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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAAGAAGATATGATTTGCTCCTGTGATGGTGATGGTGAAGTCCGCAGCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatgcaacttcatgtgtttcatggtatcttctgctttaacattcaacttctgatgcttgtctctgtttccaatcatttttgtcccaacag

Basic information

species Oryza sativa
transcript LOC_Os01g42260.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G425377_T01 (Zea mays), 5'ss of exon 7
GAACAAAGAAGATATGATTTGCTCCTGTGATGGTGATGGTGAAGTCCGCAGCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatgcaacttcatgtgtttcatggtatcttctgctttaacattca-acttctgatgcttgt----ctctgtttccaatcat-ttttgtcccaacag
 || ||||| |||||||| |||||||||||| ||||||| ||||| |||||||||||||||||||||||||||||  |||| | ||||||||| |||||||||  |   || |  |  | | ||||||||  || ||||||| | |||| | | ||   ||| |  |     |||   || |||||| |||||||    |||
AAATAAAGAGGATATGATATGCTCCTGTGATAGTGATGGGGAAGTGCGCAGCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtacacg--gctatcttttatatttcatggggtcatctgcttaatcattaagattttctatgatcatgattttcttcctcaaatcatattttgtcatcccag

upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G022383_T01 (Zea mays), 5'ss of exon 15
GAACAAAGAAGATATGATTTGCTCCTGTGATGGTGATGGTGAAGTCCGCAGCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatgcaacttcatgtgtttcatggtatcttctgctttaacattcaacttctgatgcttgtctctgtttccaatcat-ttttgtcccaacag
 |||||||| |||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||  |||| | ||||||||| |||||||||||  |||  |  |  | | ||||||||  || |  |||| | ||||         | | || |||||| |  ||||| | |||||||    |||
AAACAAAGAGGATATGATATGCTCCTGTGATGGTGATGGGGAAGTGCGCAGCTGGAGCATAAATAATGGTAGCTGTTTGACATGTGTTAAGGTGTTTAAGgtatg--atgttatctt-tatatttcatggggtcataagcttaatcatt---------aagattttctctgat--caatcgtattttgtcgtcccag
















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|88221810|gb|CI221766.1|CI221766
EST:     GAGCATAAATAATGGTAGCTGCTTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|29681692|gb|CB677967.1|CB677967
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|4714252|gb|AU058219.1|AU058219
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACNTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|86430973|gb|CI083396.1|CI083396
EST:     AGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: AGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|58608277|gb|CK036310.1|CK036310
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|58682276|gb|CK070963.1|CK070963
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|33690021|gb|CF318260.1|CF318260
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGAAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|58604540|gb|CK015068.1|CK015068
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|16575961|gb|BI803257.1|BI803257
EST:     CCTGACCTTTGTTAA-GTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTGGCA
genomic: CCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|29673281|gb|CB669556.1|CB669556
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|218488081|gb|FG946110.1|FG946110
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|29638960|gb|CB643969.1|CB643969
EST:     GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
EST: gi|3107649|gb|D43389.1|D43389
EST:     GCTGGNGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGGAGGT-CTACTCAGATGCGATTT
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGG-AGGTGCTACTCAGATGCGATTT
EST: gi|38478243|gb|CF962376.1|CF962376
EST:     GCTGGAGCATAAATAATGGTGGCTGCCTGACCTTTGTTAAGGTCTTTAAG                         GGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA
genomic: GCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatg ... gtcccaacagGGAGGTGCTACTCAGATGCGATTTCAACCTCAAAAGGGAAAATATCTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAAAGAAGATATGATTTGCTCCTGTGATGGTGATGGTGAAGTCCGCAGCTGGAGCATAAATAATGGTAGCTGCCTGACCTTTGTTAAGGTCTTTAAGgtatgcaatgcaacttcatgtgtttcatggtatcttctgctttaacattcaacttctgatgcttgtctctgtttccaatcatttttgtcccaacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC