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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggctttgatcttccactttttttcttcttctaatatctgagcttgtaatttgtgccatgtgtaatcctgaaacttttgttcttatcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g44922.2
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|117245202|gb|CT843402.1|CT843402
EST:     ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
EST: gi|88411074|gb|CI606293.1|CI606293
EST:     ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAG
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAG
EST: gi|58609232|gb|CK037265.1|CK037265
EST:     ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
EST: gi|88360390|gb|CI612109.1|CI612109
EST:     ACTTATCCCAATCCACCTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
genomic: ACTTATCCCAATCCAC-TACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
EST: gi|58668738|gb|CK057424.1|CK057424
EST:     ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
EST: gi|88399416|gb|CI606037.1|CI606037
EST:     ACTTATCCCAATCCACTACAAGATCATCAAGCCTATTCAACTGTCAA                         GCAATATTTTGTTA
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTA
EST: gi|58606730|gb|CK034763.1|CK034763
EST:     ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
EST: gi|58671614|gb|CK060300.1|CK060300
EST:     ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
EST: gi|58671004|gb|CK059690.1|CK059690
EST:     ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAA                         GCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
genomic: ACTTATCCCAATCCACTACAAGATCATCCAGCCTATTCAACTGTCAAgtaaggcttt ... tcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttgtaatttgtgccatgtgtaatcctgaaacttttgttcttatcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG
                                 cttttgttcttatc  CT-rich tract
      taatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggctttgatcttccactttttttcttcttctaatatctgagcttgtaatttgtgccatgtgtaatcctgaaacttttgttcttatcgttatcagGCAATATTTTGTTAATGAAGATGACACTGTACCCCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG