   ⟸   ENSRNOT00000082319
Ensembl Acc Id: ENSRNOP00000029378   ⟸   ENSRNOT00000038139

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5HZE8-F1-model_v2 AlphaFold Q5HZE8 1-331 view protein structure

Transcriptome

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

Promoters
RGD ID:13700030
Promoter ID:EPDNEW_R10554
Type:multiple initiation site
Name:Tmem59l_1
Description:transmembrane protein 59-like
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_6.01620,692,015 - 20,692,075EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305557 AgrOrtholog
BioCyc Gene G2FUF-11781 BioCyc
Ensembl Genes ENSRNOG00000022432 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038139.7 UniProtKB/TrEMBL
  ENSRNOT00000082319.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7315695 IMAGE-MGC_LOAD
InterPro Uncharacterised_TMEM59 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:306349 UniProtKB/TrEMBL
MGC_CLONE MGC:105747 IMAGE-MGC_LOAD
NCBI Gene 306349 ENTREZGENE
PANTHER PTHR28652 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSMEMBRANE PROTEIN 59-LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam BSMAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tmem59l PhenoGen
RatGTEx ENSRNOG00000022432 RatGTEx
UniProt A0A0G2KB04 ENTREZGENE, UniProtKB/TrEMBL
  A0A0H2UHT4 ENTREZGENE, UniProtKB/TrEMBL
  A6KA50 ENTREZGENE, UniProtKB/TrEMBL
  Q5HZE8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Tmem59l  transmembrane protein 59-like  RGD1305557  similar to Brain specific membrane-anchored protein precursor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1305557  similar to Brain specific membrane-anchored protein precursor  RGD1305557_predicted  similar to Brain specific membrane-anchored protein precursor (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305557_predicted  similar to Brain specific membrane-anchored protein precursor (predicted)  LOC306349_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC306349_predicted  similar to Brain specific membrane-anchored protein precursor (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL