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

    Gene ID: 362166, updated on 18-Sep-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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    See Phf21a in Genome Data Viewer
    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
    		  
    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

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003

    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

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

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

      Related
      ENSRNOP00000078574.2, ENSRNOT00000095030.2

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Nucleotide Protein Strain
    Heading Accession and Version

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