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    Phf20l1 PHD finger protein 20-like 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314964, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Phf20l1provided by RGD
    Official Full Name
    PHD finger protein 20-like 1provided by RGD
    Primary source
    RGD:1560141
    See related
    EnsemblRapid:ENSRNOG00000005486 AllianceGenome:RGD:1560141
    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
    Summary
    Predicted to enable methylation-dependent protein binding activity. Predicted to be involved in negative regulation of proteasomal ubiquitin-dependent protein catabolic process and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of NSL complex. Orthologous to human PHF20L1 (PHD finger protein 20 like 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 185.3), Brain (RPKM 174.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phf20l1 in Genome Data Viewer
    Location:
    7q33
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (100219598..100285580)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (98330580..98396526)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (107406948..107445219) , (108613731..108759741)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene Rab geranylgeranyltransferase subunit alpha, pseudogene 2 Neighboring gene transmembrane protein 71 Neighboring gene U2 spliceosomal RNA Neighboring gene thyroglobulin Neighboring gene src-like adaptor

    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
    • 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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    2. 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

    Clone Names

    • MGC112686

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylation-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylation-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of NSL complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 20-like protein 1
    Names
    tudor domain-containing protein PHF20L1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001271439.1 → NP_001258368.1  PHD finger protein 20-like protein 1

      See identical proteins and their annotated locations for NP_001258368.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/Swiss-Prot
      Q4V9H5
      UniProtKB/TrEMBL
      A0A8I6A3M7, A6HRR4
      Related
      ENSRNOP00000088843.1, ENSRNOT00000106420.2
      Conserved Domains (5) summary
      cd04508
      Location:90 → 135
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      cd15633
      Location:683 → 728
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam12618
      Location:210 → 317
      DUF3776; Protein of unknown function (DUF3776)
      pfam16660
      Location:318 → 383
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    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_086025.1 Reference GRCr8

      Range
      100219598..100285580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039079188.2 → XP_038935116.1  PHD finger protein 20-like protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:688 → 733
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    2. XM_063263540.1 → XP_063119610.1  PHD finger protein 20-like protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A8I6A3M7

    3. XM_063263542.1 → XP_063119612.1  PHD finger protein 20-like protein 1 isoform X6

      UniProtKB/TrEMBL
      A0A8I6A3M7

    4. XM_063263545.1 → XP_063119615.1  PHD finger protein 20-like protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A3M7

    5. XM_063263548.1 → XP_063119618.1  PHD finger protein 20-like protein 1 isoform X9

      UniProtKB/TrEMBL
      A0A8I6A3M7

    6. XM_063263551.1 → XP_063119621.1  PHD finger protein 20-like protein 1 isoform X19

    7. XM_063263553.1 → XP_063119623.1  PHD finger protein 20-like protein 1 isoform X21

    8. XM_063263554.1 → XP_063119624.1  PHD finger protein 20-like protein 1 isoform X22

      UniProtKB/TrEMBL
      A6HRR5

    9. XM_039079187.2 → XP_038935115.1  PHD finger protein 20-like protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:688 → 733
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    10. XM_063263539.1 → XP_063119609.1  PHD finger protein 20-like protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A8I6A3M7

    11. XM_063263541.1 → XP_063119611.1  PHD finger protein 20-like protein 1 isoform X6

      UniProtKB/TrEMBL
      A0A8I6A3M7

    12. XM_063263544.1 → XP_063119614.1  PHD finger protein 20-like protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A3M7

    13. XM_063263547.1 → XP_063119617.1  PHD finger protein 20-like protein 1 isoform X9

      UniProtKB/TrEMBL
      A0A8I6A3M7

    14. XM_039079186.1 → XP_038935114.1  PHD finger protein 20-like protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:688 → 733
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    15. XM_039079189.1 → XP_038935117.1  PHD finger protein 20-like protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Related
      ENSRNOP00000086359.2, ENSRNOT00000095136.2
      Conserved Domains (5) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:688 → 733
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    16. XM_039079190.1 → XP_038935118.1  PHD finger protein 20-like protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:319 → 523
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:687 → 732
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:322 → 387
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    17. XM_063263538.1 → XP_063119608.1  PHD finger protein 20-like protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A8I6A3M7

    18. XM_039079191.1 → XP_038935119.1  PHD finger protein 20-like protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:316 → 520
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:684 → 729
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:319 → 384
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    19. XM_039079192.1 → XP_038935120.1  PHD finger protein 20-like protein 1 isoform X6

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:315 → 519
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:683 → 728
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:318 → 383
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    20. XM_039079193.1 → XP_038935121.1  PHD finger protein 20-like protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:290 → 494
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:658 → 703
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:293 → 358
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 144
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    21. XM_063263546.1 → XP_063119616.1  PHD finger protein 20-like protein 1 isoform X8

      UniProtKB/TrEMBL
      A0A1W2Q6A4, A0A8I6A3M7
      Related
      ENSRNOP00000076201.2, ENSRNOT00000093254.3

    22. XM_063263549.1 → XP_063119619.1  PHD finger protein 20-like protein 1 isoform X9

      UniProtKB/TrEMBL
      A0A8I6A3M7

    23. XM_039079194.1 → XP_038935122.1  PHD finger protein 20-like protein 1 isoform X10

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (5) summary
      PTZ00449
      Location:289 → 493
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:657 → 702
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:292 → 357
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 144
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    24. XM_039079198.2 → XP_038935126.1  PHD finger protein 20-like protein 1 isoform X14

      Conserved Domains (5) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:688 → 733
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    25. XM_039079199.2 → XP_038935127.1  PHD finger protein 20-like protein 1 isoform X15

      Conserved Domains (5) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat
      cl22851
      Location:688 → 707
      PHD_SF; PHD finger superfamily

    26. XM_039079200.2 → XP_038935128.1  PHD finger protein 20-like protein 1 isoform X16

      Conserved Domains (4) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    27. XM_039079202.2 → XP_038935130.1  PHD finger protein 20-like protein 1 isoform X18

      Conserved Domains (4) summary
      PTZ00449
      Location:320 → 524
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam16660
      Location:323 → 388
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cd20454
      Location:86 → 143
      Tudor_PHF20L1; Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins
      cl17705
      Location:3 → 68
      MBT; mbt repeat

    28. XM_063263552.1 → XP_063119622.1  PHD finger protein 20-like protein 1 isoform X20

    29. XM_039079195.1 → XP_038935123.1  PHD finger protein 20-like protein 1 isoform X11

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (3) summary
      PTZ00449
      Location:190 → 394
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:558 → 603
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:193 → 258
      PHD20L1_u1; PHD finger protein 20-like protein 1

    30. XM_039079196.1 → XP_038935124.1  PHD finger protein 20-like protein 1 isoform X12

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (3) summary
      PTZ00449
      Location:186 → 390
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:554 → 599
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:189 → 254
      PHD20L1_u1; PHD finger protein 20-like protein 1

    31. XM_039079197.1 → XP_038935125.1  PHD finger protein 20-like protein 1 isoform X13

      UniProtKB/TrEMBL
      A0A8I6A3M7
      Conserved Domains (4) summary
      PTZ00449
      Location:160 → 364
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd15633
      Location:528 → 573
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)
      pfam16660
      Location:163 → 228
      PHD20L1_u1; PHD finger protein 20-like protein 1
      cl02573
      Location:1 → 14
      Tudor_SF; Tudor domain superfamily

    32. XM_039079201.2 → XP_038935129.1  PHD finger protein 20-like protein 1 isoform X17

      Conserved Domains (1) summary
      cd15633
      Location:262 → 307
      PHD_PHF20L1; PHD finger found in PHD finger protein 20-like protein 1 (P20L1)

    RNA

    1. XR_005486634.2 RNA Sequence

    2. XR_005486636.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001025702.1: Suppressed sequence

      Description
      NM_001025702.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from chicken: PHF20L1 (GeneID:420323).
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4V9H5.2 GenPept UniProtKB/Swiss-Prot:Q4V9H5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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