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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacagaagatcctttgcattctgcttttgtgttgcattgtaatcaattgcttttactactgttctgcgtcactcctcctttcaattttttaacaccattcgacattttatgatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA

Basic information

species Oryza sativa
transcript LOC_Os06g05180.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 8
gtaaacagaagatcctttgcattctgcttttgtgttgcattgtaatcaattgcttttactactgttctgcgtcactcctcctttcaattttttaacaccattcgacattttatga-tatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA
                      | |  | |  | |      |       | ||   ||  | | || |||  |  |     || | | |  | ||     |     ||||| | | | | ||||||||| ||||||||||| |||||  | || |||||||||||||| |||||||||||| | ||||| ||||||||| |||| |||||||||||||| |||
----------------------tttaatctcatttaatcacgagtggcctagcacctagcatt-ttttgcaaccttggcatttcctaatgctgaaacaagtatactattttgttactgtctagGATGGTGATTGGTTATGACGAGGGGGCCATTATGATAAAAATGGGCCGTGAAGTACCTATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 9
gtaaacagaagatcctttgcattctgcttttgtgttgcattgtaatcaattgcttttactactgttctgcgtcactcctcctttcaattttttaacaccattcgacattttat--gatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA
                    |||||   | | |  |   |  ||  |   ||   || | |  |    |   ||||     |||| | |  | || || | | ||   ||| |    | | ||||||||| ||||||||||||||||| || || |||||||||||||| |||||||||||  | ||||| ||||||||| |||| |||||||||||||| |||
-------------------gattcttggtatctagtaggtcctatccttatgtagttgccaacg----ggcccactatgtttttctaatactgaa-acaagtagattatttgtttactgtctagGATGGTGATTGGTTATGATGAGGGGACCATTATGATAAAAATGGGCCGTGAAGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
-----------gtaaacagaagatccttt-gcattctgcttttgtgttgcatt------gtaatcaattgcttttactactg------ttctgcgtcactcctcctttcaattttttaacaccattcgacattttatgatatgt------agGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA
            |  | ||||  |   |  | | | |  |     |||| ||       ||    || ||  |  | |  ||      || ||      || |   || || | |||      | || | |||||  | |   |      ||| | || ||||| |||||||| ||||| || ||| | ||| | || || |||||||||||||| |||||||| | |||||| ||||| |||||| | || 
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaaacagaagatcctttgc-at-tctgcttttgtgttgcattgtaatcaattgcttttac--------tactgttctgcgtcactcctcctttcaatttt--ttaacaccatt-cgacattttatgatatgt-agGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA
||||      |||| ||| | || ||    ||| |     |||  |   |  |   || ||        || |  | || || | |     ||||  |  |   | ||   ||  | | |  || |  | |   ||| | |||||||||||||| || ||| | |||||| | ||| | || |||||| |||| ||||| || ||||||| ||| |||||||| |||||||| |||
gtaagtttctgatcttttactatgtcaatatttattccctattaaagatatatatcttcacatcataattatttctttgtgtaaatttatgtttccttcataacttacgagatggcaataccttgtctttttccagGGTTGTAATTGGTTATGACGAAGGATCCATAATGGTGAAACTTGGCCGTGAAATACCAGTGGCTAGTATGGATAACAGCGGAAAAATTATTTGGGCTAAA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaaacagaagatcctttgcattctgcttttgtgttgcattgtaatcaattgcttttactactgttctgcgtcactcctcctttcaat--tttttaacaccattcgacattttatgatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA
                    ||| |  |||| | |   || ||| |  | |    ||   | | |  |  ||   |  || || |  |  || |     | ||      | |   | |    ||| | |  ||||| || ||||| || || || ||||| ||| | |||||||| | |||||| ||||||||||||| ||||||||| || || ||||| || 
-------------------tattgt-tttttatatcatatggtattgcact----ttgtaaatatgttaggttgtttgtcattaccgtacttatccctgctatcactgttctctcgttggccagGGTTGCGATTGGGTACGATGAAGGTACCATTATGATCAAACTTGGACGTGAGGAACCTGTTGCAAGCATGGATAACAGTGGAAAGATTATCTGGGCCAAG

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|58609972|gb|CK038005.1|CK038005
EST:     TATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG                         GATGGTAATTGGTTATGATGAGGGAACTATAATGATAAGAATGGGACGTGA
genomic: TATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAGgtaaacagaa ... tgatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGA
EST: gi|29630380|gb|CB635389.1|CB635389
EST:     GTTGGATACATGAACGGTTCAAGAAG                         GATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGA
genomic: GTTGGATACATGAAGGGTTCAAGAAGgtaaacagaa ... tgatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGA
EST: gi|58685771|gb|CK074458.1|CK074458
EST:     GAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG                         GATGGTAATTGGTTAGGATGAGGGAACTATAATGATAAAAATGGGACGTGA
genomic: GAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAGgtaaacagaa ... tgatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgtcactcctcctttcaattttttaacaccattcgacattttatgatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA
                      ttttaac  putative branch site (score: 2)
              tttcaattttttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacagaagatcctttgcattctgcttttgtgttgcattgtaatcaattgcttttactactgttctgcgtcactcctcctttcaattttttaacaccattcgacattttatgatatgtagGATGGTAATTGGTTATGATGAGGGAACTATAATGATAAAAATGGGACGTGAAGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA