Pum3l1 (pumilio RNA-binding family member 3 like 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Pum3l1 (pumilio RNA-binding family member 3 like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Pum3l1
Name: pumilio RNA-binding family member 3 like 1
RGD ID: 1308750
Description: Predicted to enable mRNA binding activity. Predicted to be involved in regulation of translation. Predicted to be active in nucleolus. Orthologous to human PUM3 (pumilio RNA binding family member 3); INTERACTS WITH (+)-schisandrin B; 4,4'-sulfonyldiphenol; aconitine.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100912029; LOC294066; pumilio domain-containing protein KIAA0020 homolog; pumilio homolog 3-like; RGD1308750; similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X154,615,637 - 154,617,736 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX154,615,648 - 154,617,733 (-)EnsemblGRCr8
mRatBN7.2X149,570,869 - 149,572,962 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX149,570,858 - 149,572,961 (-)EnsemblmRatBN7.2
Rnor_6.01670,068,390 - 70,070,486 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1670,068,378 - 70,070,470 (+)Ensemblrn6Rnor6.0
Rnor_5.01669,738,463 - 69,740,558 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X157,318,025 - 157,319,968 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
RGSC_v3.1X157,391,457 - 157,404,646 (-)NCBI
Cytogenetic MapXq37NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IEA)
nucleolus  (IBA,IEA)
nucleoplasm  (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 GOA human gene data--August 2006 GOA data from the GO Consortium
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:121
Count of miRNA genes:76
Interacting mature miRNAs:77
Transcripts:ENSRNOT00000073254, ENSRNOT00000074036
Prediction methods:Microtar, Miranda, Rnahybrid
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
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118973754157758123Rat


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
16 12 67 161 87 86 55 81 55 6 333 181 11 140 73 90 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000073254   ⟹   ENSRNOP00000064504
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX154,615,648 - 154,617,733 (-)Ensembl
mRatBN7.2 EnsemblX149,570,858 - 149,572,961 (-)Ensembl
Rnor_6.0 Ensembl1670,068,378 - 70,070,470 (+)Ensembl
RefSeq Acc Id: XM_039100243   ⟹   XP_038956171
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X154,615,637 - 154,617,736 (-)NCBI
mRatBN7.2X149,570,869 - 149,572,962 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038956171 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034834.4
  ENSRNOP00000064504
  ENSRNOP00000064504.1
Ensembl Acc Id: ENSRNOP00000064504   ⟸   ENSRNOT00000073254
RefSeq Acc Id: XP_038956171   ⟸   XM_039100243
- UniProtKB: M0R548 (UniProtKB/TrEMBL),   A0A8L2QIX0 (UniProtKB/TrEMBL)
Protein Domains
PUM-HD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R548-F1-model_v2 AlphaFold M0R548 1-647 view protein structure

Transcriptome

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

Promoters
RGD ID:13700164
Promoter ID:EPDNEW_R10682
Type:multiple initiation site
Name:RGD1308750_1
Description:similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357expressed
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_6.01670,068,385 - 70,068,445EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308750 AgrOrtholog
BioCyc Gene G2FUF-718 BioCyc
Ensembl Genes ENSRNOG00000012574 UniProtKB/TrEMBL
  ENSRNOG00000048356 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033724.6 UniProtKB/TrEMBL
  ENSRNOT00000073254 ENTREZGENE
  ENSRNOT00000073254.4 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  CPL_dom UniProtKB/TrEMBL
  PUM-HD UniProtKB/TrEMBL
  PUM3 UniProtKB/TrEMBL
  Pumilio_RNA-bd_rpt UniProtKB/TrEMBL
NCBI Gene 294066 ENTREZGENE
PANTHER PTHR13389 UniProtKB/TrEMBL
  PUMILIO HOMOLOG 3 UniProtKB/TrEMBL
Pfam CPL UniProtKB/TrEMBL
PhenoGen Pum3l1 PhenoGen
PROSITE PUM UniProtKB/TrEMBL
  PUM_HD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012574 RatGTEx
  ENSRNOG00000048356 RatGTEx
SMART Pumilio UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
UniProt A0A8L2QIX0 ENTREZGENE, UniProtKB/TrEMBL
  M0R548 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Pum3l1  pumilio RNA-binding family member 3 like 1  RGD1308750  similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed  Symbol and Name Changed 1299863 APPROVED
2021-03-09 RGD1308750  similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed  LOC100912029  pumilio domain-containing protein KIAA0020 homolog  Data merged from RGD:6489468 737654 PROVISIONAL
2013-05-24 RGD1308750  similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed  LOC683670  similar to D19Bwg1357e protein  Data merged from RGD:1584482 1643240 APPROVED
2012-07-05 LOC100912029  pumilio domain-containing protein KIAA0020 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1308750  similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed   RGD1308750_predicted  similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-19 LOC683670  similar to D19Bwg1357e protein      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1308750_predicted  similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed (predicted)  LOC294066_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC294066_predicted  similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL