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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag

Basic information

species Oryza sativa
transcript LOC_Os07g27790.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 11
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttc-ttttgtatttctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
|| ||||| ||| | || || |||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||| || | ||   | | ||  ||||| ||||||||| |||| ||||      ||||    ||    | |||||   | || |  || |   ||| | |   ||| ||| || ||||| | |  | | | |||      ||| ||| ||||||  || |  ||  | |  ||  ||||
GTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGGgtttgtgatctgctttcctttgacttcgttttgtattcctgtgcactgc----tgtgcctctgacagccagtag---ttaatatgaata---tgggc-tatctacggtattagtttatttatagcttttgcta------gaagttttaaccagaatttggcttcatgcgagtccacag

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagct-tactcctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
|| ||| | ||| |||| || ||||||||||||||||||||||||||||||||||||||||||||  |||| |||||||||||| || | ||    |||||||   || |||||||||||||| ||||                 || ||   | |||| || |  || |   ||| | |   | | |||||| |||||   ||| |  || |   |||||   ||| || |||      | || ||   ||| |||||
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcactgc------------cactgacagccacaagttaatatcaata---tggtc-tctctgcggtagtagtttat---ttctagtttttgctggaag---ttttaatcag-----aattttgtttatgtctacag

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttact----cctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtca-agtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
|||||||||||| | ||| | |||||||||||||||||||| || || ||||| |||||||||||||| ||||||||||||||  ||   |||  |    | | ||||     |||||  |    ||  || ||   | |||  |         | ||   || ||||  || |   ||                                                                                    
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttactacttctgcatgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgtcaacatcaaaatggtgtc----------------------------------------------------------------------------------

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G01750.2 (Glycine max), 5'ss of exon 11
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagctt---actcctt-tgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtca-agtagaagtaaacacaaaga--gtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
|||||||||||| ||||| | |||||||||||||||||||| || || ||||| || || |||||||| ||||||||||||||  || | |||   ||| ||| |||||    |||||  |    ||  || ||   | |||  |         | ||   || ||||  || |  ||||                                                                                     
GTCAGGCTGAAGAGATATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGGTTATGTGCTTTACCAGCATTTTGGgtgagtgacctttttactacttgtgcacgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgtcaacatcaaaatggtttc------------------------------------------------------------------------------------

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 12
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttcttttgtatttc-tgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
||  || ||||| ||||  | |||||||||||||||||||| || || ||||||||  |||||||  ||||||| || |||||   |     || |       |  | ||| ||  ||  ||   |  || ||    |   |   |||    | ||  | | |  | | | ||  |                                                                                   
GTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGGgtaactacatctattagcacatatatatttcgtgcttaatgagaatgtttcaaaaagtattgactgttgttttgattttatc-tacaaatttcag-----------------------------------------------------------------------------------

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
|||||||||||| ||||  | || ||||| ||||||||||| || || |||||||| || |||||||||||||||||||||||     || |  |  |||    ||   | | |||| |    |      |||| ||  | || |          ||||| ||  |  | |     |||  |||  | |  | | ||| | ||||                                                     
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgt-----agttagcctcttcaatctgtatatttattacaaagc------cagtttgtacatgattc--------agtaatcatcagtact-----catctgtatggaataagtgtatcttttcc-----------------------------------------------------

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 5'ss of exon 11
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttcttttgtatt---tctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
|| ||||| || || ||| | |||||||| || ||||||||||| |||||| |  |||||||||| ||||| ||||||||||| ||||  |  |   | ||   ||| |   | |     |   || |||  |||   |            |  ||   || |  || |  ||| |   ||   |    |||| ||      |  |   | | ||  || ||    ||||      || | |                   
GTGAGGCTAAAACGTTATTTGGAGATGAGGGGAGCTGATGGTGGTCCATGGCGACGATTGTGTGCATTGCCTGCATTTTGGgtacgttgacgaagctcattattcttataacgaaaacggtggatagactgagcaacttccgaccaactgaatatacttgtcataacgagcagtgtactcagacgagtggtagcaa---gcctgctttgtttactcaagaaatgcgtttg--ttgtttgtag-------------------

upper sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S28_268V6.1 (Physcomitrella patens), 5'ss of exon 11
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttcttttgtatttctg---tacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtact------gtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag
|| ||  |||| || ||  |||||||||| || ||||||||||| |||||| |  |||||||||||||||| ||||| ||||| |||||  | |||    | |  |      | || |  |   || || | |||    |  |||   ||     |  | | || |||      |   | ||| ||| |      ||   |||| ||  |   | || | | |   |   || |   |    || ||   |||    |||||     
GTGAGATTGAAACGGTACTTAGAGATGAGGGGAGCTGATGGTGGTCCATGGCGCCGATTGTGTGCTTTGCCTGCATTCTGGgtacgtta-ttcacttacattccatgaaaacgaatatgggaaatagacctggcaactcgaacttaa-gtacttcactactgaatacacttcactcaca-atgagtagttcgtgcgtgaaaattgatggcaaacttgattt-tgttacccatgtaagatt--ttctgtgtttgtcgattgtag----

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|55408876|gb|CV721252.1|CV721252
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG                         GTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagc ... ttgtatacagGTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
EST: gi|29682925|gb|CB679200.1|CB679200
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG                         GTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagc ... ttgtatacagGTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
EST: gi|572041|gb|D41552.1|D41552
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG                         GTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagc ... ttgtatacagGTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
EST: gi|218493685|gb|FG958530.1|FG958530
EST:     ATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG                         GTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
genomic: ATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagc ... ttgtatacagGTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
EST: gi|58663350|gb|CK052036.1|CK052036
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG                         GTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagc ... ttgtatacagGTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACC

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: 71 (upstream exon), 73 (downstream exon)
Score: 192

GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagc ... ttgtatacagGTTGGGCTGTTGTATGATGAGGAATCACTGCAAAGTATTTCGGACATGACCTCTGATTGGACAAATGAAGAAAGAGAAATGCTAAGGCGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttactcctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag

- - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT