Rtl3 (retrotransposon Gag like 3) - Rat Genome Database

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Gene: Rtl3 (retrotransposon Gag like 3) Rattus norvegicus
Analyze
Symbol: Rtl3
Name: retrotransposon Gag like 3
RGD ID: 1564805
Description: Predicted to enable nucleic acid binding activity and zinc ion binding activity. Orthologous to human RTL3 (retrotransposon Gag like 3); INTERACTS WITH bisphenol A; rotenone; (-)-epigallocatechin 3-gallate (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC317221; retrotransposon Gag-like protein 3; RGD1564805; similar to Hypothetical protein D430021I08; Zcchc5; zinc finger CCHC domain-containing protein 5; zinc finger CCHC-type containing 5; zinc finger, CCHC domain containing 5
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X76,020,183 - 76,023,848 (-)NCBIGRCr8
mRatBN7.2X71,947,343 - 71,951,008 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX71,948,253 - 71,950,121 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX73,451,623 - 73,455,278 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X76,963,512 - 76,967,177 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X74,531,782 - 74,535,437 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X77,953,574 - 77,957,261 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX77,954,484 - 77,956,352 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X78,149,884 - 78,153,576 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X95,091,549 - 95,093,417 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX73,247,794 - 73,251,481 (-)NCBICelera
Cytogenetic MapXq22NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Rtl3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X76,020,183 - 76,023,848 (-)NCBIGRCr8
mRatBN7.2X71,947,343 - 71,951,008 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX71,948,253 - 71,950,121 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX73,451,623 - 73,455,278 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X76,963,512 - 76,967,177 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X74,531,782 - 74,535,437 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X77,953,574 - 77,957,261 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX77,954,484 - 77,956,352 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X78,149,884 - 78,153,576 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X95,091,549 - 95,093,417 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX73,247,794 - 73,251,481 (-)NCBICelera
Cytogenetic MapXq22NCBI
RTL3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X78,656,068 - 78,659,328 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX78,656,068 - 78,659,328 (-)EnsemblGRCh38hg38GRCh38
GRCh37X77,911,565 - 77,914,825 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X77,798,222 - 77,801,481 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X77,717,710 - 77,720,970NCBI
CeleraX78,152,142 - 78,155,399 (-)NCBICelera
Cytogenetic MapXq21.1NCBI
HuRefX71,491,595 - 71,494,852 (-)NCBIHuRef
CHM1_1X77,804,581 - 77,807,838 (-)NCBICHM1_1
T2T-CHM13v2.0X77,092,886 - 77,096,144 (-)NCBIT2T-CHM13v2.0
Rtl3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X105,880,688 - 105,884,145 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX105,880,688 - 105,884,250 (-)EnsemblGRCm39 Ensembl
GRCm38X106,837,082 - 106,840,539 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX106,837,082 - 106,840,644 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X104,032,421 - 104,035,982 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X103,039,801 - 103,043,362 (-)NCBIMGSCv36mm8
CeleraX93,683,649 - 93,687,210 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.37NCBI
RTL3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X78,196,617 - 78,198,044 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X78,200,228 - 78,201,655 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X67,797,133 - 67,798,613 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X77,906,629 - 77,909,100 (-)NCBIpanpan1.1PanPan1.1panPan2
RTL3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X60,668,592 - 60,670,164 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX51,680,593 - 51,682,165 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X61,921,600 - 61,923,172 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X59,612,513 - 59,614,085 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X61,222,822 - 61,224,394 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X60,810,866 - 60,812,438 (-)NCBIUU_Cfam_GSD_1.0
Rtl3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X54,409,680 - 54,413,340 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936547731,006 - 732,745 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936547730,937 - 732,945 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTL3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X62,725,700 - 62,727,236 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X71,813,713 - 71,815,249 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RTL3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X67,686,831 - 67,690,932 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606713,759,308 - 13,760,756 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Rtl3
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:84
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000003296
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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat


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 4 9
Low 1 37 28 20 6 20 4 4 7 12 20 6 4
Below cutoff 2 2 12 8 3 8 4 7 36 6 4 3 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003296   ⟹   ENSRNOP00000003296
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX71,948,253 - 71,950,121 (-)Ensembl
Rnor_6.0 EnsemblX77,954,484 - 77,956,352 (-)Ensembl
RefSeq Acc Id: NM_001401152   ⟹   NP_001388081
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X76,020,183 - 76,023,848 (-)NCBI
mRatBN7.2X71,947,343 - 71,951,008 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001388081 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07124 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003296.6
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000003296   ⟸   ENSRNOT00000003296
RefSeq Acc Id: NP_001388081   ⟸   NM_001401152
- UniProtKB: A6IV56 (UniProtKB/TrEMBL),   D3ZH95 (UniProtKB/TrEMBL)
Protein Domains
CCHC-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZH95-F1-model_v2 AlphaFold D3ZH95 1-556 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564805 AgrOrtholog
BioCyc Gene G2FUF-1903 BioCyc
Ensembl Genes ENSRNOG00000002429 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003296.6 UniProtKB/TrEMBL
Gene3D-CATH Zinc finger, CCHC-type UniProtKB/TrEMBL
InterPro DUF4939 UniProtKB/TrEMBL
  LDOC1-rel UniProtKB/TrEMBL
  Znf_CCHC UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/TrEMBL
KEGG Report rno:317221 UniProtKB/TrEMBL
NCBI Gene 317221 ENTREZGENE
PANTHER PTHR15503 UniProtKB/TrEMBL
  RETROTRANSPOSON GAG-LIKE PROTEIN 3 UniProtKB/TrEMBL
Pfam DUF4939 UniProtKB/TrEMBL
  zf-CCHC UniProtKB/TrEMBL
PhenoGen Rtl3 PhenoGen
PROSITE ZF_CCHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002429 RatGTEx
SMART ZnF_C2HC UniProtKB/TrEMBL
Superfamily-SCOP SSF57756 UniProtKB/TrEMBL
UniProt A6IV56 ENTREZGENE, UniProtKB/TrEMBL
  D3ZH95 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-29 Rtl3  retrotransposon Gag like 3  Zcchc5  zinc finger CCHC-type containing 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-17 Zcchc5  zinc finger CCHC-type containing 5  Zcchc5  zinc finger, CCHC domain containing 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Zcchc5  zinc finger, CCHC domain containing 5   Zcchc5_predicted  zinc finger, CCHC domain containing 5 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Zcchc5_predicted  zinc finger, CCHC domain containing 5 (predicted)  RGD1564805_predicted  similar to Hypothetical protein D430021I08 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1564805_predicted  similar to Hypothetical protein D430021I08 (predicted)  LOC317221  similar to Hypothetical protein D430021I08  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317221  similar to Hypothetical protein D430021I08      Symbol and Name status set to provisional 70820 PROVISIONAL