 Gene Ontology Annotations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Cellular Component
Molecular Function
Molecular Pathway Annotations |
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Analyze GeneStrainQTL List |
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Gene Annotator (Annotation Comparison) |
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GOLF (Gene-Ortholog Location Finder) |
Cellular Component
Molecular Function
Molecular Pathway AnnotationsGene-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. | Buchman VL, etal., Nucleic Acids Res 1992 Nov 11;20(21):5579-85. |
| 2. | Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27. |
| 3. | Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1. |
| 4. | NCBI rat LocusLink and RefSeq merged data July 26, 2002 |
| 5. | RGD automated import pipeline for gene-chemical interactions |
| 6. | RGD comprehensive gene curation |
| 7. | Shain AH and Pollack JR, PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23. |
References - uncuratedGenomics
Comparative Map Data| Dpf1 (Rattus norvegicus - Norway rat) |
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| DPF1 (Homo sapiens - human) |
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| Dpf1 (Mus musculus - house mouse) |
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| Dpf1 (Chinchilla lanigera - long-tailed chinchilla) |
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| DPF1 (Pan paniscus - bonobo/pygmy chimpanzee) |
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| DPF1 (Canis lupus familiaris - dog) |
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| Dpf1 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| DPF1 (Sus scrofa - pig) |
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| DPF1 (Chlorocebus sabaeus - African green monkey) |
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| Dpf1 (Heterocephalus glaber - naked mole-rat) |
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Position Markers| BF397080 |
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| Dpf1 |
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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
| 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 | 72 | 4 | 28 | ||||||||||
| Low | 3 | 28 | 36 | 28 | 1 | 28 | 2 | 2 | 17 | 13 | 11 | ||
| Below cutoff | 15 | 17 | 9 | 18 | 9 | 8 | 9 | 13 | 8 |
View RNA-SEQ Expression Data
Sequence
Nucleotide Sequences| RefSeq Transcripts | NM_001105729 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_006228677 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_006228678 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_006228679 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_006228681 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_006228684 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_006228685 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017589599 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017589600 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017589601 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017589603 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_017589604 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AABR07002856 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AAHX01004484 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BC159415 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH473979 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CO396551 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| X66022 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
Reference Sequences
| RefSeq Acc Id: | ENSRNOT00000028091 ⟹ ENSRNOP00000028091 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | NM_001105729 ⟹ NP_001099199 | ||||||||||||||||||||
| RefSeq Status: | VALIDATED | ||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||
| Position: |
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| Sequence: |
GGCCTCAGCGCCCGCCCGACCGCTGGGAGGACCGACCCGGCAGGGACCTGCTGGGGGCAGGACChide sequence |
| RefSeq Acc Id: | XM_006228677 ⟹ XP_006228739 | ||||||||||||
| RefSeq Status: | |||||||||||||
| Type: | CODING | ||||||||||||
| Position: |
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| Sequence: |
AGATCCTCGTGCTCCCGCCCCCCGGGAATGAATGGATGGGCGGCCTCAGCGCCCGCCCGACCGChide sequence |
| RefSeq Acc Id: | XM_006228678 ⟹ XP_006228740 | ||||||||||||
| RefSeq Status: | |||||||||||||
| Type: | CODING | ||||||||||||
| Position: |
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| Sequence: |
CCCCCCGGGAATGAATGGATGGGCGGCCTCAGCGCCCGCCCGACCGCTGGGAGGACCGACCCGGhide sequence |
| RefSeq Acc Id: | XM_006228679 ⟹ XP_006228741 | ||||||||||||
| RefSeq Status: | |||||||||||||
| Type: | CODING | ||||||||||||
| Position: |
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| Sequence: |
CCGGGAATGAATGGATGGGCGGCCTCAGCGCCCGCCCGACCGCTGGGAGGACCGACCCGGCAGGhide sequence |
| RefSeq Acc Id: | XM_006228681 ⟹ XP_006228743 | ||||||||||||
| RefSeq Status: | |||||||||||||
| Type: | CODING | ||||||||||||
| Position: |
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| Sequence: |
CCCGGGAATGAATGGATGGGCGGCCTCAGCGCCCGCCCGACCGCTGGGAGGACCGACCCGGCAGhide sequence |
| RefSeq Acc Id: | XM_006228684 ⟹ XP_006228746 | ||||||||||||
| RefSeq Status: | |||||||||||||
| Type: | CODING | ||||||||||||
| Position: |
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| Sequence: |
CGCCCCCCGGGAATGAATGGATGGGCGGCCTCAGCGCCCGCCCGACCGCTGGGAGGACCGACCChide sequence |
| RefSeq Acc Id: | XM_006228685 ⟹ XP_006228747 | ||||||||||||
| RefSeq Status: | |||||||||||||
| Type: | CODING | ||||||||||||
| Position: |
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| Sequence: |
TGGGAGGACCGACCCGGCAGGGACCTGCTGGGGGCAGGACCCGGGGAGCAAGATGGCCACGGTChide sequence |
| RefSeq Acc Id: | XM_017589599 ⟹ XP_017445088 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GGGTGTCTGGCAAGAATGGTGTACGACGCGTTGCTCCTGGACGGGTGGAGGGCGTGGGGGAGGGhide sequence |
| RefSeq Acc Id: | XM_017589600 ⟹ XP_017445089 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GTGTCTGGCAAGAATGGTGTACGACGCGTTGCTCCTGGACGGGTGGAGGGCGTGGGGGAGGGGThide sequence |
| RefSeq Acc Id: | XM_017589601 ⟹ XP_017445090 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
TGGGTGTCTGGCAAGAATGGTGTACGACGCGTTGCTCCTGGACGGGTGGAGGGCGTGGGGGAGGhide sequence |
| RefSeq Acc Id: | XM_017589603 ⟹ XP_017445092 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GGTGTCTGGCAAGAATGGTGTACGACGCGTTGCTCCTGGACGGGTGGAGGGCGTGGGGGAGGGGhide sequence |
| RefSeq Acc Id: | XM_017589604 ⟹ XP_017445093 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
GTGGGTGTCTGGCAAGAATGGTGTACGACGCGTTGCTCCTGGACGGGTGGAGGGCGTGGGGGAGhide sequence |
Protein Sequences| Protein RefSeqs | NP_001099199 | (Get FASTA) | NCBI Sequence Viewer |
| XP_006228739 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_006228740 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_006228741 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_006228743 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_006228746 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_006228747 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017445088 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017445089 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017445090 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017445092 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_017445093 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | AAI59416 | (Get FASTA) | NCBI Sequence Viewer |
| EDM07826 | (Get FASTA) | NCBI Sequence Viewer | |
| EDM07827 | (Get FASTA) | NCBI Sequence Viewer | |
| EDM07828 | (Get FASTA) | NCBI Sequence Viewer | |
| P56163 | (Get FASTA) | NCBI Sequence Viewer |
Reference Sequences
| RefSeq Acc Id: | NP_001099199 ⟸ NM_001105729 |
| - UniProtKB: | B0K016 (UniProtKB/TrEMBL), A0A0H2UHS4 (UniProtKB/TrEMBL) |
| - Sequence: |
MATVIPSPLSLGEDFYREAIEHCRSYNARLCAERSLRLPFLDSQTGVAQNNCYIWMEKTHRGPGhide sequence |
| RefSeq Acc Id: | XP_006228746 ⟸ XM_006228684 |
| - Peptide Label: | isoform X8 |
| - Sequence: |
MGGLSARPTAGRTDPAGTCWGQDPGSKMATVIPSPLRCLGEDFYREAIEHCRSYNARLCAERSLhide sequence |
| RefSeq Acc Id: | XP_006228739 ⟸ XM_006228677 |
| - Peptide Label: | isoform X10 |
| - Sequence: |
MGGLSARPTAGRTDPAGTCWGQDPGSKMATVIPSPLRCLGEDFYREAIEHCRSYNARLCAERSLhide sequence |
| RefSeq Acc Id: | XP_006228740 ⟸ XM_006228678 |
| - Peptide Label: | isoform X4 |
| - Sequence: |
MGGLSARPTAGRTDPAGTCWGQDPGSKMATVIPSPLSLGEDFYREAIEHCRSYNARLCAERSLRhide sequence |
| RefSeq Acc Id: | XP_006228741 ⟸ XM_006228679 |
| - Peptide Label: | isoform X5 |
| - Sequence: |
MGGLSARPTAGRTDPAGTCWGQDPGSKMATVIPSPLRCLGEDFYREAIEHCRSYNARLCAERSLhide sequence |
| RefSeq Acc Id: | XP_006228743 ⟸ XM_006228681 |
| - Peptide Label: | isoform X11 |
| - Sequence: |
MGGLSARPTAGRTDPAGTCWGQDPGSKMATVIPSPLRCLGEDFYREAIEHCRSYNARLCAERSLhide sequence |
| RefSeq Acc Id: | XP_006228747 ⟸ XM_006228685 |
| - Peptide Label: | isoform X9 |
| - Sequence: |
MEKTHRGPGLAPGQIYTYPARCWRKKRRLNILEDPRLRPCEYKIDCEAPLKKEGGLPEGPVLEAhide sequence |
| RefSeq Acc Id: | XP_017445093 ⟸ XM_017589604 |
| - Peptide Label: | isoform X7 |
| - Sequence: |
MSVVWCVSMLWGFVDNLPLDTSGVSGYMAFIALARTSTGRPSSTAAATTRACVPSAACACPSSThide sequence |
| RefSeq Acc Id: | XP_017445090 ⟸ XM_017589601 |
| - Peptide Label: | isoform X3 |
| - Sequence: |
MSVVWCVSMLWGFVDNLPLDTSGVSGYMAFIALARTSTGRPSSTAAATTRACVPSAACACPSSThide sequence |
| RefSeq Acc Id: | XP_017445088 ⟸ XM_017589599 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MSVVWCVSMLWGFVDNLPLDTSGVSGYMAFIALARTSTGRPSSTAAATTRACVPSAACACPSSThide sequence |
| RefSeq Acc Id: | XP_017445092 ⟸ XM_017589603 |
| - Peptide Label: | isoform X6 |
| - Sequence: |
MSVVWCVSMLWGFVDNLPLDTSGVSGYMAFIALARTSTGRPSSTAAATTRACVPSAACACPSSThide sequence |
| RefSeq Acc Id: | XP_017445089 ⟸ XM_017589600 |
| - Peptide Label: | isoform X2 |
| - Sequence: |
MSVVWCVSMLWGFVDNLPLDTSGVSGYMAFIALARTSTGRPSSTAAATTRACVPSAACACPSSThide sequence |
| RefSeq Acc Id: | ENSRNOP00000028091 ⟸ ENSRNOT00000028091 |
Protein Domains
C2H2-type PHD-type
TranscriptomeStrain Variation
Strain Sequence Variants (Rnor 6.0)
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Damaging VariantsAssembly: Rnor_5.0
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 1 | 88432576 | 88432577 | G | T | snv | GK/Ox (KNAW) |
Assembly: Rnor_6.0
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 1 | 87253526 | 87253527 | G | T | snv | GK/Ox (RGD) |
Additional Information
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:61868 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000020687 | Ensembl, ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000028091 | ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Transcript | ENSRNOT00000028091 | ENTREZGENE, UniProtKB/TrEMBL |
| Gene3D-CATH | 3.30.40.10 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL |
| IMAGE_CLONE | IMAGE:8368092 | IMAGE-MGC_LOAD |
| InterPro | DPF1 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL |
| Requiem/DPF_N_dom | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| Znf_C2H2_sf | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| Znf_C2H2_type | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| Znf_FYVE_PHD | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| Znf_PHD | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| Znf_PHD-finger | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| Znf_RING/FYVE/PHD | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| KEGG Report | rno:50545 | UniProtKB/TrEMBL |
| MGC_CLONE | MGC:188698 | IMAGE-MGC_LOAD |
| NCBI Gene | 50545 | ENTREZGENE |
| PANTHER | PTHR10615:SF12 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL |
| Pfam | PHD | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL |
| Requiem_N | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| PhenoGen | Dpf1 | PhenoGen |
| PROSITE | ZF_PHD_1 | UniProtKB/Swiss-Prot |
| ZF_PHD_2 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| ZINC_FINGER_C2H2_1 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| ZINC_FINGER_C2H2_2 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| SMART | PHD | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL |
| ZnF_C2H2 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| Superfamily-SCOP | SSF57667 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL |
| SSF57903 | UniProtKB/Swiss-Prot, UniProtKB/TrEMBL | |
| UniGene | Rn.42906 | ENTREZGENE |
| UniProt | A0A0H2UHS4 | ENTREZGENE, UniProtKB/TrEMBL |
| B0K016 | ENTREZGENE, UniProtKB/TrEMBL | |
| DPF1_RAT | UniProtKB/Swiss-Prot, ENTREZGENE |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2016-02-17 | Dpf1 | double PHD fingers 1 | Dpf1 | D4, zinc and double PHD fingers family 1 | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2008-03-11 | Dpf1 | D4, zinc and double PHD fingers family 1 | Neud4 | neuronal d4 domain family member | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2002-06-10 | Neud4 | neuronal d4 domain family member | Name updated | 70584 | APPROVED |
RGD Curation Notes| Note Type | Note | Reference |
|---|---|---|
| gene_domains | contains a nuclear localization signal, a Kruppel-type zinc-finger and a cysteine/histidine-rich motif | 61670 |
| gene_expression | transcripts are expressed in neuronal cell bodies | 61670 |
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| More on Dpf1 | |
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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: | 61868 |
| Created: | 2001-04-11 |
| Species: | Rattus norvegicus |
| Last Modified: | 2020-08-20 |
| Status: | ACTIVE |
