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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcatccttcaactgtatatgctgatgctgttataaattgtgcgataatcactgcaacacatgtccaaacgtttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATGCCCATGATCGATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g64670.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------gtgatcatccttcaactgta--tatgctgatgctgttataaattgtgcgataatcactgcaacacatgtccaaacgtttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATGCCCATGATCGATCAG
                                   | | || || ||    || |  ||  | | ||  |      |   ||  |   |   | |||  |     |  || |||     ||||| |||||  |||| ||||| ||||| ||||| |||||||| || || ||||||||||| ||||||
gtagttcaaactagatagcatttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgagtagattggaagtgtttttacaa-gctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG

upper sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 4
gtgatcatccttcaactgtatatgctgatgctgttataaattgtgcgataatcactgcaacacatgtccaaacgtttaattg-cagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATGCCCATGATCGATCAG
|||| | ||| ||  || | | |  |  | |  |  |    | |    ||| | ||      || ||   ||| ||| ||   |||||||| ||  |||| ||    ||||||||||| |  |||||||| |||||||| ||||||||||||
gtgagcttccatct-ctttttttcttttttccctggttttgtct-tagtaaacgctctcggccaagt--gaacttttcatgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|218483273|gb|FG944903.1|FG944903
EST:     GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAG                         GAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATG
genomic: GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAGgtgatcatcc ... ttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATG
EST: gi|218485453|gb|FG947366.1|FG947366
EST:     GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAG                         GAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATG
genomic: GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAGgtgatcatcc ... ttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATG
EST: gi|218503045|gb|FG970333.1|FG970333
EST:     GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAG                         GAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATG
genomic: GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAGgtgatcatcc ... ttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATG
EST: gi|88395925|gb|CI593127.1|CI593127
EST:     GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAG                         GAGCCAGTGATTCCCGGCCTGCTTTCTCC
genomic: GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAGgtgatcatcc ... ttaattgcagGAGCCAGTGATTCCCGGC-TGCTTTCTCC
EST: gi|218499150|gb|FG960130.1|FG960130
EST:     GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAG                         GAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGCCTCATG
genomic: GAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGCTCATGCAGgtgatcatcc ... ttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttataaattgtgcgataatcactgcaacacatgtccaaacgtttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATGCCCATGATCGATCAG
                                           gtttaat  putative branch site (score: 4)
     ataaattgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcatccttcaactgtatatgctgatgctgttataaattgtgcgataatcactgcaacacatgtccaaacgtttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATGCCCATGATCGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT