 Gene-Chemical Interaction Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene Ontology AnnotationsMolecular Pathway Annotations |
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Analyze GeneStrainQTL List |
 Gene Annotator (Functional Annotation) unavailable |
 Gene Annotator (Annotation Distribution) unavailable |
 Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable |
Gene Annotator (Functional Annotation) |
Gene Annotator (Annotation Distribution) |
Variant Visualizer (Genomic Variants) |
 InterViewer (Protein-Protein Interactions) unavailable |
 Gviewer (Genome Viewer) unavailable |
 Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable |
InterViewer (Protein-Protein Interactions) |
GViewer (Genome Viewer) |
Variant Visualizer (Damaging Variants) |
 Gene Annotator (Annotation Comparison) unavailable |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
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MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Gene Ontology AnnotationsMolecular Pathway AnnotationsDisease Annotations
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Gene-Chemical Interaction Annotations
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Gene Ontology AnnotationsBiological Process
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Cellular Component
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Molecular Function
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Molecular Pathway AnnotationsReferences - curated| 1. | Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27. |
| 2. | RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations |
| 3. | RGD automated import pipeline for gene-chemical interactions |
| 4. | RGD comprehensive gene curation |
| 5. | Sloan KE, etal., RNA. 2014 Apr;20(4):540-50. doi: 10.1261/rna.043471.113. Epub 2014 Feb 18. |
References - uncuratedGenomics
Comparative Map Data| Fcf1 (Rattus norvegicus - Norway rat) |
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| FCF1 (Homo sapiens - human) |
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| Fcf1 (Mus musculus - house mouse) |
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| Fcf1 (Chinchilla lanigera - long-tailed chinchilla) |
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| FCF1 (Pan paniscus - bonobo/pygmy chimpanzee) |
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| FCF1 (Canis lupus familiaris - dog) |
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| Fcf1 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| FCF1 (Sus scrofa - pig) |
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Position Markers| RH127356 |
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QTLs in Region (Rnor_6.0)| The following QTLs overlap with this region. |  | Full Report | | CSV | | TAB | | Printer | | Gviewer |
miRNA Target Status
Predicted Target Of
| 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. |
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Expression
RNA-SEQ ExpressionHigh: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM
| testis | heart | brain | ovary | uterus | skeletal muscle tissue | colon | gastrocnemius | forebrain | hindbrain | lung | spleen | liver | kidney | adrenal gland | thymus | |
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| High | ||||||||||||||||
| Medium | 22 | 43 | 23 | 15 | 4 | 3 | 3 | 8 | 26 | 25 | 11 | 11 | 41 | 35 | 8 | 8 |
| Low | ||||||||||||||||
| Below cutoff |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | NM_001044235 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| GenBank Nucleotide | AABR07065089 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AAHX01045600 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AB256045 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AM258960 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH473982 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| FQ222819 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | NM_001044235 ⟹ NP_001037700 | ||||||||||||||||||||||||
| RefSeq Status: | PROVISIONAL | ||||||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||||||
| Position: |
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| Sequence: |
GAAACAGGAGTGCGTCGAGAACATGGGGAAGCAAAAGAAAACAAGGAAATATGCGACTATGAAGhide sequence |
Protein Sequences| Protein RefSeqs | NP_001037700 | (Get FASTA) | NCBI Sequence Viewer |
| GenBank Protein | BAE94255 | (Get FASTA) | NCBI Sequence Viewer |
| CAJ88856 | (Get FASTA) | NCBI Sequence Viewer | |
| EDL81537 | (Get FASTA) | NCBI Sequence Viewer | |
| EDL81538 | (Get FASTA) | NCBI Sequence Viewer | |
| EDL81539 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | NP_001037700 ⟸ NM_001044235 |
| - UniProtKB: | Q1RP75 (UniProtKB/TrEMBL) |
| - Sequence: |
MGKQKKTRKYATMKRMLSLRDERLKEKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYNTQLGhide sequence |
TranscriptomePromoters| RGD ID: | 13694733 | |||||||||
| Promoter ID: | EPDNEW_R5258 | |||||||||
| Type: | multiple initiation site | |||||||||
| Name: | Fcf1_1 | |||||||||
| Description: | FCF1 rRNA-processing protein | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/) | |||||||||
| Experiment Methods: | Single-end sequencing. | |||||||||
| Position: |
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Strain Variation
Strain Sequence Variants (Rnor 6.0)
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Damaging VariantsAssembly: Rnor_6.0
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 6 | 108807030 | 108807031 | C | T | snv | M520/N (MCW), WKY/N (MCW) |
| 6 | 108807958 | 108807959 | C | T | snv | WKY/N (MCW), M520/N (MCW), WN/N (MCW), BN/SsN (MCW), ACI/N (MCW) |
Assembly: RGSC_v3.4
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 6 | 109019407 | 109019408 | C | T | snv | BN/NHsdMcwi (KNAW) |
| 6 | 109027418 | 109027419 | C | T | snv | M520/N (KNAW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), BN/NHsdMcwi (KNAW), WKY/N (KNAW) |
| 6 | 109028325 | 109028326 | G | A | snv | ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), LCR/2Mco (UMich), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SR/JrHsd (MCW), HCR/1Mco (UMich), LCR/1Mco (UMich), BN/NHsdMcwi (KNAW), FHH/EurMcwi (MCW), HCR/2Mco (UMich) |
| 6 | 109028346 | 109028347 | C | T | snv | LCR/2Mco (UMich), WKY/N (KNAW), BN/NHsdMcwi (KNAW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW), LE/Stm (KNAW), LCR/1Mco (UMich), FHL/EurMcwi (MCW), WN/N (KNAW), BN/SsN (KNAW), HCR/2Mco (UMich), HCR/1Mco (UMich), GH/OmrMcwi (MCW), ACI/N (KNAW), M520/N (KNAW), ACI/EurMcwi (MCW) |
Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:1310899 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000004723 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000006297 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Transcript | ENSRNOT00000006297 | ENTREZGENE, UniProtKB/TrEMBL |
| InterPro | DUF652 | UniProtKB/TrEMBL |
| PIN_dom | UniProtKB/TrEMBL | |
| PIN_domain-like | UniProtKB/TrEMBL | |
| KEGG Report | rno:299198 | UniProtKB/TrEMBL |
| NCBI Gene | 299198 | ENTREZGENE |
| Pfam | Fcf1 | UniProtKB/TrEMBL |
| PhenoGen | Fcf1 | PhenoGen |
| SMART | PINc | UniProtKB/TrEMBL |
| Superfamily-SCOP | SSF88723 | UniProtKB/TrEMBL |
| UniGene | Rn.1198 | ENTREZGENE |
| UniProt | Q1RP75 | ENTREZGENE, UniProtKB/TrEMBL |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2013-09-16 | Fcf1 | FCF1 rRNA-processing protein | Fcf1 | FCF1 small subunit (SSU) processome component homolog (S. cerevisiae) | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2011-05-25 | Fcf1 | FCF1 small subunit (SSU) processome component homolog (S. cerevisiae) | RGD1310899 | similar to CGI-35 protein | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2008-04-30 | RGD1310899 | similar to CGI-35 protein | RGD1310899_predicted | similar to CGI-35 protein (predicted) | 'predicted' is removed | 2292626 | APPROVED |
| 2005-01-20 | RGD1310899_predicted | similar to CGI-35 protein (predicted) | LOC299198_predicted | Symbol and Name status set to approved | 1331353 | APPROVED | |
| 2005-01-12 | LOC299198_predicted | similar to CGI-35 protein (predicted) | Symbol and Name status set to provisional | 70820 | PROVISIONAL |
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| More on Fcf1 | |
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Alliance Gene |
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NCBI Gene |
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Ensembl Gene |
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JBrowse: rn5 rn6 |
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NCBI Genome Data Viewer |
| RGD Object Information | |
| RGD ID: | 1310899 |
| Created: | 2005-01-12 |
| Species: | Rattus norvegicus |
| Last Modified: | 2019-08-20 |
| Status: | ACTIVE |
