Xlr4a (X-linked lymphocyte-regulated 4A) - Rat Genome Database

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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 FAM9B (family with sequence similarity 9 member B); INTERACTS WITH bisphenol A; fenvalerate; Monobutylphthalate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC293841; RGD1565442; similar to X-linked lymphocyte regulated gene 4; X-linked lymphocyte-regulated protein 3A
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X155,958,900 - 155,967,302 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX155,958,756 - 155,967,276 (-)EnsemblGRCr8
mRatBN7.2X150,916,647 - 150,925,201 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX150,916,932 - 150,929,786 (-)EnsemblmRatBN7.2
Rnor_6.0X153,072,965 - 153,081,324 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX153,072,908 - 153,080,915 (-)Ensemblrn6Rnor6.0
Rnor_5.01148,801,991 - 148,816,935 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X159,068,518 - 159,075,735 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1131,880,644 - 131,898,301 (-)NCBICelera
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

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

miRNA Target Status (No longer updated)

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 (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

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

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 10 60 155 86 86 55 71 55 6 301 158 7 135 64 77 31 15 15

Sequence


Ensembl Acc Id: ENSRNOT00000091365   ⟹   ENSRNOP00000069444
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX155,958,756 - 155,967,276 (-)Ensembl
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X155,958,900 - 155,967,300 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X155,958,900 - 155,967,301 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X155,958,900 - 155,967,302 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X155,958,900 - 155,967,302 (-)NCBI
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:
RefSeq Acc Id: XP_219738   ⟸   XM_219738
- Peptide Label: isoform X2
- UniProtKB: D4A7L7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229590   ⟸   XM_006229528
- Peptide Label: isoform X1
- UniProtKB: D4A7L7 (UniProtKB/TrEMBL),   A6KSZ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229585   ⟸   XM_006229523
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006229586   ⟸   XM_006229524
- Peptide Label: isoform X1
- Sequence:
Ensembl 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 Transcript ENSRNOT00000091365 ENTREZGENE
  ENSRNOT00000091365.3 UniProtKB/TrEMBL
InterPro Cor1/Xlr/Xmr UniProtKB/TrEMBL
  XLR/SYCP3 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
RatGTEx ENSRNOG00000055822 RatGTEx
UniProt A6KSZ1 ENTREZGENE, UniProtKB/TrEMBL
  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