RGD1306474 (similar to RIKEN cDNA 9530003J23) - Rat Genome Database

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Gene: RGD1306474 (similar to RIKEN cDNA 9530003J23) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RGD1306474
Name: similar to RIKEN cDNA 9530003J23
RGD ID: 1306474
Description: Predicted to enable lysozyme activity. Predicted to be involved in defense response to Gram-negative bacterium and defense response to Gram-positive bacterium. Orthologous to human LYZ (lysozyme); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PREDICTED
Previously known as: hypothetical protein LOC362881; LOC362881; lysozyme f1; Lyzf1; uncharacterized protein LOC362881
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8754,761,063 - 54,772,664 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl754,761,749 - 54,766,621 (-)EnsemblGRCr8
mRatBN7.2752,875,842 - 52,880,716 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl752,875,842 - 52,880,716 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx754,782,566 - 54,787,436 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0756,985,673 - 56,990,545 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0756,763,554 - 56,768,424 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0760,305,006 - 60,309,878 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl760,305,006 - 60,309,878 (-)Ensemblrn6Rnor6.0
Rnor_5.0760,306,988 - 60,311,860 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4756,576,837 - 56,581,709 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera749,649,679 - 49,654,551 (-)NCBICelera
RGSC_v3.1756,598,146 - 56,602,373 (-)NCBI
Cytogenetic Map7q22NCBI
JBrowse:




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

Biological Process

Cellular Component

Molecular Function
lysozyme activity  (IBA,IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in RGD1306474
46 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:101
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000007610
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
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72380760668807606Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74511390390113903Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71051708662346019Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72663805771638057Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72417947886817926Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74913799967614020Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)75170064396700643Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)731770293110435881Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73984590284845902Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73299870277998702Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)74968283263890004Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73617876481178764Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74847504993475049Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73617876481178764Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74299622658678836Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72862457565788017Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)749682832115766396Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72154197786817926Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)749682832115766396Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)71049882055498820Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71746044762460447Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)749682832115766396Rat
2303582Gluco53Glucose level QTL 533blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)74860308793603087Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)72005723265057232Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)72718291472182914Rat


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
8 10 16 59 91 90 59 63 59 6 191 101 1 39 15 39 31

Sequence


Ensembl Acc Id: ENSRNOT00000007610   ⟹   ENSRNOP00000007610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl754,761,749 - 54,766,621 (-)Ensembl
mRatBN7.2 Ensembl752,875,842 - 52,880,716 (-)Ensembl
Rnor_6.0 Ensembl760,305,006 - 60,309,878 (-)Ensembl
RefSeq Acc Id: NM_001108746   ⟹   NP_001102216
RefSeq Status: PREDICTED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8754,761,749 - 54,766,621 (-)NCBI
mRatBN7.2752,875,842 - 52,880,716 (-)NCBI
Rnor_6.0760,305,006 - 60,309,878 (-)NCBI
Rnor_5.0760,306,988 - 60,311,860 (-)NCBI
RGSC_v3.4756,576,837 - 56,581,709 (-)RGD
Celera749,649,679 - 49,654,551 (-)RGD
Sequence:
RefSeq Acc Id: XM_063263797   ⟹   XP_063119867
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8754,761,063 - 54,772,664 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001102216 (Get FASTA)   NCBI Sequence Viewer  
  XP_063119867 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CDM98786 (Get FASTA)   NCBI Sequence Viewer  
  EDM16626 (Get FASTA)   NCBI Sequence Viewer  
  EDM16627 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000007610
  ENSRNOP00000007610.4
RefSeq Acc Id: NP_001102216   ⟸   NM_001108746
- Peptide Label: precursor
- UniProtKB: D4A0W2 (UniProtKB/TrEMBL),   A6IGS1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000007610   ⟸   ENSRNOT00000007610
RefSeq Acc Id: XP_063119867   ⟸   XM_063263797
- Peptide Label: isoform X1
Protein Domains
Glycosyl hydrolases family 22 (GH22)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A0W2-F1-model_v2 AlphaFold D4A0W2 1-151 view protein structure

Transcriptome

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

Promoters
RGD ID:13695210
Promoter ID:EPDNEW_R5735
Type:initiation region
Name:RGD1306474_1
Description:similar to RIKEN cDNA 9530003J23
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_6.0760,309,829 - 60,309,889EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306474 AgrOrtholog
BioCyc Gene G2FUF-34010 BioCyc
Ensembl Genes ENSRNOG00000005790 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007610 ENTREZGENE
  ENSRNOT00000007610.6 UniProtKB/TrEMBL
Gene3D-CATH 1.10.530.10 UniProtKB/TrEMBL
InterPro Glyco_hydro_22 UniProtKB/TrEMBL
  Glyco_hydro_22_CS UniProtKB/TrEMBL
  Glyco_hydro_22_lys UniProtKB/TrEMBL
  Lysozyme-like_dom UniProtKB/TrEMBL
KEGG Report rno:362881 UniProtKB/TrEMBL
NCBI Gene 362881 ENTREZGENE
PANTHER 9530003J23RIK PROTEIN UniProtKB/TrEMBL
  PTHR11407 UniProtKB/TrEMBL
Pfam Lys UniProtKB/TrEMBL
PhenoGen RGD1306474 PhenoGen
PRINTS LYSOZYME UniProtKB/TrEMBL
  LYZLACT UniProtKB/TrEMBL
PROSITE LACTALBUMIN_LYSOZYME_1 UniProtKB/TrEMBL
  LACTALBUMIN_LYSOZYME_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005790 RatGTEx
SMART LYZ1 UniProtKB/TrEMBL
Superfamily-SCOP SSF53955 UniProtKB/TrEMBL
UniProt A6IGS1 ENTREZGENE, UniProtKB/TrEMBL
  D4A0W2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 RGD1306474  similar to RIKEN cDNA 9530003J23   RGD1306474_predicted  similar to RIKEN cDNA 9530003J23 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1306474_predicted  similar to RIKEN cDNA 9530003J23 (predicted)  LOC362881_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362881_predicted  similar to RIKEN cDNA 9530003J23 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL