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 1.9e-11
    FPrintScan Cold-shock protein, DNA-binding 1.9e-11
    FPrintScan Cold-shock protein, DNA-binding 1.9e-11
    HMMSmart Cold shock protein 1e-21
    HMMSmart Zinc finger, CCHC-type 0.00012
    HMMSmart Zinc finger, CCHC-type 8.5e-05
    HMMSmart Zinc finger, CCHC-type 0.00021
    HMMSmart Zinc finger, CCHC-type 6e-05
    HMMSmart Zinc finger, CCHC-type 0.00051
    HMMSmart Zinc finger, CCHC-type 0.00073
    HMMSmart Zinc finger, CCHC-type 8e-06
    Gene3D Nucleic acid-binding, OB-fold 6.9e-13
    Gene3D Zinc finger, CCHC retroviral-type 4.6e-06
    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 7.8e-07
    HMMPfam Zinc finger, CCHC-type 2.5e-05
    HMMPfam Zinc finger, CCHC-type 1.3e-06
    HMMPfam Zinc finger, CCHC-type 1.5e-05
    HMMPfam Zinc finger, CCHC-type 1.5e-05
    HMMPfam Zinc finger, CCHC-type 4.3e-06
    HMMPfam Zinc finger, CCHC-type 9.9e-08
    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 3.4e-11
    superfamily Retrovirus zinc finger-like domains 8e-10
    superfamily Retrovirus zinc finger-like domains 3.1e-09
    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