Rpl39l1 (ribosomal protein L39 like 1) - Rat Genome Database

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Gene: Rpl39l1 (ribosomal protein L39 like 1) Rattus norvegicus
Analyze
Symbol: Rpl39l1
Name: ribosomal protein L39 like 1
RGD ID: 1561345
Description: Predicted to be a structural constituent of ribosome. Predicted to be involved in cytoplasmic translation and spermatogenesis. Predicted to be located in cytoplasm and ribosome. Predicted to be part of cytosolic large ribosomal subunit. Orthologous to human RPL39L (ribosomal protein L39 like); INTERACTS WITH 1,2-dimethylhydrazine; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC497860; MGC125234; ribosomal protein L39-like; ribosomal protein L39-like protein; Rpl39l; similar to RIKEN cDNA 4930517K11
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,962,506 - 5,966,621 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl105,962,515 - 5,966,621 (-)EnsemblGRCr8
mRatBN7.2105,455,712 - 5,459,828 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl105,454,559 - 5,462,029 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1010,151,694 - 10,155,820 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,673,153 - 9,677,269 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0105,311,187 - 5,315,326 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,529,580 - 5,533,695 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,529,589 - 5,533,695 (-)Ensemblrn6Rnor6.0
Rnor_5.0104,350,262 - 4,354,377 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4105,409,437 - 5,413,552 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera104,471,705 - 4,475,820 (-)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cytoplasmic translation  (IBA,IEA,ISO)
spermatogenesis  (IBA,IEA,ISO)
translation  (IEA)

Cellular Component

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:12490704  


Genomics

Comparative Map Data
Rpl39l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,962,506 - 5,966,621 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl105,962,515 - 5,966,621 (-)EnsemblGRCr8
mRatBN7.2105,455,712 - 5,459,828 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl105,454,559 - 5,462,029 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1010,151,694 - 10,155,820 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,673,153 - 9,677,269 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0105,311,187 - 5,315,326 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,529,580 - 5,533,695 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,529,589 - 5,533,695 (-)Ensemblrn6Rnor6.0
Rnor_5.0104,350,262 - 4,354,377 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4105,409,437 - 5,413,552 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera104,471,705 - 4,475,820 (-)NCBICelera
Cytogenetic Map10q11NCBI
RPL39L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383187,120,948 - 187,139,496 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3187,120,927 - 187,180,972 (-)Ensemblhg38GRCh38
GRCh373186,838,736 - 186,857,284 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363188,321,435 - 188,339,957 (-)NCBIBuild 36Build 36hg18NCBI36
Build 343188,321,442 - 188,339,965NCBI
Celera3185,270,573 - 185,289,095 (-)NCBICelera
Cytogenetic Map3q27.3NCBI
HuRef3184,243,217 - 184,261,742 (-)NCBIHuRef
CHM1_13186,802,108 - 186,820,629 (-)NCBICHM1_1
T2T-CHM13v2.03189,938,378 - 189,956,928 (-)NCBIT2T-CHM13v2.0
Rpl39l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39169,988,061 - 9,992,775 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl169,988,090 - 9,992,775 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381610,170,197 - 10,174,911 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1610,170,226 - 10,174,911 (+)Ensemblmm10GRCm38
MGSCv371610,170,321 - 10,175,004 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361610,083,806 - 10,088,489 (+)NCBIMGSCv36mm8
Celera1610,803,453 - 10,808,136 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map165.49NCBI
RPL39L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22184,990,800 - 185,009,429 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13184,995,517 - 185,014,111 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03184,146,722 - 184,165,326 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13192,612,140 - 192,630,507 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3192,612,337 - 192,612,492 (-)EnsemblpanPan2panpan1.1
LOC100682542
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11049,680,765 - 49,681,175 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1049,535,774 - 49,536,185 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01050,554,149 - 50,554,547 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11050,261,380 - 50,261,791 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01050,548,040 - 50,548,451 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01050,735,942 - 50,736,353 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC100525679
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX98,178,150 - 98,181,332 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1214,814,759 - 14,815,155 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2216,026,697 - 16,027,096 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RPL39L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1581,390,733 - 81,390,885 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604154,880,086 - 54,899,943 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Rpl39l1
60 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:76
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000051564
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
15 11 61 136 79 78 51 18 51 5 224 103 11 115 47 74 27 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000051564   ⟹   ENSRNOP00000040295
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,455,245 - 5,462,029 (-)Ensembl
Rnor_6.0 Ensembl105,529,589 - 5,533,695 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105843   ⟹   ENSRNOP00000095440
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,454,559 - 5,459,994 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118208   ⟹   ENSRNOP00000091729
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,455,195 - 5,460,501 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000135412   ⟹   ENSRNOP00000111248
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl105,962,515 - 5,966,621 (-)Ensembl
RefSeq Acc Id: NM_001195471   ⟹   NP_001182400
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,962,506 - 5,966,621 (-)NCBI
mRatBN7.2105,455,712 - 5,459,828 (-)NCBI
Rnor_6.0105,529,580 - 5,533,695 (-)NCBI
Rnor_5.0104,350,262 - 4,354,377 (-)NCBI
Celera104,471,705 - 4,475,820 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001182400 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI03491 (Get FASTA)   NCBI Sequence Viewer  
  EDL96232 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000111248
  ENSRNOP00000111248.1
RefSeq Acc Id: NP_001182400   ⟸   NM_001195471
- UniProtKB: Q3ZB89 (UniProtKB/TrEMBL),   A0A8I6ATH3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000040295   ⟸   ENSRNOT00000051564
Ensembl Acc Id: ENSRNOP00000091729   ⟸   ENSRNOT00000118208
Ensembl Acc Id: ENSRNOP00000095440   ⟸   ENSRNOT00000105843
Ensembl Acc Id: ENSRNOP00000111248   ⟸   ENSRNOT00000135412

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3ZB89-F1-model_v2 AlphaFold Q3ZB89 1-51 view protein structure

Transcriptome

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

Promoters
RGD ID:13696948
Promoter ID:EPDNEW_R7473
Type:multiple initiation site
Name:Rpl39l_1
Description:ribosomal protein L39-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_6.0105,533,716 - 5,533,776EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561345 AgrOrtholog
BioCyc Gene G2FUF-26125 BioCyc
Ensembl Genes ENSRNOG00000032300 Ensembl
  ENSRNOG00000089495 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000135412 ENTREZGENE
  ENSRNOT00000135412.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1620.10 UniProtKB/TrEMBL
InterPro Ribosomal_L39 UniProtKB/TrEMBL
  Ribosomal_L39_CS UniProtKB/TrEMBL
  Ribosomal_L39e_dom UniProtKB/TrEMBL
KEGG Report rno:497860 UniProtKB/TrEMBL
NCBI Gene 497860 ENTREZGENE
PANTHER 60S RIBOSOMAL PROTEIN L39-LIKE UniProtKB/TrEMBL
  RIBOSOMAL PROTEIN L39E UniProtKB/TrEMBL
Pfam Ribosomal_L39 UniProtKB/TrEMBL
PhenoGen Rpl39l1 PhenoGen
PROSITE RIBOSOMAL_L39E UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032300 RatGTEx
  ENSRNOG00000089495 RatGTEx
Superfamily-SCOP Ribosomal_L39 UniProtKB/TrEMBL
UniProt A0A8I6ATH3 ENTREZGENE, UniProtKB/TrEMBL
  Q3ZB89 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-07-21 Rpl39l1  ribosomal protein L39 like 1  Rpl39l  ribosomal protein L39-like  Name and Symbol changed 629549 APPROVED
2012-09-18 Rpl39l  ribosomal protein L39-like  LOC497860  similar to RIKEN cDNA 4930517K11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC497860  similar to RIKEN cDNA 4930517K11      Symbol and Name status set to provisional 70820 PROVISIONAL