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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttgttattgtttgttctatcaatttgacatccaggtaatacaacgccaactaactattttgcactctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g16900.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 6
-----------------gtaaatttgttattgtttgttctatcaatttgac-atccaggtaatacaacgccaactaac---tattt-tgcactctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG
                  || |      || |      ||| || |  | | ||||   | |||   |     || ||   | ||| |    | | |||| ||||| ||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||
gctcggttattttttccctagaccccacatgggagccgctagcactaggtctatccgattgatatggcaaatgctcacatttgtttgtttctttttccagTTGCAATATTGGTGAAGGTGGCATTTGTCTAGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 6
gtaaatttgttattgtttgttctatcaatttgacatccaggtaatacaacgccaactaactattt-tgcactctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG
||||| ||| | ||||||  ||||      |    |   | ||   |||   |    |  | ||| |  | | |||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
gtaaacttgct-ttgtttaatctaatttccttgggtattgatacagcaaaagctcacatttgtttgtttattttcccagTTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaa-atttgttatt--gtttgttctatca--atttgacatccaggtaatacaacg---ccaactaactattttgcactctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG
|||| |||||||  |  || |     || |   | |   ||  |  | |  |||       |      |||| ||   | | ||||    || ||||| || | ||| |||   || || |||||||||||||| ||||| |||||||||||||| | |
gtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccagTATGAATATTGGGGAGGATGGTATTGCCCTTGCTGAAGCTGTTCACGGCTCTGCACCTGATATTGCTGGAATG

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|27920689|gb|CB096497.1|CB096497
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|55410982|gb|CV723358.1|CV723358
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29640079|gb|CB645088.1|CB645088
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|218503212|gb|FG950056.1|FG950056
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|27554418|gb|CA998318.1|CA998318
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|41883639|gb|BX928526.1|BX928526
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|33799865|gb|CF325799.1|CF325799
EST:     CTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: CTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29673427|gb|CB669702.1|CB669702
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29616639|gb|CB621651.1|CB621651
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|87036093|gb|CI189540.1|CI189540
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29639682|gb|CB644691.1|CB644691
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|55410961|gb|CV723337.1|CV723337
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29619531|gb|CB624543.1|CB624543
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29664535|gb|CB660810.1|CB660810
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|86495897|gb|CI138530.1|CI138530
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|27554444|gb|CA998344.1|CA998344
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29616640|gb|CB621652.1|CB621652
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|4714232|gb|AU058199.1|AU058199
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|29671573|gb|CB667848.1|CB667848
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
EST: gi|86900281|gb|CI296324.1|CI296324
EST:     ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAG                         CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC
genomic: ATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttgt ... actctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaatttgacatccaggtaatacaacgccaactaactattttgcactctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG
                              aactaac  putative branch site (score: 1)
                                       ttttgcactctccc  putative PPT
                                 taactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttgttattgtttgttctatcaatttgacatccaggtaatacaacgccaactaactattttgcactctcccagCTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT