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    Ikzf1 IKAROS family zinc finger 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305501, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Ikzf1provided by RGD
    Official Full Name
    IKAROS family zinc finger 1provided by RGD
    Primary source
    RGD:1562979
    See related
    EnsemblRapid:ENSRNOG00000004444 AllianceGenome:RGD:1562979
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1562979
    Summary
    Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; identical protein binding activity; and nucleic acid binding activity. Predicted to be involved in erythrocyte differentiation; lymphocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including hematopoietic or lymphoid organ development; lymphocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to be located in cytosol; nucleoplasm; and pericentric heterochromatin. Predicted to be part of protein-DNA complex. Human ortholog(s) of this gene implicated in B-lymphoblastic leukemia/lymphoma; acute lymphoblastic leukemia; colorectal cancer; and common variable immunodeficiency 13. Orthologous to human IKZF1 (IKAROS family zinc finger 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 276.1), Spleen (RPKM 257.4) and 3 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ikzf1 in Genome Data Viewer
    Location:
    14q21
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (90468696..90556522)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (86255065..86340839)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (91782281..91867828)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120096664 Neighboring gene sperm microtubule inner protein 7 Neighboring gene phosphoglucomutase 1, pseudogene 1 Neighboring gene uncharacterized LOC120096666 Neighboring gene fidgetin-like 1 Neighboring gene uncharacterized LOC120096667 Neighboring gene dopa decarboxylase

    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. Evaluation of a panel of tumor-specific differentially-methylated DNA regions in IRF4, IKZF1 and BCAT1 for blood-based detection of colorectal cancer. Young GP, et al. Clin Epigenetics, 2021 Jan 21. PMID 33478584, Free PMC Article
    2. Disease risk factors identified through shared genetic architecture and electronic medical records. Li L, et al. Sci Transl Med, 2014 Apr 30. PMID 24786325, Free PMC Article
    3. A two-gene blood test for methylated DNA sensitive for colorectal cancer. Pedersen SK, et al. PLoS One, 2015. PMID 25928810, Free PMC Article
    4. A cross-sectional study comparing a blood test for methylated BCAT1 and IKZF1 tumor-derived DNA with CEA for detection of recurrent colorectal cancer. Young GP, et al. Cancer Med, 2016 Oct. PMID 27726312, Free PMC Article
    5. Methylation and Gene Expression of BCAT1 and IKZF1 in Colorectal Cancer Tissues. Jedi M, et al. Clin Med Insights Oncol, 2018. PMID 29780264, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly-pyrimidine tract binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within B cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within Peyer's patch development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within amacrine cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in erythrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within establishment of protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within forebrain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within gland development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hemopoiesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lymph node development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lymphocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within natural killer cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of RNA polymerase II transcription preinitiation complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of multicellular organism growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of neutrophil differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription elongation by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription 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
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within retinal bipolar neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within thymus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in pericentric heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-DNA complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DNA-binding protein Ikaros

    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_001107237.1 → NP_001100707.1  DNA-binding protein Ikaros

      See identical proteins and their annotated locations for NP_001100707.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474055
      UniProtKB/TrEMBL
      A0A8I5ZVE4, A6KJA9
      Conserved Domains (4) summary
      COG5048
      Location:1 → 130
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:59 → 79
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:57 → 79
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:71 → 96
      zf-H2C2_2; Zinc-finger double domain

    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_086032.1 Reference GRCr8

      Range
      90468696..90556522
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006251494.5 → XP_006251556.4  DNA-binding protein Ikaros isoform X1

      UniProtKB/TrEMBL
      A0A0G2JVD9
      Related
      ENSRNOP00000069446.2, ENSRNOT00000080753.3

    2. XM_039092066.2 → XP_038947994.2  DNA-binding protein Ikaros isoform X12

    3. XM_063273234.1 → XP_063129304.1  DNA-binding protein Ikaros isoform X13

    4. XM_039092063.2 → XP_038947991.2  DNA-binding protein Ikaros isoform X6

    5. XM_008770318.4 → XP_008768540.3  DNA-binding protein Ikaros isoform X10

      Related
      ENSRNOP00000112759.1, ENSRNOT00000161801.1

    6. XM_039092065.2 → XP_038947993.2  DNA-binding protein Ikaros isoform X9

    7. XM_063273233.1 → XP_063129303.1  DNA-binding protein Ikaros isoform X11

    8. XM_008770316.4 → XP_008768538.3  DNA-binding protein Ikaros isoform X8

    9. XM_008770313.4 → XP_008768535.3  DNA-binding protein Ikaros isoform X3

      Related
      ENSRNOP00000106731.1, ENSRNOT00000129081.1

    10. XM_039092062.2 → XP_038947990.2  DNA-binding protein Ikaros isoform X2

    11. XM_008770314.4 → XP_008768536.3  DNA-binding protein Ikaros isoform X4

      Related
      ENSRNOP00000086084.1, ENSRNOT00000097538.2

    12. XM_008770315.4 → XP_008768537.2  DNA-binding protein Ikaros isoform X7

      UniProtKB/TrEMBL
      A0A8I5ZVE4, A6KJA9
      Related
      ENSRNOP00000111933.1, ENSRNOT00000129247.1
      Conserved Domains (4) summary
      COG5048
      Location:1 → 130
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:59 → 79
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:57 → 79
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:71 → 96
      zf-H2C2_2; Zinc-finger double domain

    13. XM_006251491.5 → XP_006251553.1  DNA-binding protein Ikaros isoform X5

      See identical proteins and their annotated locations for XP_006251553.1

      UniProtKB/TrEMBL
      A6KJA7, D4A9W4
      Related
      ENSRNOP00000105080.1, ENSRNOT00000133484.1
      Conserved Domains (3) summary
      COG5048
      Location:141 → 420
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:117 → 137
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:130 → 154
      zf-H2C2_2; Zinc-finger double domain

    14. XM_006251492.5 → XP_006251554.1  DNA-binding protein Ikaros isoform X5

      See identical proteins and their annotated locations for XP_006251554.1

      UniProtKB/TrEMBL
      A6KJA7, D4A9W4
      Conserved Domains (3) summary
      COG5048
      Location:141 → 420
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:117 → 137
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:130 → 154
      zf-H2C2_2; Zinc-finger double domain
    Nucleotide Protein Strain
    Heading Accession and Version

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