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    Dpf1 double PHD fingers 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 50545, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Dpf1provided by RGD
    Official Full Name
    double PHD fingers 1provided by RGD
    Primary source
    RGD:61868
    See related
    EnsemblRapid:ENSRNOG00000020687 AllianceGenome:RGD:61868
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Neud4
    Summary
    Predicted to enable sequence-specific double-stranded DNA binding activity. Involved in nervous system development. Predicted to be located in cytoplasm and nucleus. Predicted to be part of nBAF complex. Orthologous to human DPF1 (double PHD fingers 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 57.0), Uterus (RPKM 7.8) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dpf1 in Genome Data Viewer
    Location:
    1q21
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (93729683..93743425)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (84602212..84615954)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (87248448..87258070)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene MARCKS-related protein-like Neighboring gene protein phosphatase 1, regulatory (inhibitor) subunit 14A Neighboring gene serine peptidase inhibitor, Kunitz type, 2 Neighboring gene signal-induced proliferation-associated 1 like 3 Neighboring gene WD repeat domain 87

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Differential splicing creates a diversity of transcripts from a neurospecific developmentally regulated gene encoding a protein with new zinc-finger motifs. Buchman VL, et al. Nucleic Acids Res, 1992 Nov 11. PMID 1454523, Free PMC Article
    2. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. Shain AH, et al. PLoS One, 2013. PMID 23355908, Free PMC Article
    3. Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. Staahl BT, et al. J Neurosci, 2013 Jun 19. PMID 23785148, Free PMC Article
    4. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Lessard J, et al. Neuron, 2007 Jul 19. PMID 17640523, Free PMC Article
    5. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Hargreaves DC, et al. Cell Res, 2011 Mar. PMID 21358755, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in nervous system development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of nBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of nBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein neuro-d4
    Names
    BAF45B
    BRG1-associated factor 45B
    D4, zinc and double PHD fingers family 1
    neuro-d4
    neuronal d4 domain family member

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001105729.3 → NP_001099199.2  zinc finger protein neuro-d4

      Status: VALIDATED

      Source sequence(s)
      BC159415, CO396551, JAXUCZ010000001
      UniProtKB/Swiss-Prot
      P56163
      UniProtKB/TrEMBL
      A0A0H2UHS4
      Related
      ENSRNOP00000028091.7, ENSRNOT00000028091.10
      Conserved Domains (3) summary
      cd15530
      Location:327 → 372
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:269 → 326
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:12 → 83
      Requiem_N; N-terminal domain of DPF2/REQ

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      93729683..93743425
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039088375.2 → XP_038944303.1  zinc finger protein neuro-d4 isoform X1

      UniProtKB/Swiss-Prot
      P56163
      Conserved Domains (4) summary
      COG5189
      Location:249 → 277
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:385 → 440
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:327 → 384
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    2. XM_039088394.2 → XP_038944322.1  zinc finger protein neuro-d4 isoform X5

      UniProtKB/Swiss-Prot
      P56163
      Conserved Domains (4) summary
      COG5189
      Location:249 → 277
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:368 → 423
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:310 → 367
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    3. XM_039088425.2 → XP_038944353.1  zinc finger protein neuro-d4 isoform X17

      UniProtKB/TrEMBL
      A0A8I6AHA1
      Conserved Domains (4) summary
      COG5189
      Location:201 → 229
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:320 → 375
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:262 → 319
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    4. XM_039088377.2 → XP_038944305.1  zinc finger protein neuro-d4 isoform X2

      UniProtKB/Swiss-Prot
      P56163
      Conserved Domains (4) summary
      COG5189
      Location:249 → 277
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:385 → 430
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:327 → 384
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    5. XM_039088402.2 → XP_038944330.1  zinc finger protein neuro-d4 isoform X7

      UniProtKB/Swiss-Prot
      P56163
      Conserved Domains (4) summary
      COG5189
      Location:249 → 277
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:368 → 413
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:310 → 367
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    6. XM_039088397.2 → XP_038944325.1  zinc finger protein neuro-d4 isoform X6

      UniProtKB/Swiss-Prot
      P56163
      Related
      ENSRNOP00000103561.1, ENSRNOT00000144956.1
      Conserved Domains (4) summary
      COG5189
      Location:231 → 259
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:367 → 422
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:309 → 366
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    7. XM_039088407.2 → XP_038944335.1  zinc finger protein neuro-d4 isoform X8

      UniProtKB/Swiss-Prot
      P56163
      Conserved Domains (4) summary
      COG5189
      Location:231 → 259
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:367 → 412
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:309 → 366
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    8. XM_063271900.1 → XP_063127970.1  zinc finger protein neuro-d4 isoform X10

    9. XM_063271901.1 → XP_063127971.1  zinc finger protein neuro-d4 isoform X11

    10. XM_039088421.2 → XP_038944349.1  zinc finger protein neuro-d4 isoform X14

      UniProtKB/TrEMBL
      A0A8I6AHA1
      Conserved Domains (4) summary
      COG5189
      Location:201 → 229
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:337 → 392
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:279 → 336
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:52 → 118
      Requiem_N; N-terminal domain of DPF2/REQ

    11. XM_063271908.1 → XP_063127978.1  zinc finger protein neuro-d4 isoform X16

      Related
      ENSRNOP00000092298.2, ENSRNOT00000098222.2

    12. XM_063271916.1 → XP_063127986.1  zinc finger protein neuro-d4 isoform X19

    13. XM_039088390.2 → XP_038944318.1  zinc finger protein neuro-d4 isoform X4

      UniProtKB/Swiss-Prot
      P56163
      Conserved Domains (4) summary
      COG5189
      Location:236 → 264
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:372 → 427
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:314 → 371
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:39 → 105
      Requiem_N; N-terminal domain of DPF2/REQ

    14. XM_006228678.5 → XP_006228740.1  zinc finger protein neuro-d4 isoform X9

      UniProtKB/Swiss-Prot
      P56163
      Related
      ENSRNOP00000089460.1, ENSRNOT00000118174.2
      Conserved Domains (4) summary
      COG5189
      Location:218 → 246
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:354 → 409
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:296 → 353
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:39 → 105
      Requiem_N; N-terminal domain of DPF2/REQ

    15. XM_063271903.1 → XP_063127973.1  zinc finger protein neuro-d4 isoform X13

    16. XM_063271905.1 → XP_063127975.1  zinc finger protein neuro-d4 isoform X15

      Related
      ENSRNOP00000098892.1, ENSRNOT00000144320.1

    17. XM_063271913.1 → XP_063127983.1  zinc finger protein neuro-d4 isoform X18

    18. XM_063271921.1 → XP_063127991.1  zinc finger protein neuro-d4 isoform X22

    19. XM_039088383.2 → XP_038944311.1  zinc finger protein neuro-d4 isoform X3

      UniProtKB/Swiss-Prot
      P56163
      Conserved Domains (4) summary
      COG5189
      Location:237 → 265
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:373 → 428
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:315 → 372
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:40 → 106
      Requiem_N; N-terminal domain of DPF2/REQ

    20. XM_063271917.1 → XP_063127987.1  zinc finger protein neuro-d4 isoform X20

    21. XM_063271920.1 → XP_063127990.1  zinc finger protein neuro-d4 isoform X21

    22. XM_039088431.2 → XP_038944359.1  zinc finger protein neuro-d4 isoform X24

      UniProtKB/TrEMBL
      B0K016
      Conserved Domains (4) summary
      COG5189
      Location:154 → 182
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:290 → 345
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:232 → 289
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:1 → 23
      Requiem_N; N-terminal domain of DPF2/REQ

    23. XM_039088416.2 → XP_038944344.1  zinc finger protein neuro-d4 isoform X12

      UniProtKB/TrEMBL
      A0A8I6GFF6
      Conserved Domains (4) summary
      COG5189
      Location:202 → 230
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:338 → 393
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:280 → 337
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:5 → 71
      Requiem_N; N-terminal domain of DPF2/REQ

    24. XM_063271924.1 → XP_063127994.1  zinc finger protein neuro-d4 isoform X23

    25. XM_039088436.2 → XP_038944364.1  zinc finger protein neuro-d4 isoform X24

      UniProtKB/TrEMBL
      B0K016
      Conserved Domains (4) summary
      COG5189
      Location:154 → 182
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:290 → 345
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15690
      Location:232 → 289
      PHD1_DPF1; PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1)
      pfam14051
      Location:1 → 23
      Requiem_N; N-terminal domain of DPF2/REQ
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P56163.1 GenPept UniProtKB/Swiss-Prot:P56163

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