A630001G21Rikl (RIKEN cDNA A630001G21 gene like) - Rat Genome Database

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Gene: A630001G21Rikl (RIKEN cDNA A630001G21 gene like) Rattus norvegicus
Analyze
No known orthologs.
Symbol: A630001G21Rikl (Ensembl: RGD1563917)
Name: RIKEN cDNA A630001G21 gene like (Ensembl:similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa))
RGD ID: 1563917
Description: Predicted to be located in nucleus; INTERACTS WITH cadmium dichloride; copper atom; copper(0).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC501176; nuclear autoantigen Sp-100; RGD1563917; similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa); similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Lysp100b)
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8993,831,074 - 93,853,415 (-)NCBIGRCr8
mRatBN7.2986,381,777 - 86,405,385 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl986,383,201 - 86,405,361 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0992,753,666 - 92,775,830 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl992,753,957 - 92,775,816 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0992,484,422 - 92,506,425 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4984,446,691 - 84,468,821 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera983,805,908 - 83,828,076 (-)NCBICelera
Cytogenetic Map9q35NCBI
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

Cellular Component
nucleus  (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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Variants

.
Variants in A630001G21Rikl
261 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:234
Count of miRNA genes:165
Interacting mature miRNAs:185
Transcripts:ENSRNOT00000029635
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
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)98636963192058970Rat


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 2 11 1
Low 9 30 19 8 19 2 2 74 20 34 10 2
Below cutoff 1 28 25 20 20 6 9 14 5 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029635   ⟹   ENSRNOP00000036936
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl986,383,201 - 86,405,361 (-)Ensembl
Rnor_6.0 Ensembl992,753,957 - 92,775,816 (-)Ensembl
RefSeq Acc Id: XM_056984622   ⟹   XP_056840602
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,831,074 - 93,853,410 (-)NCBI
mRatBN7.2986,381,785 - 86,405,381 (-)NCBI
RefSeq Acc Id: XM_056984623   ⟹   XP_056840603
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,831,074 - 93,853,413 (-)NCBI
mRatBN7.2986,381,777 - 86,405,385 (-)NCBI
RefSeq Acc Id: XM_056984625   ⟹   XP_056840605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,836,637 - 93,853,410 (-)NCBI
mRatBN7.2986,391,341 - 86,405,381 (-)NCBI
RefSeq Acc Id: XM_056984626   ⟹   XP_056840606
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,831,074 - 93,853,410 (-)NCBI
mRatBN7.2986,381,781 - 86,405,381 (-)NCBI
RefSeq Acc Id: XM_056984627   ⟹   XP_056840607
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,831,074 - 93,853,409 (-)NCBI
mRatBN7.2986,381,781 - 86,405,380 (-)NCBI
RefSeq Acc Id: XM_056984628   ⟹   XP_056840608
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,831,074 - 93,853,411 (-)NCBI
mRatBN7.2986,381,781 - 86,405,382 (-)NCBI
RefSeq Acc Id: XM_063268166   ⟹   XP_063124236
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,831,074 - 93,853,415 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000036936   ⟸   ENSRNOT00000029635
RefSeq Acc Id: XP_056840603   ⟸   XM_056984623
- Peptide Label: isoform X2
RefSeq Acc Id: XP_056840608   ⟸   XM_056984628
- Peptide Label: isoform X6
RefSeq Acc Id: XP_056840606   ⟸   XM_056984626
- Peptide Label: isoform X4
RefSeq Acc Id: XP_056840607   ⟸   XM_056984627
- Peptide Label: isoform X5
RefSeq Acc Id: XP_056840602   ⟸   XM_056984622
- Peptide Label: isoform X1
- UniProtKB: D4ACI5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_056840605   ⟸   XM_056984625
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063124236   ⟸   XM_063268166
- Peptide Label: isoform X7
Protein Domains
HSR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACI5-F1-model_v2 AlphaFold D4ACI5 1-177 view protein structure

Transcriptome

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

Promoters
RGD ID:13696819
Promoter ID:EPDNEW_R7340
Type:single initiation site
Name:RGD1563917_1
Description:similar to Nuclear autoantigen Sp-100
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_6.0992,775,786 - 92,775,846EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563917 AgrOrtholog
BioCyc Gene G2FUF-26931 BioCyc
Ensembl Genes ENSRNOG00000017273 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029635.7 UniProtKB/TrEMBL
InterPro Sp100 UniProtKB/TrEMBL
  Sp110/Sp140/Sp140L UniProtKB/TrEMBL
NCBI Gene 501176 ENTREZGENE
PANTHER PTHR46386 UniProtKB/TrEMBL
  RIKEN CDNA A630001G21 GENE UniProtKB/TrEMBL
Pfam Sp100 UniProtKB/TrEMBL
PhenoGen A630001G21Rikl PhenoGen
PROSITE HSR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017273 RatGTEx
UniProt D4ACI5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 A630001G21Rikl  RIKEN cDNA A630001G21 gene like  RGD1563917  similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa)  Symbol and Name Changed 1299863 APPROVED
2008-04-30 RGD1563917  similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa)   RGD1563917_predicted  similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1563917_predicted  similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa) (predicted)    similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Lysp100b) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1563917_predicted  similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Lysp100b) (predicted)  LOC501176  similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Lysp100b)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501176  similar to Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Lysp100b)      Symbol and Name status set to provisional 70820 PROVISIONAL