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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggaaatcatgtattaaaatgggtcctcttgttgtaatttagttttcagattttgcctcaccattgattatgctgatggtaattttttactctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG

Basic information

species Oryza sativa
transcript LOC_Os11g43620.2
intron # 2
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|87018205|gb|CI297418.1|CI297418
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|86418484|gb|CI032693.1|CI032693
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|117223750|gb|CT842091.1|CT842091
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|86537089|gb|CI177295.1|CI177295
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55442446|gb|CV734541.1|CV734541
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55439258|gb|CV732932.1|CV732932
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|55439260|gb|CV732933.1|CV732933
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|8528391|gb|AU093206.1|AU093206
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|15846851|gb|BI795127.1|BI795127
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
EST: gi|163921024|gb|EG710124.1|EG710124
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... actctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagattttgcctcaccattgattatgctgatggtaattttttactctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG
                           tgctgat  putative branch site (score: 3)
                                       ttttttactcttt  putative PPT
                                    taattttttactcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggaaatcatgtattaaaatgggtcctcttgttgtaatttagttttcagattttgcctcaccattgattatgctgatggtaattttttactctttaagGATACCTTGTTTCTGTGGACTCTTATATGAATCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
aatggaaa
- - - - -catgtat
- - - - - - - - - - - - - - -cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat