Rfpl4a (ret finger protein-like 4A) - Rat Genome Database

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Gene: Rfpl4a (ret finger protein-like 4A) Rattus norvegicus
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Symbol: Rfpl4a
Name: ret finger protein-like 4A
RGD ID: 1307409
Description: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response and regulation of gene expression. Predicted to be located in female germ cell nucleus. Predicted to be active in cytoplasm. Orthologous to several human genes including RFPL4A (ret finger protein like 4A); INTERACTS WITH bisphenol A; 2,3,7,8-tetrachlorodibenzodioxine (ortholog); acrylamide (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC292583; ret finger protein-like 4; Rfpl4
RGD Orthologs
Human
Mouse
Bonobo
Dog
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8177,757,811 - 77,764,270 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl177,757,811 - 77,764,270 (+)EnsemblGRCr8
mRatBN7.2168,728,964 - 68,735,423 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl168,728,964 - 68,735,423 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx174,074,050 - 74,080,509 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0182,638,359 - 82,644,818 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0175,786,916 - 75,793,489 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0172,280,117 - 72,286,784 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl172,280,117 - 72,286,576 (+)Ensemblrn6Rnor6.0
Rnor_5.0176,249,814 - 76,256,273 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4167,465,024 - 67,471,483 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera168,383,757 - 68,390,216 (-)NCBICelera
RGSC_v3.1167,544,565 - 67,549,278 (+)NCBI
Cytogenetic Map1q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,IEA)
nucleus  (IEA)

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. 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:12525704  


Genomics

Comparative Map Data
Rfpl4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8177,757,811 - 77,764,270 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl177,757,811 - 77,764,270 (+)EnsemblGRCr8
mRatBN7.2168,728,964 - 68,735,423 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl168,728,964 - 68,735,423 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx174,074,050 - 74,080,509 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0182,638,359 - 82,644,818 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0175,786,916 - 75,793,489 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0172,280,117 - 72,286,784 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl172,280,117 - 72,286,576 (+)Ensemblrn6Rnor6.0
Rnor_5.0176,249,814 - 76,256,273 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4167,465,024 - 67,471,483 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera168,383,757 - 68,390,216 (-)NCBICelera
RGSC_v3.1167,544,565 - 67,549,278 (+)NCBI
Cytogenetic Map1q12NCBI
RFPL4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381955,757,294 - 55,763,421 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1955,759,043 - 55,763,424 (+)Ensemblhg38GRCh38
GRCh371956,270,463 - 56,274,787 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361960,962,192 - 60,966,353 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1953,315,258 - 53,319,293 (+)NCBICelera
Cytogenetic Map19q13.42NCBI
CHM1_11956,264,056 - 56,268,090 (+)NCBICHM1_1
T2T-CHM13v2.01958,856,647 - 58,862,774 (+)NCBIT2T-CHM13v2.0
Rfpl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3975,112,786 - 5,119,910 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl75,112,786 - 5,119,949 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm3875,109,787 - 5,116,911 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl75,109,787 - 5,116,950 (-)Ensemblmm10GRCm38
MGSCv3775,061,389 - 5,068,513 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3674,712,953 - 4,719,983 (-)NCBIMGSCv36mm8
Celera74,851,872 - 4,858,996 (-)NCBICelera
Cytogenetic Map7A1NCBI
cM Map72.96NCBI
LOC100989536
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22062,062,221 - 62,063,595 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11963,852,418 - 63,853,792 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01952,810,147 - 52,813,283 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11961,604,316 - 61,605,636 (+)NCBIPanPan1.1PanPan1.1panPan2
RFPL4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11102,053,068 - 102,056,986 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1102,110,277 - 102,114,195 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01102,706,670 - 102,710,588 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1102,707,976 - 102,710,190 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11102,344,266 - 102,348,184 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01102,056,166 - 102,060,083 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01102,819,213 - 102,823,131 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
RFPL4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1648,347,654 - 48,354,622 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660451,017,096 - 1,021,489 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Rfpl4a
46 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:277
Count of miRNA genes:192
Interacting mature miRNAs:213
Transcripts:ENSRNOT00000021077
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
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)14345783787558729Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)151940904101229020Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14630261591302615Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)14345783787558729Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)14630261591302615Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)14350995288509952Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)14212296887122968Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)14630261591302615Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14345783787558729Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)14630261591302615Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13070837587558729Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16540563796805205Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13456572679565726Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15190920691302615Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)158769992103769992Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)14630261591302615Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)14350995288509952Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)14212296887122968Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)14630261591302615Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)14350995288509952Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
3 5 12 23 15 14 53 91 73 19 12 32 14 6 6

Sequence


Ensembl Acc Id: ENSRNOT00000021077   ⟹   ENSRNOP00000021077
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl177,757,811 - 77,764,270 (+)Ensembl
mRatBN7.2 Ensembl168,728,964 - 68,735,423 (+)Ensembl
Rnor_6.0 Ensembl172,280,117 - 72,286,576 (+)Ensembl
RefSeq Acc Id: NM_001106222   ⟹   NP_001099692
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8177,757,811 - 77,764,270 (+)NCBI
mRatBN7.2168,728,964 - 68,735,423 (+)NCBI
Rnor_6.0172,280,117 - 72,286,576 (+)NCBI
Rnor_5.0176,249,814 - 76,256,273 (-)NCBI
RGSC_v3.4167,465,024 - 67,471,483 (+)RGD
Celera168,383,757 - 68,390,216 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099692 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4ABM4 (Get FASTA)   NCBI Sequence Viewer  
  EDL75888 (Get FASTA)   NCBI Sequence Viewer  
  EDL75889 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021077
  ENSRNOP00000021077.4
RefSeq Acc Id: NP_001099692   ⟸   NM_001106222
- UniProtKB: D4ABM4 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000021077   ⟸   ENSRNOT00000021077
Protein Domains
B30.2/SPRY

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ABM4-F1-model_v2 AlphaFold D4ABM4 1-285 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:1307409 AgrOrtholog
BioCyc Gene G2FUF-60885 BioCyc
Ensembl Genes ENSRNOG00000015743 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000021077 ENTREZGENE
  ENSRNOT00000021077.5 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.920 UniProtKB/Swiss-Prot
  3.30.40.10 UniProtKB/Swiss-Prot
InterPro B30.2/SPRY UniProtKB/Swiss-Prot
  B30.2/SPRY_sf UniProtKB/Swiss-Prot
  Butyrophylin_SPRY UniProtKB/Swiss-Prot
  ConA-like_dom_sf UniProtKB/Swiss-Prot
  PRY UniProtKB/Swiss-Prot
  RDM_domain_RFPL UniProtKB/Swiss-Prot
  SPRY/PRY_RFPL UniProtKB/Swiss-Prot
  SPRY_dom UniProtKB/Swiss-Prot
  TRIM/RBCC UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
KEGG Report rno:292583 UniProtKB/Swiss-Prot
NCBI Gene 292583 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM UniProtKB/Swiss-Prot
Pfam PRY UniProtKB/Swiss-Prot
  RDM UniProtKB/Swiss-Prot
  SPRY UniProtKB/Swiss-Prot
  zf-C3HC4_4 UniProtKB/Swiss-Prot
PhenoGen Rfpl4a PhenoGen
PRINTS BUTYPHLNCDUF UniProtKB/Swiss-Prot
PROSITE B302_SPRY UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000015743 RatGTEx
SMART PRY UniProtKB/Swiss-Prot
  SPRY UniProtKB/Swiss-Prot
Superfamily-SCOP RING/U-box UniProtKB/Swiss-Prot
  SSF49899 UniProtKB/Swiss-Prot
UniProt D4ABM4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Rfpl4a  ret finger protein-like 4A  Rfpl4  ret finger protein-like 4   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Rfpl4  ret finger protein-like 4   Rfpl4_predicted  ret finger protein-like 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rfpl4_predicted  ret finger protein-like 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED