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    LOC4340493 peptidyl-prolyl cis-trans isomerase CYP40 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4340493, updated on 21-Dec-2023

    Summary

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    Gene symbol
    LOC4340493
    Gene description
    peptidyl-prolyl cis-trans isomerase CYP40
    Locus tag
    OSNPB_060216800
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Oryza sativa Japonica Group
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
    Expression
    Ubiquitous expression in roots before flowering (RPKM 14.4), flower buds (RPKM 12.5) and 6 other tissues See more
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    Genomic context

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    See LOC4340493 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    102 current IRGSP-1.0 (GCF_001433935.1) 6 NC_029261.1 (5933796..5939640, complement)

    Chromosome 6 - NC_029261.1Genomic Context describing neighboring genes Neighboring gene pentatricopeptide repeat-containing protein At3g29230 Neighboring gene uncharacterized LOC4340492 Neighboring gene transfer RNA valine (anticodon AAC) Neighboring gene MADS-box transcription factor 55-like

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_029261.1 Chromosome 6 Reference IRGSP-1.0 Primary Assembly

    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Transcriptome profiling of various organs at different developmental stages in rice
    • Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
    • BioProject: PRJNA243371
    • Publication: PMID 26387578
    • Analysis date: Fri Dec 15 20:02:59 2017

    Bibliography

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    Related articles in PubMed

    1. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Rice Full-Length cDNA Consortium, et al. Science, 2003 Jul 18. PMID 12869764

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables peptidyl-prolyl cis-trans isomerase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein folding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in protein peptidyl-prolyl isomerization IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    peptidyl-prolyl cis-trans isomerase CYP40
    Names
    OSJNBb0024N18.19
    Os06g0216800
    putative cyclophilin-40

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Oryza sativa Japonica Group Annotation Release 102 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference IRGSP-1.0 Primary Assembly

    Genomic

    1. NC_029261.1 Reference IRGSP-1.0 Primary Assembly

      Range
      5933796..5939640 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_026026544.1 → XP_025882329.1  peptidyl-prolyl cis-trans isomerase CYP40 isoform X1

      UniProtKB/TrEMBL
      B9FS72
      Conserved Domains (4) summary
      smart00028
      Location:353 → 386
      TPR; Tetratricopeptide repeats
      cd01926
      Location:26 → 193
      cyclophilin_ABH_like; Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain. This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding ...
      sd00006
      Location:352 → 382
      TPR; TPR repeat [structural motif]
      cl26005
      Location:330 → 427
      PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional

    2. XM_026026545.1 → XP_025882330.1  peptidyl-prolyl cis-trans isomerase CYP40 isoform X2

      UniProtKB/TrEMBL
      B9FS72, Q0DDL1, Q69TG8
      Conserved Domains (3) summary
      COG0457
      Location:231 → 378
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      cd01926
      Location:26 → 193
      cyclophilin_ABH_like; Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain. This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding ...
      sd00006
      Location:234 → 262
      TPR; TPR repeat [structural motif]

    3. XM_026026543.1 → XP_025882328.1  peptidyl-prolyl cis-trans isomerase CYP40 isoform X1

      UniProtKB/TrEMBL
      B9FS72
      Conserved Domains (4) summary
      smart00028
      Location:353 → 386
      TPR; Tetratricopeptide repeats
      cd01926
      Location:26 → 193
      cyclophilin_ABH_like; Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain. This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding ...
      sd00006
      Location:352 → 382
      TPR; TPR repeat [structural motif]
      cl26005
      Location:330 → 427
      PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional
    Nucleotide Protein
    Heading Accession and Version

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