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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttaaattgggaaaaaaaccgagtactatatttatattatattaatttttttttaaaaaaatcctcggtgaccttacaagtaaaatttactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTAGTCCTGGGATATGTCACAGGCCTTGTTGTTGATCTTGCTATTCTAATTG

Basic information

species Oryza sativa
transcript LOC_Os08g34060.3
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34060.3 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 8
------------------------------------------------------------------------------------tgttttaaattgggaaaaaaaccgagtac----tatatttatattatattaattttttttt----aaaaaaatcctcgg--tgacct------tacaagtaaaatttactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTAGTCCTGGGATATGTCACAGGCCTTGTTGTTGATCTTGCTATTCTAATTG
                                                                                      | | ||| |     | ||      ||     |||||| |||||   ||  ||||| |||    |   || || |     ||   |      || || | |||| |||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||  |||||||||||||| || | |||||||||||||||||||| ||||
gtaaattcattatgaaaaaaataatcagcaccttccctaaaccaccttaggaagcactgtgttgggtagcaaattttgatgtttaatataaaactacatcagaatttacctatatcatatattgatatttcctttctttttcttttgttatttaagtctttcacctgttttgtctactataaatgaaatgtactttgcagATAGATGTTGACATCGGTTCATCATCCGTTGCCCGGAGCATTATTGGTCTAGTATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTG
















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|157650644|gb|EX450278.1|EX450278
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|86870886|gb|CI326712.1|CI326712
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|88958682|gb|CI096197.1|CI096197
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|88964786|gb|CI084784.1|CI084784
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTCGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|29630515|gb|CB635524.1|CB635524
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|29622067|gb|CB627078.1|CB627078
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|29623531|gb|CB628542.1|CB628542
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|86430572|gb|CI082995.1|CI082995
EST:     TGGGAAAAGCAGTAACATGCAATAACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|12622371|gb|AU172584.1|AU172584
EST:     CATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: CATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|88252721|gb|CI351149.1|CI351149
EST:     AACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: AACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|86862408|gb|CI345515.1|CI345515
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|88271238|gb|CI387291.1|CI387291
EST:     CAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: CAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
EST: gi|86499063|gb|CI141696.1|CI141696
EST:     TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG                         ATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA
genomic: TGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAGgtgatctagt ... tactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttttttttaaaaaaatcctcggtgaccttacaagtaaaatttactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTAGTCCTGGGATATGTCACAGGCCTTGTTGTTGATCTTGCTATTCTAATTG
                                           tttacttt  CT-rich tract
     tttttttaaaaaaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttaaattgggaaaaaaaccgagtactatatttatattatattaatttttttttaaaaaaatcctcggtgaccttacaagtaaaatttactttgcagATAGATGTTGACATTGGTTCTTCATCCGTTGCACGGAGCATTATTGGTCTAGTCCTGGGATATGTCACAGGCCTTGTTGTTGATCTTGCTATTCTAATTG

- - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtaaaa