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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC

Basic information

species Oryza sativa
transcript LOC_Os06g03760.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 7
gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagctt-gaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
||||  ||||| || || |||| || | ||||  | ||  |||    |  |  ||  |  ||| ||||| ||| ||||  ||||||||||||||||||||| || ||||||||||| |||||||| || || ||||||||||||||||| |||||||| || |||||  ||||||| |||||
gtat-cttctgatc-ttccattcttgtcaacttatgctgctgagccgaacaaattcaattaatcttctgatttatgtaccagGTCTGCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCAC

upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 9
gtatatttc---tgttcat--tacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
|||| ||     |  ||||  | || | || | ||||  |  |  |||||| |  |     |  ||| ||||  ||| ||||  |||||| |||||||||||||| || ||||||||||| ||||||||||| || ||||||||||||||||| |||||||| ||||||||| | |||||||||||
gtatcttctgaattctcatcttccagtcttgtcaacttatggtgctgatgagaacaatccaattaatcttctaatttgtgtaccagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC

upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
--------------------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatat------tctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
                                 |  | || |||  | ||  |  | |   |   ||  |||| ||     ||   |     ||||      | |||| | |  || |||||| ||||| |||||||| |||||||| ||||| ||||| || ||| | || ||||||||||| |  |||||||| ||  ||| | |||| ||||| ||
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgcaatttgttcttt-catcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC

upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 8
--------------------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatat------tctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
                                 |  | || |||  | ||  |  | |   |   ||  |||| ||     ||   |     ||||      | |||| | |  || |||||| ||||| |||||||| |||||||| ||||| ||||| || ||| | || ||||||||||| |  |||||||| ||  ||| | |||||||||| ||
gtatgttggaaagctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatctagatgatatatgtaatttgttcttt-catcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC

upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 9
------------------------------------------gtatatt--tctgttcattacattgttctgaactcgtcctattgatgacagtagcttgacca-atattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
                                          ||||| |  |   | ||||| ||| |    ||    | || |  || |   ||| |     |  || | |||| | |  || |||||| ||||| |||||||| |||||||| ||||| ||||| || ||| | || ||||||||||| |  |||||||| ||  ||| | |||||||||| ||
gtatgttggaaaactcaggctatttttctttccttcagttatgtataataattgatacattatattatatgtaat--attctttcaattaatctagatgatatatgtaatttgttcttt-catcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC

upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
--------gtatatttctgttcattacattgttctgaactcgtcct--attgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
         ||  ||| |  |  |||   |||       |  | ||   ||  | || |   |    |   ||   |||          ||||||  | || |||||||||||||| |||||||||||||| || ||  | || || || ||||||| ||||||||||||||||||  | || ||||| ||
gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactgactccatgctggtacg-tgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC

upper sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctg---tattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
                    | |  | ||  ||  ||| ||||||       |||  |    || |  |   || |   || |    ||||||     | ||||||| ||||| || ||||||||||| ||||||||||||||||||||  | || || |||||||||| ||||||||| ||||||||  | || ||||| ||
gtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacc--tggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC

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|58684950|gb|CK073637.1|CK073637
EST:     TTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGATGGTGTTTGGG                         GTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG
genomic: TTTGTCCTCCTTCCTGAATGAAATCTTCGTAAAATTGGATGGTGTTTGGGgtatatttct ... tctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG
EST: gi|55827892|gb|AU063117.2|AU063117
EST:     GTAAAATTGGATGGTGTTTGGG                         GTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG
genomic: GTAAAATTGGATGGTGTTTGGGgtatatttct ... tctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
                                     ttctgttttct  CT-rich tract
                                 aatattct  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctgtattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG