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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcagttcactgttttctagaatccaattgctttgtactatcgtgctacgctgagagtggatataatcagagctaactaagatgcttttctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG

Basic information

species Oryza sativa
transcript LOC_Os07g43060.2
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|88212631|gb|CI212271.1|CI212271
EST:     TCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: TCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|55431292|gb|CV728660.1|CV728660
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|55431294|gb|CV728661.1|CV728661
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|88838475|gb|CI375023.1|CI375023
EST:     GGATCACGACAACGT-GTCAACTGCACCACCCCCAAGTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|88976243|gb|CI024460.1|CI024460
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|163919996|gb|EG709802.1|EG709802
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTCGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|87019382|gb|CI279892.1|CI279892
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|86423375|gb|CI060948.1|CI060948
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|58610018|gb|CK038051.1|CK038051
EST:     AACGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGTG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGA
genomic: AAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAG-Ggtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGA
EST: gi|11610378|gb|AU166054.1|AU166054
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|8857385|gb|AU094703.1|AU094703
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|163928022|gb|EG709470.1|EG709470
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
EST: gi|88833830|gb|CI077311.1|CI077311
EST:     GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGG                         AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG
genomic: GAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 56 (downstream exon)
Score: 32

TTCATGGAGCAAGGCTGCGAGAACTGCCCCTTCCTCGACATGGAAAGGGATCACGACAACGTCGTCAACTGCACCACCCCCAACTTCACAGGgtaacgtcca ... ctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacgctgagagtggatataatcagagctaactaagatgcttttctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG
                          agctaac  putative branch site (score: 32)
                                      tgcttttct  putative PPT
                atataatca  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcagttcactgttttctagaatccaattgctttgtactatcgtgctacgctgagagtggatataatcagagctaactaagatgcttttctgtgctcagAATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT