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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtaagccagccgccgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC

Basic information

species Oryza sativa
transcript LOC_Os05g38520.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38520.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009936_T01 (Zea mays), 3'ss of exon 1
gtaaggtaagccagccgccgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
| ||| |   |   ||  ||||||| ||  | ||| | | |||||||||||| ||| | |||||| | |   | | | |        | |   ||||         ||  |||||||  |  |  ||  ||||||||| ||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||| |  |||
gcaag-tccccattcccgcgccgccgccgtcgccgtcgctgatctgaaaccc-agcgtatctcctgcttatcctcggtt-------gtttgtccccg---------cgcacagGAAAGTGTTCGTCCTCATGGCGCCGCCGCAGCCGAAGTCGGGCCTCTTCGTGGGCATCAACAAGGGCCATGTCGTCACCAAGCGCGAGCTGCCTCTGCGC

upper sequence: LOC_Os05g38520.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009936_T03 (Zea mays), 3'ss of exon 1
gtaaggtaag---ccagccgc-cgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
|||||| |||   |||  | | ||||||| ||  | ||| | | |||||||||||| ||| | |||||| | |   | | | |        | |   ||||         ||  |||||||  |  |  ||  ||||||||| ||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||| |  |||
gtaaggcaagtccccattcccgcgccgccgccgtcgccgtcgctgatctgaaaccc-agcgtatctcctgcttatcctcggtt-------gtttgtccccg---------cgcacagGAAAGTGTTCGTCCTCATGGCGCCGCCGCAGCCGAAGTCGGGCCTCTTCGTGGGCATCAACAAGGGCCATGTCGTCACCAAGCGCGAGCTGCCTCTGCGC

upper sequence: LOC_Os05g38520.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G850966_T01 (Zea mays), 3'ss of exon 1
gtaaggtaagccagccgc-cgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
|||||||||||||||| | ||||||| || || ||||| | ||||||||||| ||   ||||||||  |        || | | |    ||     |  || |||  ||  |||||||  |  |   |  ||||||||| ||||||| ||||| || || ||||| |||||||||||||| || ||||||||||||||||||||||| || |||
gtaaggtaagccagccccgcgccgccgccgccgccgccgc-gatctgaaacc-tactttctctccttgcgta----tgccctcat---cctcgcttctttgtttgg-cgcacagGAAAGGGTTCGTACTCATGGCGCCGCCGCAGCCAAAGTCGGGCCTTTTCGTTGGCATCAACAAGGGTCATGTCGTCACCAAGCGCGAGCTGCCTCCCCGC

upper sequence: LOC_Os05g38520.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G850966_T03 (Zea mays), 3'ss of exon 1
gtaaggtaagccagccgc-cgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
     ||||||||||| | ||||||| || || ||||| | ||||||||||| ||   ||||||||  |        || | | |    ||     |  || |||  ||  |||||||  |  |   |  ||||||||| ||||||| ||||| || || ||||| |||||||||||||| || ||||||||||||||||||||||| || |||
-----gtaagccagccccgcgccgccgccgccgccgccgc-gatctgaaacc-tactttctctccttgcgta----tgccctcat---cctcgcttctttgtttgg-cgcacagGAAAGGGTTCGTACTCATGGCGCCGCCGCAGCCAAAGTCGGGCCTTTTCGTTGGCATCAACAAGGGTCATGTCGTCACCAAGCGCGAGCTGCCTCCCCGC

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|88724915|gb|CI748174.1|CI748174
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: TAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88348393|gb|CI639052.1|CI639052
EST:     AGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: AGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88327174|gb|CI652214.1|CI652214
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: TAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|163922854|gb|EG714230.1|EG714230
EST:     AGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: AGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88719521|gb|CI743031.1|CI743031
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: GCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88334064|gb|CI641115.1|CI641115
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: TAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88347746|gb|CI655099.1|CI655099
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: TAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|38477139|gb|CF961272.1|CF961272
EST:     CTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88575340|gb|CI669485.1|CI669485
EST:     AGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: AGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|33680377|gb|CF308616.1|CF308616
EST:     CCCTAGCCGCCGCCGCTTCATTTCTCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
genomic: CCCTAGCCGCCGCCGCTTCATTTCTCC----CAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
EST: gi|88327829|gb|CI657873.1|CI657873
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: GCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|86900242|gb|CI296285.1|CI296285
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|33806404|gb|CF329080.1|CF329080
EST:     GCCGCCGCCGCTT-ATTTCTCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
genomic: GCCGCCGCCGCTTCATTTCTCC----CAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
EST: gi|88305783|gb|CI633354.1|CI633354
EST:     AGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: AGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88728828|gb|CI752338.1|CI752338
EST:     GCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88342060|gb|CI644397.1|CI644397
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: TAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|55435920|gb|CV731097.1|CV731097
EST:     CTCCCTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTCCCTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88416945|gb|CI573660.1|CI573660
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|33658651|gb|CF281264.1|CF281264
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88575782|gb|CI669927.1|CI669927
EST:     AGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: AGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88338563|gb|CI645817.1|CI645817
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: TAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88904096|gb|CI006329.1|CI006329
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88346074|gb|CI633947.1|CI633947
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: TAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|55408754|gb|CV721130.1|CV721130
EST:     GCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|55436210|gb|CV731242.1|CV731242
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88727025|gb|CI750680.1|CI750680
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: TAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|33653498|gb|CF276112.1|CF276112
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGTAAG                      
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC----AGgtaaggtaag ... gttcgtg
EST: gi|86415680|gb|CI029691.1|CI029691
EST:     CTAGCCGCCGCCGCTTCATTTCTCTCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
genomic: CTAGCCGCCGCCGCTTCATTTCTC-C----CAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
EST: gi|218480671|gb|FG953809.1|FG953809
EST:     CCGCTTCATTTCTCCCAGTAAG                      
genomic: CCGCTTCATTTCTCCC----AGgtaaggtaag ... gttcgtg
EST: gi|33804492|gb|CF328121.1|CF328121
EST:     AGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: AGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|55413378|gb|CV725754.1|CV725754
EST:     CCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|58597901|gb|CK008429.1|CK008429
EST:     CATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|55440035|gb|CV733328.1|CV733328
EST:     CCCTAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CCCTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88977309|gb|CI025046.1|CI025046
EST:     ATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: ATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88332653|gb|CI660171.1|CI660171
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: GCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88207348|gb|CI207197.1|CI207197
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88294295|gb|CI667269.1|CI667269
EST:     GCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|86421154|gb|CI057143.1|CI057143
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88347011|gb|CI628681.1|CI628681
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: GCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|568404|gb|D39253.1|D39253
EST:     CGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88728042|gb|CI751552.1|CI751552
EST:     GCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|55438722|gb|CV732658.1|CV732658
EST:     TCCCTA-CCGCCGCCG-TT-ATTTCTCCCAG                         GTAAGGAAAAAGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCT
genomic: TCCCTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagG--A--AAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCT
EST: gi|88422114|gb|CI688909.1|CI688909
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: GCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88335958|gb|CI645559.1|CI645559
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: TAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|87022433|gb|CI267570.1|CI267570
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|86821168|gb|CI266735.1|CI266735
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88212927|gb|CI210778.1|CI210778
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|33654987|gb|CF277601.1|CF277601
EST:     CCCTAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CCCTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88310442|gb|CI659232.1|CI659232
EST:     GCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88331889|gb|CI642114.1|CI642114
EST:     CGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88573811|gb|CI665580.1|CI665580
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: TAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|38475070|gb|CF959203.1|CF959203
EST:     GCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88369460|gb|CI580482.1|CI580482
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                     
genomic: CTAGCCGCCGCCGCTTCATTTCTCCC-----AGgtaaggtaag ... gttcgt
EST: gi|88343333|gb|CI627293.1|CI627293
EST:     GCCGCCGCCGCTTCATTTCTACCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
genomic: GCCGCCGCCGCTTCATTTCT-CC----CAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCG
EST: gi|86418411|gb|CI032620.1|CI032620
EST:     CTAGCCGCCGCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|58590943|gb|CF989251.1|CF989251
EST:     GCCGCTTCATTTCTCCCAG                         GAAAAAGGGCTCCCCGATGGCGCCGT--C-G-CGAAGTCCGGGCGCTTCGT
genomic: GCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT

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: 26 (upstream exon), 75 (downstream exon)
Score: 28

GGTTTCCTCCCTAGCCGCCGCCGCTTCATTTCTCCCAGgtaaggtaag ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
                 cgctcac  putative branch site (score: 28)
                                          cttgttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtaagccagccgccgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC