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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCTCTTGCAATGTCAATGGAGGAGGGTTCTTCAGGGGCTGCAGCGGCTGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtccttttctccgctgagctctttcattcttctataactttaatttaattcattcaaacgacaatgattcaggacttactagttcataggtgtatc...

Basic information

species Oryza sativa
transcript LOC_Os03g13970.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G165926_T01 (Zea mays), 5'ss of exon 7
---------------------CAGGCTCTTGCAATGTCAATGGAGGAGGGTTCTTCAGGGGCTGCAGC---GGCTGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtccttttctccgctgagctctttcattcttctataactttaatttaattcattcaaacgacaatgattcaggacttactagttcataggtgtatc
                     ||||| |||||||||||||||||||  ||| |||||||  |||||||   | ||||  ||||||||||||| |||| || || |||||  ||||||||| | |||  ||  | |  |  | |     | |  |   || ||  || |  | |  ||| |||   |  | | | ||||                          
GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGTGGTGCTTCAGGATCTGCAGCTGTGACTGACTCTGCTATGGCAGAAGCTGgtgcagttgaccctgacttggcattgggtgtgttttctcttatgtttgcagcctcaaaaattgtagcacatacagt--atttattgctatca-attaattcta------------------------
















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|88845879|gb|CI084609.1|CI084609
EST:     ACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: ACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86431099|gb|CI083522.1|CI083522
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|218485696|gb|FG969920.1|FG969920
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88831185|gb|CI081995.1|CI081995
EST:     TGATGCTGCTATGGCAGAGTCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86538942|gb|CI179148.1|CI179148
EST:     AGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: AGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86478545|gb|CI121178.1|CI121178
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|94362977|gb|CI053138.1|CI053138
EST:     CTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: CTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88203319|gb|CI203168.1|CI203168
EST:     TGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88344598|gb|CI637207.1|CI637207
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGCACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|218483651|gb|FG955547.1|FG955547
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86259614|gb|CI065487.1|CI065487
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGAGGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|29673812|gb|CB670087.1|CB670087
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|24468801|gb|CA305750.1|CA305750
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86435819|gb|CI107052.1|CI107052
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CCCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|29686951|gb|CB683226.1|CB683226
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|88960606|gb|CI006567.1|CI006567
EST:     ATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: ATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86255672|gb|CI066735.1|CI066735
EST:     CTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: CTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|86492426|gb|CI135059.1|CI135059
EST:     CCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: CCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
EST: gi|29638893|gb|CB643902.1|CB643902
EST:     TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAG                         CTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA
genomic: TGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtcctt ... ttctgcgcagCTCTTCAAATGTCTGTCCAGGACGCAGGCGGGTCTAGTCAGTCTGATATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGCTCTTGCAATGTCAATGGAGGAGGGTTCTTCAGGGGCTGCAGCGGCTGATGCTGCTATGGCAGAGGCTGCTGTAGATGACCAGGACTTGGCACTAGgtaggtccttttctccgctgagctctttcattcttctataactttaatttaattcattcaaacgacaatgattcaggacttactagttcataggtgtatc

- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT