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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagtttatgtaagccagtatattttggtctgacatgcttcttttgttgcaaaagacactcttatgagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG

Basic information

species Oryza sativa
transcript LOC_Os02g02750.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02750.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G466281_T01 (Zea mays), 3'ss of exon 13
-atagtttatgtaagccagtatattttggtctgacatgcttcttttgttgcaaaaga-cactcttatgagcattacctaatatctacttctatta-tgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG
 || | |||| | |     |    ||     || | |  |||  ||  || |    |  |    ||||| |||||| | | |||| ||| ||||  | ||||||| |||||||||||||||||||| |||||||| ||||| ||| |||| |||||||||||||||
cat-gcttattttattt--ttctcttacagatgccctctttcagttactgtagtgcagtaaaaatatgaacattactttacatctgcttatattgctccacagGGAAGAATGATTCTGGCTCACTTGTGTGATGAACCCAAGGGTTTGAAAACAGGGATGTGCATG

upper sequence: LOC_Os02g02750.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 14
atagtttatgta-agccagtatattttggtctgacatgcttcttttgttgcaaaagacactct-tatgagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG
| | |   ||||  |  | |  || ||    || |       |  | ||||| |   | |  | ||| |  |||  || || |      || | ||   ||||| || |||||| |||| |||||||||||||| || || |||||||| || ||||||||||||
aaaatgcttgtacggttattgaatcttatattgcctcttgcttccttttgcatatatctccatatattatgatt-tcttatgtgggaagct-taatttgcagGGGAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG

upper sequence: LOC_Os02g02750.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 14
ata-gtttatgtaagccagtatattttggtctgacatgcttcttttgttgcaaaagacactct-tatgagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG
| | | || | |  |  | |  || ||  | || |       |  | ||| | |  || |  | ||| |  ||| | ||  |   |    || | |   ||||| || |||||| |||| |||||||||||||| || || |||||||| || ||||||||||||
acatgcttgtatg-gttattgaatcttattttgcctctggcttccttttgtatacaactccatatattatgatttcttatgagggaagcttaat-tttgcagGGAAGGATGATTTTGGCACACTTATGTGATGAACCTAAGGGTCTGAAAACTGGGATGTGCATG

upper sequence: LOC_Os02g02750.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 13
atagtttatgtaagccagtatattttggtctgac--atgcttcttttgttgcaaaagacactcttat-gagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG
   || | | |      | |   ||  ||  ||   ||  | |  || |||| ||| |   | | || || ||  |  || ||| |  |||  || |   ||||| ||||||||||| |||||||| ||||||||||| ||||| || || |||   |||||||||
---gtatgtcttgattcgaaatcttaagttagatcaatagtacaattattgcgaaaaa-gttgtgatagaacaaaagttactatgtttttccttttt---cagGGAAGAATGATTCTTGCTCACTTGTGTGATGAGCCTAAAGGACTAAAAACAAACATGTGCATG

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|33803550|gb|CF327650.1|CF327650
EST:     AGCCACATCTTCTAGTTATTGGAACTGGTTTTGCATTTGGCTTTCTTGTG                         GGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACA
genomic: AGCCACATCTTCTAGTTATTGGAACTGGTTTTGCATTTGGCTTTCTTGTGgtaaggcctt ... ttatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACA
EST: gi|88691614|gb|CI733692.1|CI733692
EST:     AGCCACATCTTCTAGTTATTGGAACTGGTTTTGCATTTGGCTTTCTTGTG                         GGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACA
genomic: AGCCACATCTTCTAGTTATTGGAACTGGTTTTGCATTTGGCTTTCTTGTGgtaaggcctt ... ttatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcaaaagacactcttatgagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG
                           acctaat  putative branch site (score: 3)
                                       cttctatt  putative PPT
                              taatatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagtttatgtaagccagtatattttggtctgacatgcttcttttgttgcaaaagacactcttatgagcattacctaatatctacttctattatgcacagGGCAGAATGATTCTGGCTCACTTATGTGATGAGCCCAAAGGTCTGAAGACAGGGATGTGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA