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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCGATGGCGCTGGCCATCGCCCTCGCGGCGCTCTGCCTCGCGGGGCTGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccactccttcctctactctcccctttatcctctttcacggcatgatctctccgctgcgtttgttttttttttgtcggatctggggttggggtgg...

Basic information

species Oryza sativa
transcript LOC_Os08g17370.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g17370.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G146951_T01 (Zea mays), 5'ss of exon 1
GGCGGCGATGGCGCTGGCCATCGCCCTCGCGGCGCTCTGC---------CTCGCGGGGCTGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgccca---ctccttcctctactctcccctttatcctctttcacggcatgatctctccgctgcgtttgttttttttttgtcggatctggggttggggtgg
         ||||  |||| ||||| |||| || ||||||         ||||||  || |||| | |||||||||||||| ||||||||||||||  ||||||| |||||  ||  |   |  |  ||  |  |||| |||   |      ||  ||  |  |  | |     |   |   |     ||   |  | ||||| | | |   
---------GGCGTGGGCCGTCGCCTTCGCCGCACTCTGCATCGTCGCGCTCGCGCCGCCGGCCTCAGGGTTCTACCTCCCCGGCGTCGCGCCCAATGACTTCGAGAAGgtacgcgtaagacagccaccctttgtctcgcctccgtttctcctcctgggctcctggcacgagatctcctccctagcgctttgtgtgtttggggatcgcg---
















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|88592890|gb|CI711026.1|CI711026
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88337348|gb|CI629638.1|CI629638
EST:     TGGCCGCCGGGTTCTANCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88585110|gb|CI702718.1|CI702718
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88316794|gb|CI624236.1|CI624236
EST:     TGGCCGCGGGGTTCTACCTCCCAGGCGTCGCGCCCAAAAACTTCGAAAAG                         AAAGATCCTCTTAAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88728293|gb|CI751803.1|CI751803
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88440826|gb|CI693395.1|CI693395
EST:     TGGCCGNCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88332849|gb|CI639697.1|CI639697
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88336798|gb|CI644225.1|CI644225
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88587991|gb|CI705778.1|CI705778
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88728674|gb|CI752184.1|CI752184
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88461579|gb|CI695415.1|CI695415
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88401829|gb|CI591156.1|CI591156
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88727824|gb|CI749336.1|CI749336
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88726936|gb|CI750591.1|CI750591
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88573197|gb|CI664768.1|CI664768
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88311138|gb|CI658051.1|CI658051
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88434670|gb|CI690951.1|CI690951
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88570641|gb|CI662014.1|CI662014
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGAAAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88352519|gb|CI654344.1|CI654344
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACCAAATTGACATCAATCAAGACCCA
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAAC-AAATTGACATCAATCAAGACCCA
EST: gi|88347827|gb|CI655180.1|CI655180
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCCTCAAGTGAAAGTCAACAAATGGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88392216|gb|CI684058.1|CI684058
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88725941|gb|CI747453.1|CI747453
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAANAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88719060|gb|CI742570.1|CI742570
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGAACCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|95100589|gb|CI692289.1|CI692289
EST:     TGGCCGNCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88350578|gb|CI630022.1|CI630022
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATTCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88337332|gb|CI629622.1|CI629622
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88338701|gb|CI644158.1|CI644158
EST:     TGGNCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88448583|gb|CI693973.1|CI693973
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88329322|gb|CI653236.1|CI653236
EST:     TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGANATCAATCAAGACCCAC
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
EST: gi|88726478|gb|CI750133.1|CI750133
EST:     TGGNCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAG                         AAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG
genomic: TGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAG

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: 56 (upstream exon), 67 (downstream exon)
Score: 27

GGCGGCGATGGCGCTGGCCATCGCCCTCGCGGCGCTCTGCCTCGCGGGGCTGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccac ... ttgtttacagAAAGATCCTCTTCAAGTGAAAGTCAACAAATTGACATCAATCAAGACCCAGCTTCCCTACTCTTATGTCGACAGTGCTCAAAATCTCGGTGAAGTTCTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGCGATGGCGCTGGCCATCGCCCTCGCGGCGCTCTGCCTCGCGGGGCTGGCCGCCGGGTTCTACCTCCCAGGCGTCGCGCCCAACAACTTCGACAAGgtgtgcccactccttcctctactctcccctttatcctctttcacggcatgatctctccgctgcgtttgttttttttttgtcggatctggggttggggtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccgc