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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACCCAGATGGCCGGACATTCGCGACTGGTAACCAAGACAAGACATGCA

Basic information

species Oryza sativa
transcript LOC_Os08g38880.6
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G113726_T02 (Zea mays), 3'ss of exon 8
gtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgttt-ctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACCCAGATGGCCGGACATTCGCGACTGGTAACCAAGACAAGACATGCA
|||||| ||| |||  || |||  | | | |||            | | ||   |  ||| | |    | ||   |    | || ||||||||| |||||  ||||||  || ||| |||| ||||| || ||||| || ||||| ||||| ||||| |||||||| || || |||||||||||||| ||||
gtaagcggaacgcagtgcacagtaactgatttct---------ttttatat---aataaatgcacgattgatatatacaagcttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA
















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|38477499|gb|CF961632.1|CF961632
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|29640281|gb|CB645290.1|CB645290
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|88267006|gb|CI378941.1|CI378941
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGG--AA                         A-A-TTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|6984506|gb|AU082482.1|AU082482
EST:     TGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         NCAGTTCATGAAATCCGCGGTCATCTGGACTACTCTTTCGCGTCCAGCGTG
genomic: TGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGT-CAGCGTG
EST: gi|29677554|gb|CB673829.1|CB673829
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|88271495|gb|CI387548.1|CI387548
EST:     TTGTTGGGGACAACCCTGAA-GACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|88272502|gb|CI386357.1|CI386357
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|218498616|gb|FG945329.1|FG945329
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|29669309|gb|CB665584.1|CB665584
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|29621086|gb|CB626097.1|CB626097
EST:     TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|86499824|gb|CI142457.1|CI142457
EST:     AGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: AGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|218505284|gb|FG952914.1|FG952914
EST:     CAACCCTGAAAGGACTTATAGTCGATACTAATTCAGGAAAA                         ACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: CAACCCTG-AAGGACTTATAGTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
EST: gi|88271367|gb|CI387420.1|CI387420
EST:     TGTTGGGGACAACCCTGAAGGACTTATAGGTCGATACTAATTCAGGAAAA                         ACAATTCATGAACTCCCCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG
genomic: TGTTGGGGACAACCCTGAAGGACTTATA-GTCGATACTAATTCAGGAAAAgtaagcagaa ... tttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACCCAGATGGCCGGACATTCGCGACTGGTAACCAAGACAAGACATGCA
                                         tttgtttctc  CT-rich tract
                    aaaaagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACCCAGATGGCCGGACATTCGCGACTGGTAACCAAGACAAGACATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG