RGD1306474 (similar to RIKEN cDNA 9530003J23) - 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 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   new 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
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. Predicted to be located in extracellular space. Human ortholog(s) of this gene implicated in familial visceral amyloidosis. Orthologous to human LYZ (lysozyme); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; cobalt dichloride.
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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8754,761,063 - 54,772,664 (-)NCBIGRCr8
mRatBN7.2752,875,842 - 52,880,716 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl752,875,842 - 52,880,716 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx754,782,566 - 54,787,436 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0756,985,673 - 56,990,545 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0756,763,554 - 56,768,424 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0760,305,006 - 60,309,878 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl760,305,006 - 60,309,878 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0760,306,988 - 60,311,860 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4756,576,837 - 56,581,709 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1756,598,146 - 56,602,373 (-)NCBI
Celera749,649,679 - 49,654,551 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

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
22 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74725178365728867Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74110969256793354Rat
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)73429328279293282Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat


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
Low 2 9 53 37 18 37 8 9 11 10 8 10 8
Below cutoff 1 4 4 4 1 14 13 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007610   ⟹   ENSRNOP00000007610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Reference Protein Sequences
RefSeq Acc Id: NP_001102216   ⟸   NM_001108746
- Peptide Label: precursor
- UniProtKB: D4A0W2 (UniProtKB/TrEMBL),   A6IGS1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq 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
  ENSRNOT00000007610.5 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