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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgattgtgtttggtgtcctgcaccgtttgtgaagaaaaaaaatgtttataactgtccacctttcagttcagttaaattacttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG

Basic information

species Oryza sativa
transcript LOC_Os01g60660.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 9
atttgattgtgtt-tggt--gtcctgcaccgtttgtgaagaaaaaaaatgtttataactgtccacctttcagttcagttaaattac-ttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG
 ||   | | ||| | ||  ||  ||| | |  | | || ||  |   ||||||  | |    |  ||   |||   ||  ||||| || |  || |  | |||||||||||||||||| ||||||||||| ||||| ||||| || ||||| |||||||| || |||
-ttctctcgagttatagtttgtattgccctgcattttaacaacgatcttgtttaccagt---tatgttctggttgttttttattacattgttattgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG

upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G166345_T03 (Zea mays), 3'ss of exon 9
atttgattgtgtt-tggt--gtcctgcaccgtttgtgaagaaaaaaaatgtttataactgtccacctttcagttcagttaaattac-ttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG------------------------------------
 ||   | | ||| | ||  ||  ||| | |  | | || ||  |   ||||||  | |    |  ||   |||   ||  ||||| || |  || |  | |||||||||||||||||| ||||||||||| ||||| ||||| || ||||| |||||||| || |||                                    
-ttctctcgagttatagtttgtattgccctgcattttaacaacgatcttgtttaccagt---tatgttctggttgttttttattacattgttattgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGGTACACTTCAGTGGCCTGTTTGATATGATGTAACAT

upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA04G40090.1 (Glycine max), 3'ss of exon 10
atttgattgtgtttggtgtcctgcaccgtttgtgaagaaaaaaaatgtttataactgtcc----acctttcagttcagttaaattacttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG
  | | |    ||| || |   ||||   ||||           ||   |||||||  |     |   |||| |  |  ||   |  || || |||  ||||||| ||||||| |||||||||||||| || || || || ||||||||||| || ||||| ||||||
--tggttcaaatttagtttgtagcacttgttgtcttattgtgctatagatataacttacttgagatgattcattatacctatgct--ttgtcgttctaatatagGATTGATGGAAAGCCAGAAGATGTACTAAACCCAAAAAAGAAACAGCTGGAGAAGATTACACCG

upper sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G14760.1 (Glycine max), 3'ss of exon 10
atttgattgtgtttggtgtcctgcaccgt-ttgtgaagaaaaaaaatgtttataactgtccacctttcagttcagttaaattacttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG
 |   ||| |  |||||  |      | | |||||      | | |   ||| |    |  |  |      | |     ||   || || |||  || |||| ||||||| |||||||||||||| || || || || ||||||||||| || ||||| ||||||
ttcaaattttagttggtagcacttgtcttattgtgctttggatata-acttacagtacttgagatcattaattatgcctatgctttgtcgttctaatttagGATTGATGGAAAGCCAGAAGATGTACTAAACCCAAAAAAGAAACAGCTGGATAAGATTACACCG

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|89189180|gb|CI048719.1|CI048719
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|86594926|gb|CI258180.1|CI258180
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGA-GTCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCG
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAG-CCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCG
EST: gi|58688789|gb|CK077476.1|CK077476
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|88272357|gb|CI386212.1|CI386212
EST:     GCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: GCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|86418870|gb|CI053671.1|CI053671
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|86492758|gb|CI135391.1|CI135391
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|86429228|gb|CI075909.1|CI075909
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|88206615|gb|CI206464.1|CI206464
EST:     TTGATTCCTCCAGAAGGAGTTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|86834522|gb|CI344453.1|CI344453
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|88408821|gb|CI554143.1|CI554143
EST:     GAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: GAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|86434980|gb|CI106213.1|CI106213
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|29672822|gb|CB669097.1|CB669097
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|88959962|gb|CI381840.1|CI381840
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|86823873|gb|CI258854.1|CI258854
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|89198563|gb|CI016648.1|CI016648
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|88448867|gb|CI557939.1|CI557939
EST:     TTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|29642064|gb|CB647071.1|CB647071
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|88831359|gb|CI083753.1|CI083753
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|29642108|gb|CB647115.1|CB647115
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|58694983|gb|CK083670.1|CK083670
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|15852252|gb|BI805048.1|BI805048
EST:     TGATTCCTCCACGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TGATTCCTCCA-GAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
EST: gi|88380986|gb|CI523557.1|CI523557
EST:     TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGG                         GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA
genomic: TTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaatta ... tcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttataactgtccacctttcagttcagttaaattacttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG
   ttataac  putative branch site (score: 2)
                                     cttatccttc  putative PPT
                           agttaaattacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgattgtgtttggtgtcctgcaccgtttgtgaagaaaaaaaatgtttataactgtccacctttcagttcagttaaattacttatccttcacatatagGTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- -tgattgt
- - - - - -tttggtg
- - - - - - - - - tcctgca
- - - - - - - - - - - - - - - - - - -aaaaaaa