Xlr4a (X-linked lymphocyte-regulated 4A) - 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 QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap)  (beta) 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) Overgo Probe Designer
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease COVID-19 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   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) 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 Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Xlr4a (X-linked lymphocyte-regulated 4A) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Xlr4a
Name: X-linked lymphocyte-regulated 4A
RGD ID: 1565442
Description: Predicted to be involved in meiotic cell cycle and spermatid development. Predicted to be active in synaptonemal complex. Orthologous to human FAM9A (family with sequence similarity 9 member A).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC293841; RGD1565442; similar to X-linked lymphocyte regulated gene 4; X-linked lymphocyte-regulated protein 3A
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X150,916,647 - 150,925,201 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX150,916,932 - 150,929,786 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X153,072,965 - 153,081,324 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX153,072,908 - 153,080,915 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01148,801,991 - 148,816,935 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,068,518 - 159,075,735 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1131,880,644 - 131,898,301 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Xlr4a
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:18
Count of miRNA genes:18
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000023158
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
BI288653  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X150,916,925 - 150,917,222 (+)MAPPERmRatBN7.2
Rnor_6.0X153,073,088 - 153,073,384NCBIRnor6.0
Rnor_5.01148,802,113 - 148,802,409UniSTSRnor5.0
RGSC_v3.4X159,068,797 - 159,069,093UniSTSRGSC3.4
Celera1131,880,923 - 131,881,219UniSTS
Cytogenetic MapXq37UniSTS


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 12
Low 2 15 13 3 13 61 4 26 6
Below cutoff 1 41 40 26 15 26 8 10 13 30 3 5 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000091365   ⟹   ENSRNOP00000069444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX150,916,932 - 150,929,786 (-)Ensembl
Rnor_6.0 EnsemblX153,072,908 - 153,080,915 (-)Ensembl
RefSeq Acc Id: XM_006229523   ⟹   XP_006229585
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X150,916,647 - 150,925,200 (-)NCBI
Rnor_6.0X153,072,965 - 153,081,324 (-)NCBI
Rnor_5.01148,801,991 - 148,816,935 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229524   ⟹   XP_006229586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X150,916,647 - 150,925,200 (-)NCBI
Rnor_6.0X153,072,965 - 153,081,324 (-)NCBI
Rnor_5.01148,801,991 - 148,816,935 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229527   ⟹   XP_006229589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X150,916,647 - 150,925,200 (-)NCBI
Rnor_6.0X153,072,965 - 153,081,324 (-)NCBI
Rnor_5.01148,801,991 - 148,816,935 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229528   ⟹   XP_006229590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X150,916,647 - 150,925,201 (-)NCBI
Rnor_6.0X153,072,965 - 153,081,324 (-)NCBI
Rnor_5.01148,801,991 - 148,816,935 (-)NCBI
Sequence:
RefSeq Acc Id: XM_219738   ⟹   XP_219738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X150,916,647 - 150,924,534 (-)NCBI
Rnor_6.0X153,072,965 - 153,080,700 (-)NCBI
Rnor_5.01148,801,991 - 148,816,935 (-)NCBI
RGSC_v3.4X159,068,518 - 159,075,735 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_219738   ⟸   XM_219738
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006229590   ⟸   XM_006229528
- Peptide Label: isoform X2
- UniProtKB: D4A7L7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229585   ⟸   XM_006229523
- Peptide Label: isoform X2
- UniProtKB: D4A7L7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229586   ⟸   XM_006229524
- Peptide Label: isoform X2
- UniProtKB: D4A7L7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229589   ⟸   XM_006229527
- Peptide Label: isoform X2
- UniProtKB: D4A7L7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069444   ⟸   ENSRNOT00000091365
Protein Domains
XLR/SYCP3/FAM9

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7L7-F1-model_v2 AlphaFold D4A7L7 1-215 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:1565442 AgrOrtholog
BioCyc Gene G2FUF-688 BioCyc
Ensembl Genes ENSRNOG00000055822 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069444 ENTREZGENE
  ENSRNOP00000069444.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000091365 ENTREZGENE
  ENSRNOT00000091365.2 UniProtKB/TrEMBL
InterPro Cor1/Xlr/Xmr UniProtKB/TrEMBL
KEGG Report rno:293841 UniProtKB/TrEMBL
NCBI Gene 293841 ENTREZGENE
PANTHER X-LINKED LYMPHOCYTE REGULATED GENE 4-RELATED UniProtKB/TrEMBL
  XLR/SCP3/FAM9 UniProtKB/TrEMBL
Pfam Cor1 UniProtKB/TrEMBL
PhenoGen Xlr4a PhenoGen
UniProt D4A7L7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Xlr4a  X-linked lymphocyte-regulated 4A  RGD1565442_predicted  similar to X-linked lymphocyte regulated gene 4 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565442_predicted  similar to X-linked lymphocyte regulated gene 4 (predicted)  LOC293841  similar to X-linked lymphocyte regulated gene 4  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC293841  similar to X-linked lymphocyte regulated gene 4      Symbol and Name status set to provisional 70820 PROVISIONAL