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Phf21a PHD finger protein 21A [ Rattus norvegicus (Norway rat) ]

Gene ID: 362166, updated on 17-Aug-2024

Summary

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Official Symbol
Phf21aprovided by RGD
Official Full Name
PHD finger protein 21Aprovided by RGD
Primary source
RGD:1560612
See related
EnsemblRapid:ENSRNOG00000006063 AllianceGenome:RGD:1560612
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
RGD1560612
Summary
Enables chromatin binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within suckling behavior. Located in nucleus. Orthologous to human PHF21A (PHD finger protein 21A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 123.0), Thymus (RPKM 101.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
3q24
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (98600933..98791132)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (78158760..78331903)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (81099765..81271841)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene cAMP responsive element binding protein 3-like 1 Neighboring gene uncharacterized LOC103691847 Neighboring gene uncharacterized LOC120101597 Neighboring gene large ribosomal subunit protein eL34-like Neighboring gene small nucleolar RNA SNORA21 Neighboring gene uncharacterized LOC134486123 Neighboring gene LARGE xylosyl- and glucuronyltransferase 2 Neighboring gene peroxisomal biogenesis factor 16

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. The rest repression of the neurosecretory phenotype is negatively modulated by BHC80, a protein of the BRAF/HDAC complex. Klajn A, et al. J Neurosci, 2009 May 13. PMID 19439607, Free PMC Article
  2. A component of BRAF-HDAC complex, BHC80, is required for neonatal survival in mice. Iwase S, et al. FEBS Lett, 2006 May 29. PMID 16684532
  3. Characterization of BHC80 in BRAF-HDAC complex, involved in neuron-specific gene repression. Iwase S, et al. Biochem Biophys Res Commun, 2004 Sep 17. PMID 15325272
  4. The histone demethylase LSD1/KDM1A promotes the DNA damage response. Mosammaparast N, et al. J Cell Biol, 2013 Nov 11. PMID 24217620, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within suckling behavior ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of DNA repair complex ISO
Inferred from Sequence Orthology
more info
  
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone deacetylase complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
PHD finger protein 21A

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_001428967.1 → NP_001415896.1  PHD finger protein 21A isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    F1M6K4

  2. NM_001428968.1 → NP_001415897.1  PHD finger protein 21A isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    F1M6K4

  3. NM_001428969.1 → NP_001415898.1  PHD finger protein 21A isoform 3

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A6HNF8

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_086021.1 Reference GRCr8

    Range
    98600933..98791132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063284918.1 → XP_063140988.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  2. XM_063284925.1 → XP_063140995.1  PHD finger protein 21A isoform X5

    UniProtKB/TrEMBL
    F1M6K4

  3. XM_063284930.1 → XP_063141000.1  PHD finger protein 21A isoform X7

    UniProtKB/TrEMBL
    A6HNF8
    Related
    ENSRNOP00000078574.2, ENSRNOT00000095030.2

  4. XM_063284933.1 → XP_063141003.1  PHD finger protein 21A isoform X10

    UniProtKB/TrEMBL
    F1M6K4

  5. XM_063284932.1 → XP_063141002.1  PHD finger protein 21A isoform X9

    UniProtKB/TrEMBL
    A6HNF8

  6. XM_063284931.1 → XP_063141001.1  PHD finger protein 21A isoform X8

    UniProtKB/TrEMBL
    A6HNF8

  7. XM_063284900.1 → XP_063140970.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  8. XM_063284903.1 → XP_063140973.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  9. XM_063284893.1 → XP_063140963.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  10. XM_063284908.1 → XP_063140978.1  PHD finger protein 21A isoform X3

    UniProtKB/TrEMBL
    F1M6K4

  11. XM_063284907.1 → XP_063140977.1  PHD finger protein 21A isoform X2

    UniProtKB/TrEMBL
    F1M6K4

  12. XM_063284939.1 → XP_063141009.1  PHD finger protein 21A isoform X13

    UniProtKB/TrEMBL
    A6HNF8

  13. XM_063284941.1 → XP_063141011.1  PHD finger protein 21A isoform X14

    UniProtKB/TrEMBL
    A6HNF8

  14. XM_063284904.1 → XP_063140974.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  15. XM_063284936.1 → XP_063141006.1  PHD finger protein 21A isoform X11

    UniProtKB/TrEMBL
    A6HNF8

  16. XM_063284940.1 → XP_063141010.1  PHD finger protein 21A isoform X12

    UniProtKB/TrEMBL
    A6HNF8

  17. XM_063284914.1 → XP_063140984.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  18. XM_063284917.1 → XP_063140987.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4
    Related
    ENSRNOP00000061099.5, ENSRNOT00000067664.6

  19. XM_063284934.1 → XP_063141004.1  PHD finger protein 21A isoform X11

  20. XM_063284909.1 → XP_063140979.1  PHD finger protein 21A isoform X4

  21. XM_063284923.1 → XP_063140993.1  PHD finger protein 21A isoform X6

  22. XM_063284920.1 → XP_063140990.1  PHD finger protein 21A isoform X5

    UniProtKB/TrEMBL
    F1M6K4

  23. XM_063284919.1 → XP_063140989.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  24. XM_063284927.1 → XP_063140997.1  PHD finger protein 21A isoform X6

    UniProtKB/TrEMBL
    F1M6K4

  25. XM_063284926.1 → XP_063140996.1  PHD finger protein 21A isoform X5

    UniProtKB/TrEMBL
    F1M6K4

  26. XM_063284915.1 → XP_063140985.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  27. XM_063284894.1 → XP_063140964.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  28. XM_063284935.1 → XP_063141005.1  PHD finger protein 21A isoform X11

    UniProtKB/TrEMBL
    A6HNF8

  29. XM_063284910.1 → XP_063140980.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  30. XM_063284924.1 → XP_063140994.1  PHD finger protein 21A isoform X6

    UniProtKB/TrEMBL
    F1M6K4

  31. XM_063284928.1 → XP_063140998.1  PHD finger protein 21A isoform X5

    UniProtKB/TrEMBL
    F1M6K4

  32. XM_063284897.1 → XP_063140967.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  33. XM_063284911.1 → XP_063140981.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  34. XM_063284929.1 → XP_063140999.1  PHD finger protein 21A isoform X6

    UniProtKB/TrEMBL
    F1M6K4

  35. XM_063284921.1 → XP_063140991.1  PHD finger protein 21A isoform X5

    UniProtKB/TrEMBL
    F1M6K4

  36. XM_063284899.1 → XP_063140969.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  37. XM_063284922.1 → XP_063140992.1  PHD finger protein 21A isoform X5

    UniProtKB/TrEMBL
    F1M6K4

  38. XM_063284895.1 → XP_063140965.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  39. XM_063284938.1 → XP_063141008.1  PHD finger protein 21A isoform X12

    UniProtKB/TrEMBL
    A6HNF8

  40. XM_063284896.1 → XP_063140966.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  41. XM_063284898.1 → XP_063140968.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  42. XM_063284913.1 → XP_063140983.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  43. XM_039106451.2 → XP_038962379.2  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  44. XM_063284906.1 → XP_063140976.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  45. XM_063284905.1 → XP_063140975.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  46. XM_063284902.1 → XP_063140972.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  47. XM_063284937.1 → XP_063141007.1  PHD finger protein 21A isoform X11

    UniProtKB/TrEMBL
    A6HNF8

  48. XM_063284901.1 → XP_063140971.1  PHD finger protein 21A isoform X1

    UniProtKB/TrEMBL
    F1M6K4

  49. XM_063284912.1 → XP_063140982.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4

  50. XM_063284916.1 → XP_063140986.1  PHD finger protein 21A isoform X4

    UniProtKB/TrEMBL
    F1M6K4
Nucleotide Protein Strain
Heading Accession and Version

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