S03430

RIKEN rice full-length cDNA overexpressed Arabidopsis lines

Original: S03430

Phenotypes

Morphological phenotypes

Specific phenotypess were NOT observed.

Invisible phenotypes

Specific phenotypes were NOT observed.

Original: S03430

Determination of introduced cDNA(s)

  • J023041B11 - Rice Full-length cDNAs - Original: J023041B11

    full reading [+] show sequence

    Nucleotide sequence: J023041B11 - full reading 
    GGGACTCTCC CGATCCTTCC CCAACTCGGC GTCGCGCCGC CTCAACCGAA 
    GCAAGGAGCA AAGCGGGGAT TCAGAACGGG AAGGAGAAGG TCCGGTTCGT 
    CCGCTCTCGA GCTCAAGTGT CAGTTGAAGT GTTTTGAAAG TCATGGCGGA 
    GCATTTGGCT TCAATATTTG GGACTGAGAA GGATAGGGTT AACTGCCCCT 
    TTTACTTCAA GATTGGGGCT TGCCGTCATG GGGATCGTTG CTCCCGTCTG 
    CACAACAGGC CAACTGTGTC GCCGACAATT GTGCTTGCTA ACATGTATCA 
    GCGCCCTGAT ATGATCACAC CAGGAGTCGA TGCTCAAGGC CAACCTATTG 
    ATCCTGAAAA GATGCAGGAG CACTTTGAGG ATTTCTATGA GGATATCTAT 
    GAGGAGCTGA GCAAGTTTGG TGAGGTTGAG ACCCTCAATG TCTGTGATAA 
    CCTTGCTGAC CACATGATAG GCAATGTGTA TGTCCAGTTC AGGGAGGAAG 
    AACAGGCAGT CGCTGCGCAT AATGCCCTTC AAGGTCGCTT CTACTCAGGG 
    CGCCCAATAA TTGTTGAGTA TTCCCCTGTG ACTGATTTCC GTGAGGCGAC 
    CTGTAGGCAG TTTGAGGAGA ACAGCTGCAA CCGTGGGGGC TACTGTAATT 
    TTATGCATGT AAAGCAGATT GGCAGGGAGC TCAGGAGGAA GCTTTATGGG 
    GGGCGATCCA GGAGGAGCCA TGGGAGAAGC CGCAGCCCAA GCCCACGCCA 
    CAGGAGGGGC AATCGTGACC GTGATGATTT CCGCCGTGAA CGTGATGGTT 
    ATCGTGGTGG TGGTGATGGT TACCGTGGCG GCGGCGGTGG CGGTGGTGGT 
    GACGGTTACC GCGGCGGTGA TAGTTACCGT GGTGGTGGTG GTGGTGGACG 
    CAGGGGTGGG GGCAGCAGGT ATGACAGGTA TGATGATGGA GGAAGGCGCA 
    GGCATGGCAG CCCCCCAAGG CGTGCAAGGA GCCCAGTCAG GGAAAGCAGC 
    GAGGAACGCA GGGCGAAGAT TGAACAGTGG AACCGTGAAC GGGAGGAAAA 
    GCCTTGAACG AAAGCAGTGA TATCTCTATG GATGGCCGGT TCATGCCTTC 
    ATGGCAATCA CTATCCGCTG GAGTCGTGGT GTGCTGCTAT GTTCTAAGTG 
    GATATTTAGT GTGTGTCGTT TGGTACTCAT GCTTGGCTGA GTAACCCTTT 
    TAAATGCAGG ATTCTGGATT CTATTTACAT TGTGTTTCGT TTGACGTGTA 
    AACCGCCGTT TGTTTTTAAA TATGCAATAT TGGATCTTTT GTCAGTCTAT 
    TATCCTGTC

    Gene models with high sequence identity

    1. AT5G42820.2 [+] show detail - Zinc finger C-x8-C-x5-C-x3-H type family protein
      E-value: 4e-97; Score: 352.00

     

    InterPro Scan Digest

    Program Description E-value
    Gene3D Nucleotide-binding, alpha-beta plait 5.4e-38
    ProfileScan RNA recognition motif, RNP-1 11.145
    ProfileScan Zinc finger, CCCH-type 13.065
    ProfileScan Zinc finger, CCCH-type 11.892
    FPrintScan U2 auxiliary factor small subunit 3.4e-64
    FPrintScan U2 auxiliary factor small subunit 3.4e-64
    FPrintScan U2 auxiliary factor small subunit 3.4e-64
    FPrintScan U2 auxiliary factor small subunit 3.4e-64
    FPrintScan U2 auxiliary factor small subunit 3.4e-64
    FPrintScan U2 auxiliary factor small subunit 3.4e-64
    HMMPanther U2 auxiliary factor small subunit 5.6e-120
    HMMSmart Zinc finger, CCCH-type 0.0068
    HMMSmart Zinc finger, CCCH-type 0.014
    superfamily RNA-binding domain, RBD 8.3e-25
    superfamily CCCH zinc finger 0.00056
    superfamily CCCH zinc finger 0.0031
    HMMPfam Zinc finger, CCCH-type 0.00000036
    HMMPfam Zinc finger, CCCH-type 0.00021
    HMMPfam RNA recognition motif, RNP-1 0.000013

    See the detailed result >

    AT5G42820.2

    Model type
    Protein coding
    Short Description
    Zinc finger C-x8-C-x5-C-x3-H type family protein
    Curator Summary
    U2 auxiliary factor small subunit. The atU2AF35b protein and its homolog, atU2AF35a, contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83% identical, and each Arabidopsis homolog shows approximately 70% similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots: atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions.
    Computational Description
    U2AF35B; FUNCTIONS IN: RNA binding, zinc ion binding, nucleotide binding, nucleic acid binding; INVOLVED IN: photoperiodism, flowering; LOCATED IN: nucleus; EXPRESSED IN: 28 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, CCCH-type (InterPro:IPR000571), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677), U2 auxiliary factor small subunit (InterPro:IPR009145); BEST Arabidopsis thaliana protein match is: U2 snRNP auxiliary factor small subunit, putative (TAIR:AT1G27650.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    Link
    InterPro Scan - TAIR