2610008E11Rikl (RIKEN cDNA 2610008E11 gene like) - Rat Genome Database

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Gene: 2610008E11Rikl (RIKEN cDNA 2610008E11 gene like) Rattus norvegicus
Analyze
No known orthologs.
Symbol: 2610008E11Rikl (Ensembl: LOC691170)
Name: RIKEN cDNA 2610008E11 gene like (Ensembl:similar to zinc finger protein 84 (HPF2))
RGD ID: 1587418
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC691170; similar to zinc finger protein 84 (HPF2); zinc finger protein 39-like; zinc finger protein 883-like
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8711,080,766 - 11,102,013 (+)NCBIGRCr8
mRatBN7.2710,430,177 - 10,451,419 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl710,430,206 - 10,451,406 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0713,318,520 - 13,339,755 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl713,318,533 - 13,337,858 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0713,514,582 - 13,536,060 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,956,516 - 11,975,595 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera78,575,509 - 8,597,078 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)

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

Genomics

Variants

.
Variants in 2610008E11Rikl
144 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:99
Interacting mature miRNAs:104
Transcripts:ENSRNOT00000034545
Prediction methods:Microtar, 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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat

Markers in Region
BE106376  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2710,449,591 - 10,449,743 (+)MAPPERmRatBN7.2
Rnor_6.0713,337,932 - 13,338,083NCBIRnor6.0
Rnor_5.0713,534,237 - 13,534,388UniSTSRnor5.0
RGSC_v3.4711,975,867 - 11,976,018UniSTSRGSC3.4
Celera78,595,255 - 8,595,406UniSTS
RH 3.4 Map752.0UniSTS
Cytogenetic Map7q11UniSTS
BF406083  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2710,449,389 - 10,449,581 (+)MAPPERmRatBN7.2
Rnor_6.0713,337,730 - 13,337,921NCBIRnor6.0
Rnor_5.0713,534,035 - 13,534,226UniSTSRnor5.0
RGSC_v3.4711,975,665 - 11,975,856UniSTSRGSC3.4
Celera78,595,053 - 8,595,244UniSTS
RH 3.4 Map750.8UniSTS
Cytogenetic Map7q11UniSTS
RH138941  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2710,451,126 - 10,451,341 (+)MAPPERmRatBN7.2
Rnor_6.0713,339,467 - 13,339,681NCBIRnor6.0
Rnor_5.0713,535,772 - 13,535,986UniSTSRnor5.0
RGSC_v3.4711,977,402 - 11,977,616UniSTSRGSC3.4
Celera78,596,790 - 8,597,004UniSTS
RH 3.4 Map753.9UniSTS
Cytogenetic Map7q11UniSTS


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 30 25 9 18 9 8 8 73 28 34 11 8
Low 3 13 32 32 1 32 3 1 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034545   ⟹   ENSRNOP00000034574
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl710,430,206 - 10,451,406 (+)Ensembl
Rnor_6.0 Ensembl713,318,533 - 13,337,858 (+)Ensembl
RefSeq Acc Id: XM_001077082   ⟹   XP_001077082
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8711,080,768 - 11,102,013 (+)NCBI
mRatBN7.2710,430,177 - 10,451,419 (+)NCBI
Rnor_6.0713,318,520 - 13,339,755 (+)NCBI
Rnor_5.0713,514,582 - 13,536,060 (+)NCBI
RGSC_v3.4711,956,516 - 11,975,595 (+)RGD
Sequence:
RefSeq Acc Id: XM_039080027   ⟹   XP_038935955
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8711,085,213 - 11,102,013 (+)NCBI
mRatBN7.2710,434,618 - 10,451,419 (+)NCBI
RefSeq Acc Id: XM_063264397   ⟹   XP_063120467
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8711,080,766 - 11,102,013 (+)NCBI
Protein Sequences
Protein RefSeqs XP_001077082 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935955 (Get FASTA)   NCBI Sequence Viewer  
  XP_063120467 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034574
  ENSRNOP00000034574.7
Reference Protein Sequences
RefSeq Acc Id: XP_001077082   ⟸   XM_001077082
- Peptide Label: isoform X1
- UniProtKB: D3ZKP7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000034574   ⟸   ENSRNOT00000034545
RefSeq Acc Id: XP_038935955   ⟸   XM_039080027
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063120467   ⟸   XM_063264397
- Peptide Label: isoform X2
Protein Domains
C2H2-type   KRAB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKP7-F1-model_v2 AlphaFold D3ZKP7 1-669 view protein structure

Transcriptome

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

Promoters
RGD ID:13695066
Promoter ID:EPDNEW_R5586
Type:multiple initiation site
Name:LOC691170_1
Description:similar to zinc finger protein 84
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_6.0713,318,559 - 13,318,619EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587418 AgrOrtholog
BioCyc Gene G2FUF-34863 BioCyc
Ensembl Genes ENSRNOG00000022871 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034545.7 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.140 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro KRAB_dom_sf UniProtKB/TrEMBL
  Krueppel-associated_box UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
NCBI Gene 691170 ENTREZGENE
PANTHER FINGER PUTATIVE TRANSCRIPTION FACTOR FAMILY-RELATED UniProtKB/TrEMBL
  ZINC FINGER PROTEIN 768 UniProtKB/TrEMBL
Pfam KRAB UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
PhenoGen 2610008E11Rikl PhenoGen
PROSITE KRAB UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022871 RatGTEx
SMART KRAB UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP Krueppel-associated_box UniProtKB/TrEMBL
  SSF57667 UniProtKB/TrEMBL
UniProt D3ZKP7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 2610008E11Rikl  RIKEN cDNA 2610008E11 gene like  LOC691170  similar to zinc finger protein 84 (HPF2)  Symbol and Name Changed 1299863 APPROVED
2013-05-24 LOC691170  similar to zinc finger protein 84 (HPF2)  LOC687219  similar to zinc finger protein 84 (HPF2)  Data merged from RGD:1587759 1643240 APPROVED
2006-11-19 LOC691170  similar to zinc finger protein 84 (HPF2)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687219  similar to zinc finger protein 84 (HPF2)      Symbol and Name status set to provisional 70820 PROVISIONAL