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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatacaaatgtcctatccatacctgttttcttttcatggtgtaatgctcataactaaacaatcttctctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCATGCTGATGACTTACTCCTAGGGGACAGCCAGAATAGTTGGAACCGCATGA

Basic information

species Oryza sativa
transcript LOC_Os03g13790.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G104255_T01 (Zea mays), 3'ss of exon 3
gtactatacaaatgtcctatccatacctgttttcttttcatggtgtaatgctcat--aactaaacaatcttctctc--ctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCATGCTGATGACTTACTCCTAGGGGACAGCCAGAATAGTTGGAACCGCATGA
         |  ||    |  ||||  |||| | || |  | |  | ||  |     | || | |  | || | |    || |||||||||||||| |||||| ||||||||||||||||||| | || |||| | || |||||| ||||  |||||||||| || ||||||||||||||  | |
-------gtacttgaagaaatcataa-tgttcttttgtactagcattatcttagctgagcttaccctttttttattaattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAAGCCGATGACATACTTATAGGGGACAGTCAAAATAGTTGGAACCGTCTAA

upper sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G152319_T02 (Zea mays), 3'ss of exon 13
gtactatacaaatgtcctatccatacctgttttcttttcatggt-gtaatgctcataactaaacaatcttctctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCATGCTGATGACTTACTCCTAGGGGACAGCCAGAATAGTTGGAACCGCATGA
|||||  |  ||  |   ||       |||  |    | ||  | |    ||| | |  |      | |  | || || |||||||||||||| |||||| ||||||||||||||||| ||| || ||| ||  | |||||| ||||  |||||||||| || | |||||||||  | |   
gtacttgatgaaattataatgttcttttgtactggcattatcttagctgagcttacatttt-----tttcttttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC
















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|29617185|gb|CB622197.1|CB622197
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|86257214|gb|CI004032.1|CI004032
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|86592896|gb|CI270453.1|CI270453
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCCAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|29618832|gb|CB623844.1|CB623844
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|29621696|gb|CB626707.1|CB626707
EST:     GTGACCACGATTTTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|15854139|gb|BI806935.1|BI806935
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|87022124|gb|CI259196.1|CI259196
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|86478667|gb|CI121300.1|CI121300
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|29621640|gb|CB626651.1|CB626651
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|88841876|gb|CI081132.1|CI081132
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|88197571|gb|CI197421.1|CI197421
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|87014871|gb|CI271470.1|CI271470
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|86477380|gb|CI120013.1|CI120013
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|29626961|gb|CB631972.1|CB631972
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|29626892|gb|CB631903.1|CB631903
EST:     GTGACCACGATTTTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CATGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|29644351|gb|CB649358.1|CB649358
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
EST: gi|86482080|gb|CI124713.1|CI124713
EST:     GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGG                         CCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT
genomic: GTGACCACGATTCTGCTCCGAAGGATCAATCTCTAGCTGACTTATACTGGgtactataca ... ctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttcttttcatggtgtaatgctcataactaaacaatcttctctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCATGCTGATGACTTACTCCTAGGGGACAGCCAGAATAGTTGGAACCGCATGA
                             aactaaa  putative branch site (score: 2)
                                    caatcttctctcct  CT-rich tract
                           ataactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatacaaatgtcctatccatacctgttttcttttcatggtgtaatgctcataactaaacaatcttctctcctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCATGCTGATGACTTACTCCTAGGGGACAGCCAGAATAGTTGGAACCGCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT