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

Gene ID: 50545, updated on 17-Aug-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 histone binding activity; sequence-specific double-stranded DNA binding activity; and transcription coregulator activity. Involved in nervous system development. Predicted to be located in cytoplasm. Predicted to be part of nBAF complex. Orthologous to human DPF1 (double PHD fingers 1). [provided by Alliance of Genome Resources, Apr 2022]
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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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

    UniProtKB/Swiss-Prot
    P56163

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

    UniProtKB/Swiss-Prot
    P56163

  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

    UniProtKB/TrEMBL
    A0A8I6AHA1
    Related
    ENSRNOP00000092298.2, ENSRNOT00000098222.2

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

    UniProtKB/TrEMBL
    A0A8I6AHA1

  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

    UniProtKB/Swiss-Prot
    P56163

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

    UniProtKB/Swiss-Prot
    P56163
    Related
    ENSRNOP00000098892.1, ENSRNOT00000144320.1

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

    UniProtKB/TrEMBL
    A0A8I6AHA1

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

    UniProtKB/TrEMBL
    A0A8I6AHA1

  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

    UniProtKB/Swiss-Prot
    P56163

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

    UniProtKB/TrEMBL
    A0A8I6AHA1

  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

    UniProtKB/TrEMBL
    A0A8I6GFF6

  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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