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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctcattctccaagttattttttttcttaaaagtatgtactatgttttggtagattttagttcttctgggggctactaaacttttagttccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTATCGACCTCCAGGAATAAAATCTCTGAAGTTCAGCAAATTCTCTCTTGGAA

Basic information

species Oryza sativa
transcript LOC_Os07g22640.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22640.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G092129_T01 (Zea mays), 3'ss of exon 4
---aatctcattctccaagttattttttttcttaaaagtatgtactatgttttggtagattttagttcttctgggggctactaaacttttagttccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTATCGACCTCCAGGAATAAAATCTCTGAAGTTCAGCAAATTCTCTCTTGGAA
     |   |    || || | | | ||||  |  ||   ||| |  |    |  |   |  ||   | | |  |     || |  ||| | ||  |||| ||||||| || | ||| || |||||||| ||||| ||||||||||||||||| || |||||||||||||||||| |||||||||||||||| ||||||||||
tttgttaagacatgcctagctgtatgttttgctgcaatcttgtgccctaccctact---tcataagccatatatgctgagcttacttttcattttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTACCGGCCTCCAGGAATAAAATCTTTGAAGTTCAGCAAATTTTCTCTTGGAA

upper sequence: LOC_Os07g22640.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G02370.2 (Glycine max), 3'ss of exon 3
-----aatctcattctccaagttatttttttt-cttaaaagtatgtactatgttttggtagattttagttcttctgggggctactaaacttttagttccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTATCGACCTCCAGGAATAAAATCTCTGAAGTTCAGCAAATTCTCTCTTGGAA
      | ||  | |   || ||   ||     | || | || | | |  ||||||| |  |   ||| |    |       | | |   ||| |||   ||| |||| || ||    ||  |||  ||||||||||| ||||||||||| || ||  ||||||||||||| |  ||  |||||||||||||  | || |||||||
ttggagaccttttacattaaatttccttgcaaacatagaggtgtattcc-tgttttgcttaaa--tagatgacataatattgattga---ttttgttttcttttagGCAGCAACCTTGGTGATCAGAGAATCTGTTGAACCACTGCTAGAAGAGTACAGACCTCCAGGAATTACTTCATTGAAGTTCAGCAAGCTGTCACTTGGAA

upper sequence: LOC_Os07g22640.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G09070.1 (Glycine max), 3'ss of exon 4
aatctcattctccaagttatttttttt-cttaaaagtatgtactatgttttggtagattt--tagttcttctgggggctactaaacttttagttccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTATCGACCTCCAGGAATAAAATCTCTGAAGTTCAGCAAATTCTCTCTTGGAA
 | ||  | |   || ||   ||     | || | || | | |  ||||||| |  | |   |  |     | |    |  |  | |||  |||   ||| |||| || ||    ||  | |  ||||||||||| ||||||||||| || ||  ||||||||||||| |  ||  |||||||||||||  | || |||||||
gaccttttacgttaaatttccttgcaaacatagaggtgttttcc-tgttttgcttaaatagatgatgtgatttgatattgattgatttt--gttttcttttagGCAGCAACCATGGTGATAAGAGAATCTGTTGAACCACTGCTAGAAGAGTACAGACCTCCAGGAATTACTTCATTGAAGTTCAGCAAGCTGTCACTTGGAA

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|29655975|gb|CB652250.1|CB652250
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
EST: gi|29624991|gb|CB630002.1|CB630002
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
EST: gi|86904903|gb|CI310696.1|CI310696
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
EST: gi|44674448|gb|CR287882.1|CR287882
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
EST: gi|29630138|gb|CB635147.1|CB635147
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
EST: gi|58606676|gb|CK034709.1|CK034709
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
EST: gi|29662931|gb|CB659206.1|CB659206
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
EST: gi|29624993|gb|CB630004.1|CB630004
EST:     TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAA                         GCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT
genomic: TGAAATGGCTGAACAAGCATCTCAGCAAACTCTGGCCTTTCGTTGATCAAgtaagacaaa ... tccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggtagattttagttcttctgggggctactaaacttttagttccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTATCGACCTCCAGGAATAAAATCTCTGAAGTTCAGCAAATTCTCTCTTGGAA
                              tactaaa  putative branch site (score: 1)
                                            ttccatttc  putative PPT
                                 taaactttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctcattctccaagttattttttttcttaaaagtatgtactatgttttggtagattttagttcttctgggggctactaaacttttagttccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTATCGACCTCCAGGAATAAAATCTCTGAAGTTCAGCAAATTCTCTCTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG