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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtattgtgacagttttcagttttcattcagcttaattttggatgaaaaaggattaatacaggcttcatttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAGATCGAGAAGCTGTTCGAGTCTGTTGCAAGGTCTTGTGGAGGAAAAGGGG

Basic information

species Oryza sativa
transcript LOC_Os10g40780.1
intron # 50
splice site 3'
intron type U2

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|29644838|gb|CB649845.1|CB649845
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|29686205|gb|CB682480.1|CB682480
EST:     CCCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|38471984|gb|CF956115.1|CF956115
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|58679929|gb|CK068616.1|CK068616
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|29686204|gb|CB682479.1|CB682479
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|29616068|gb|CB621080.1|CB621080
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|58670528|gb|CK059214.1|CK059214
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|29674319|gb|CB670594.1|CB670594
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|89198422|gb|CI007482.1|CI007482
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|29629738|gb|CB634747.1|CB634747
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|29629914|gb|CB634923.1|CB634923
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
EST: gi|3767891|gb|AU031918.1|AU031918
EST:     CCCGCCTTCACCCGTGGGGNCTACTAATTACTTTCATTGAGCTTATAAAG                         -ATCCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGA
genomic: -CCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAAT-CCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGA
EST: gi|88220672|gb|CI220232.1|CI220232
EST:     ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAG                         AATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG
genomic: ACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAAAGgtatggtatt ... tttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcagcttaattttggatgaaaaaggattaatacaggcttcatttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAGATCGAGAAGCTGTTCGAGTCTGTTGCAAGGTCTTGTGGAGGAAAAGGGG
                            gattaat  putative branch site (score: 3)
                                        cttcatttccttc  putative PPT
                      aaaaaggattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtattgtgacagttttcagttttcattcagcttaattttggatgaaaaaggattaatacaggcttcatttccttcagAATCCACGCTACAGTTTTTGGGCTCGATCATTTACTCGCTGTGCACCTGAGATCGAGAAGCTGTTCGAGTCTGTTGCAAGGTCTTGTGGAGGAAAAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA