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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcactttctggtaatgttttgttacctaaccaagtgatgcaccattactgaagttgtaaagttacag

Basic information

species Oryza sativa
transcript LOC_Os10g35960.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G085747_T04 (Zea mays), 5'ss of exon 7
AGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcactttctggtaatgttttgttacctaaccaagtgatgcaccattac-tgaagttgtaaagttacag----------------------------
|||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||   ||  ||||   |  |  |     | | |     |    ||| || || |    ||||| |  ||| ||                             
AGGACTGAGGCAACCTCGGCTGGAAGGAGAAGAATACTTGGCTGTTGTAGATGAATTCATGGAGGCTGTCCATGCACGTTGGCCTAAAGCAGTTGTGCAGgtat-tgtgctttaaagccacctccatgtgctttgttcaagattgctccttttcactgagttgaattgtt-catttcttcttggatctgatcacttgttagt

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G08110.1 (Glycine max), 5'ss of exon 7
AGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcactt-tctggtaatgttttgttacctaaccaagtgatgcaccattactgaagttgtaaagttacag----------------------------------------------------------------
||||||  | ||||| ||| ||||||| ||||| ||  | ||  || |||||||||||||||||||||||||||| || ||||| || ||  ||||||||||  |     || | |  | |  ||||   |   |      |      | |||  |        | | |||| |                                                                
AGGACTTCGACAACCAAGGTTGGAAGGTGAAGAGTATCTATCAATTATAGATGAATTCATGGAAGCTGTTCATGCTCGATGGCCCAAGGCTATTGTGCAGgtatggttgtttattttttcaccttttcccattgatatgcattggtttctattttttctagcacata-ttactgactctcaatgttctttttagattttatcaattttgtaactagattgttgtgttaatgttatcag

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA03G01680.1 (Glycine max), 5'ss of exon 8
AGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcactttctggtaatgttttgttacctaaccaagtgatgcaccattactgaagttgtaaa-gttacag-----------------------------------------------------------------
||||||  | ||||| ||||||||||| ||||| ||  | ||  ||||||||||||| ||||||||||||||||| || ||||| || ||  ||||||||||  |   | ||  |  |  |  ||| |  | |    | |   ||     |   |    | | | |  |||| |                                                                 
AGGACTTCGACAACCAAGGCTGGAAGGTGAAGAGTATCTATCAATTGTAGATGAATTTATGGAAGCTGTTCATGCTCGATGGCCCAAGGCTATTGTGCAGgtatgcttatttattttttctccttt-tcccattgatatgcattggtttgtatttattctagcacatattactgactcccaatgttctatttagattatatcaatttttgtaactagattgttgtgttaatgttatcag

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|58687567|gb|CK076254.1|CK076254
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGT
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|58673493|gb|CK062179.1|CK062179
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGT
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|58665242|gb|CK053928.1|CK053928
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGT
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|58694574|gb|CK083261.1|CK083261
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGT
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|88414501|gb|CI698600.1|CI698600
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAA
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAA
EST: gi|58659006|gb|CK047686.1|CK047686
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAGGGGGCCTTTGAAACTCTTCAGAGGTATCGT
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|29664101|gb|CB660376.1|CB660376
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|29671880|gb|CB668155.1|CB668155
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCNCAA-TGAAATGGGCCTTTGAAACTCTTC
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTC-CAAATGAAATGGGCCTTTGAAACTCTTC
EST: gi|29624067|gb|CB629078.1|CB629078
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|29656255|gb|CB652530.1|CB652530
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|29687359|gb|CB683634.1|CB683634
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|88342733|gb|CI677737.1|CI677737
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAA
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAA
EST: gi|88386729|gb|CI682882.1|CI682882
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTT
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTT
EST: gi|58604291|gb|CK014819.1|CK014819
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGT
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|29624065|gb|CB629076.1|CB629076
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
EST: gi|29678813|gb|CB675088.1|CB675088
EST:     ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAG                         TTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG
genomic: ATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGG

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: 69 (upstream exon), 75 (downstream exon)
Score: 83

AGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcac ... aaagttacagTTTGAAGACTTCCAAATGAAATGGGCCTTTGAAACTCTTCAGAGGTATCGGAACCGATTTTGTATGTTCAATGATGACGTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGACTGAGGCAACCTAGGCTGGAAGGAGAAGAATACTTGTCTGTTGTAGATGAATTCATGGAAGCTGTTCATGCACGTTGGCCGAAAGCAGTTGTGCAGgttcgtgcactttctggtaatgttttgttacctaaccaagtgatgcaccattactgaagttgtaaagttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT