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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttatttttcctgtaaactttcagtatgcatttatcaatgtgttcttaccaggtttgactttgagttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA

Basic information

species Oryza sativa
transcript LOC_Os08g07960.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 3
gtaagtttatttttcctgta-aactttcagtatgcatttatcaatgtgttctt----accagg----------tttgactttgagttttgtg---cagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA
|||  |||  || | ||||  ||  | ||||  || ||| | | |||| | |     ||| ||          |||| |||||  ||||||    |||||| |||||||||||||||||||||| |  ||||| |||||||| || || || ||||| ||||| 
gtagctttgcttatgctgtgtaatctgcagttggcctttgtaactgtgatgtatggaacccggattgtttggctttggctttgtattttgtctaccagGTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCG
















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|88451540|gb|CI565593.1|CI565593
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|25799251|gb|CA755212.1|CA755212
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|29681300|gb|CB677575.1|CB677575
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|10794894|gb|AU108860.1|AU108860
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCANCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|29615879|gb|CB620891.1|CB620891
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGGGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88394449|gb|CI605790.1|CI605790
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|33793654|gb|CF322711.1|CF322711
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88417412|gb|CI579073.1|CI579073
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88356897|gb|CI620785.1|CI620785
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88394469|gb|CI605810.1|CI605810
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88399681|gb|CI583415.1|CI583415
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|33795033|gb|CF323392.1|CF323392
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88397869|gb|CI583187.1|CI583187
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTA
EST: gi|58598341|gb|CK008869.1|CK008869
EST:     TTTAGCCCAGAGAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: TTTAGCCCA-A-AGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
EST: gi|88417428|gb|CI579089.1|CI579089
EST:     GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAG                         GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA
genomic: GTTTTAGCCCAAAGAGCAACCTTCTGGTGGCAACTTCCTGGGATAACCAGgtaagtttat ... ttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtatgcatttatcaatgtgttcttaccaggtttgactttgagttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA
         atttatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttatttttcctgtaaactttcagtatgcatttatcaatgtgttcttaccaggtttgactttgagttttgtgcagGTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG