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  3. RAFL05-08-O16

RAFL05-08-O16

RIKEN Arabidopsis Full-length cDNAs

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

Mutant lines with RAFL05-08-O16 introduced

  • F20310 - rosette leaf::decreased size / rosette leaf::increased width / rosette leaf::present in fewer numbers in organism / whole plant::decreased height / rosette leaf::epinastic / rosette leaf::abnormal / rosette leaf::abnormal / stem::present in fewer numbers in organism
  • F20640 - Specific phenotypes were NOT observed.

Mutant lines with disrupted or induced

3 mutant lines found