F20310

RIKEN Arabidopsis full-length cDNA overexpressed Arabidopsis lines

Original: F20310

Phenotypes

Morphological phenotypes

Generation Anatomical entity
/structure development stage		 Phenotypes
T1  
whole plant (PO:0000003)
  • decreased height (PATO:0000569)
    (Adult plant::Plant height::short)
rosette leaf (PO:0000014)
  • decreased size (PATO:0000587)
    (Rosette leaf::Shape::small)
  • increased width (PATO:0000600)
    (Rosette leaf::Shape::wide)
  • present in fewer numbers in organism (PATO:0001997)
    (Rosette leaf::Number::few)
T2  
rosette leaf (PO:0000014)
  • epinastic (PATO:0000945)
    (Rosette leaf::Shape::epinastic)
  • abnormal (PATO:0000460)
    (Rosette leaf::Others)
  • abnormal (PATO:0000460)
    (Rosette leaf::Others)
stem (PO:0009047)
  • present in fewer numbers in organism (PATO:0001997)
    (Stem::Number::few)

Invisible phenotypes

Specific phenotypes were NOT observed.

Original: F20310

Determination of introduced cDNA(s)

  • RAFL05-08-O16 - RIKEN Arabidopsis Full-length cDNAs - Original: RAFL05-08-O16 - Resource: pda00927

    full reading [+] show sequence

    Nucleotide sequence: RAFL05-08-O16 - full reading 
    AAAAGTGCTT CGAGTTTTTG TTAACCTTTT TCTCTGATCT AATGGCGATG 
    GAAGATCAAT CGGCGGCGAG ATCTATCGGA AAAGTTAGTT GGTTTAGCGA 
    TGGAAAAGGC TACGGTTTCA TTACTCCCGA TGATGGCGGC GAAGAGCTTT 
    TTGTTCATCA ATCCTCAATT GTCTCCGATG GATTCCGTAG CTTGACTCTT 
    GGTGAATCGG TTGAATACGA AATCGCGCTT GGAAGCGACG GAAAGACTAA 
    GGCCATTGAA GTTACTGCTC CCGGCGGCGG TTCACTTAAT AAGAAGGAAA 
    ACAGCTCCCG TGGATCCGGA GGTAATTGTT TTAATTGCGG TGAGGTTGGT 
    CATATGGCTA AGGATTGTGA CGGTGGAAGT GGTGGGAAAA GCTTTGGAGG 
    TGGTGGTGGT CGTAGATCTG GCGGCGAAGG TGAATGTTAC ATGTGTGGTG 
    ATGTGGGACA CTTCGCTAGG GATTGTAGGC AAAGCGGTGG TGGAAACAGC 
    GGCGGAGGAG GAGGAGGTGG TCGTCCGTGT TACAGTTGCG GTGAGGTTGG 
    TCATTTGGCA AAGGATTGTC GTGGTGGTTC TGGTGGAAAC AGATACGGAG 
    GAGGTGGTGG TCGTGGATCT GGCGGTGATG GATGCTACAT GTGTGGTGGT 
    GTGGGACATT TCGCTAGGGA TTGTAGGCAA AACGGCGGTG GAAACGTTGG 
    AGGTGGTGGA AGCACTTGTT ATACCTGTGG CGGAGTTGGC CACATTGCGA 
    AAGTTTGCAC CAGCAAGATA CCTTCTGGTG GTGGTGGTGG TGGTCGTGCT 
    TGTTACGAAT GTGGAGGAAC TGGCCATTTG GCTCGTGACT GTGATCGGAG 
    AGGAAGTGGA AGCAGCGGAG GTGGCGGTGG CAGTAACAAG TGCTTCATCT 
    GCGGCAAGGA AGGTCACTTT GCGAGGGAAT GTACTTCGGT TGCTTAACAA 
    AAAGATGCAA AGAAGAAGAG TAATGTTCAT AAACCTCTTT TGTTTTCTAT 
    TAAAATCTAC CTAATGCTCC TTTTTGGTGA CTATAATGTG ATTGCTAAAG 
    TCGTTTAGGA TGTTTAAGAA TGGTTGTTTT GGGAGTTTTT GATCTCTCTA 
    TATTACTCTT TTGACTGGTT TATGCAACCT GTTCACTGCT TTTGTTGATG 
    CCATAAGTTT GAGATCTTGA ATGATATGTG TGCTTGCGAA AAAAAAAAAA 
    AAAA

    Gene models with high sequence identity

    1. AT2G17870.1 [+] show detail - cold shock domain protein 3
      E-value: 0; Score: 100.00

     

    InterPro Scan Digest

    Program Description E-value
    ProfileScan Zinc finger, CCHC-type 10.79
    ProfileScan Zinc finger, CCHC-type 10.526
    ProfileScan Zinc finger, CCHC-type 10.691
    ProfileScan Zinc finger, CCHC-type 10.263
    ProfileScan Zinc finger, CCHC-type 9.175
    ProfileScan Zinc finger, CCHC-type 10.46
    ProfileScan Zinc finger, CCHC-type 10.493
    FPrintScan Cold-shock protein, DNA-binding 0.000000000019
    FPrintScan Cold-shock protein, DNA-binding 0.000000000019
    FPrintScan Cold-shock protein, DNA-binding 0.000000000019
    HMMSmart Cold shock protein 1e-21
    HMMSmart Zinc finger, CCHC-type 0.00012
    HMMSmart Zinc finger, CCHC-type 0.000085
    HMMSmart Zinc finger, CCHC-type 0.00021
    HMMSmart Zinc finger, CCHC-type 0.00006
    HMMSmart Zinc finger, CCHC-type 0.00051
    HMMSmart Zinc finger, CCHC-type 0.00073
    HMMSmart Zinc finger, CCHC-type 0.000008
    Gene3D Nucleic acid-binding, OB-fold 0.00000000000069
    Gene3D Zinc finger, CCHC retroviral-type 0.0000046
    Gene3D Zinc finger, CCHC retroviral-type 0.00027
    Gene3D Zinc finger, CCHC retroviral-type 0.0002
    HMMPanther CELLULAR NUCLEIC ACID BINDING PROTEIN 7.5e-44
    HMMPanther ZINC FINGER CCHC DOMAIN CONTAINING PROTEIN 7.5e-44
    HMMPfam Zinc finger, CCHC-type 0.00000078
    HMMPfam Zinc finger, CCHC-type 0.000025
    HMMPfam Zinc finger, CCHC-type 0.0000013
    HMMPfam Zinc finger, CCHC-type 0.000015
    HMMPfam Zinc finger, CCHC-type 0.000015
    HMMPfam Zinc finger, CCHC-type 0.0000043
    HMMPfam Zinc finger, CCHC-type 0.000000099
    HMMPfam Cold-shock protein, DNA-binding 9.3e-23
    superfamily Nucleic acid-binding, OB-fold-like 1.8e-20
    superfamily Retrovirus zinc finger-like domains 0.000000000034
    superfamily Retrovirus zinc finger-like domains 0.0000000008
    superfamily Retrovirus zinc finger-like domains 0.0000000031
    superfamily Retrovirus zinc finger-like domains 0.00022
    PatternScan Cold-shock conserved site 0

    See the detailed result >

    AT2G17870.1

    Model type
    Protein coding
    Short Description
    cold shock domain protein 3
    Curator Summary
    Encodes COLD SHOCK DOMAIN PROTEIN 3 (CSP3), involved in the acquisition of freezing tolerance.
    Computational Description
    cold shock domain protein 3 (CSP3); FUNCTIONS IN: DNA binding, zinc ion binding, nucleic acid binding; INVOLVED IN: response to cold, DNA duplex unwinding; LOCATED IN: nucleus, cytoplasm; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Nucleic acid-binding, OB-fold (InterPro:IPR012340), Cold-shock conserved site (InterPro:IPR019844), Zinc finger, CCHC retroviral-type (InterPro:IPR013084), Cold shock protein (InterPro:IPR011129), Nucleic acid-binding, OB-fold-like (InterPro:IPR016027), Zinc finger, CCHC-type (InterPro:IPR001878), Cold-shock protein, DNA-binding (InterPro:IPR002059); BEST Arabidopsis thaliana protein match is: cold shock domain protein 1 (TAIR:AT4G36020.1); Has 72472 Blast hits to 41123 proteins in 2889 species: Archae - 51; Bacteria - 27281; Metazoa - 11105; Fungi - 2852; Plants - 6181; Viruses - 14957; Other Eukaryotes - 10045 (source: NCBI BLink).
    Link
    InterPro Scan - TAIR