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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggattaaaacttaatctatatgtggttctgttattcttgagcctgcatcttactattttgtttcatttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAACTTTGGAAGCCAGTAAAAATCCAATGAG

Basic information

species Glycine max
transcript GLYMA08G20830.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 11
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 13
------------gtatgggattaaaacttaatctatatgtggttctgttattcttgagcctgcatcttactattttgtttcatttgat------tccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAACTTTGGAAGCCAGTAAAAATCCAATGAG
            | |  | ||   |  ||  | |     |  |||   |     |||  |    | | | |  ||||||   ||| ||      ||||||||||| |||||||||||||||  ||  || |||||||||||| |  |||| || ||||| || | ||| ||||||||
gtatgccaagaagcagagcatcttattttgttattcgcatt-ttcgaatgactatgattccttgtataaatcatttgttcggtttcatacactttccagCAATCTGTTCCGTGTGTTTGGTGTTGCCCCCGGAAGTACTGAGACGGCAACCTTAGAAGCAAGCAGAAACCCAATGAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 11
gtatgggattaaaacttaatctatatg----tggttctgttattcttgagcctgcatcttactattttgtttcatttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAACTTTGGAAGCCAGTAAAAATCCAATGAG
||  |   || ||| ||  | |||       || ||||   |  ||  | | ||  |  ||  ||     || || |||| |||||||||| ||||| || |||||||||   || || || |||||||| ||||| |||||||||||||||||||| |||||
gtccgttttttaaattttctttatccaccattgtttcttgaaccctctaccatgagtactaacataa-aattgatgtgatcccagCAATCTTTTCCGAGTTTTTGGTTGTTCCCCAGGGAGCACTGAGGCAACAACCTTGGAAGCCAGTAAAAATCCCATGAG
















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|193311638|gb|FK275534.1|FK275534
EST:     GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG                         CAATCTATTCCGTGTGTTTGGTTGTGTTCCTGG
genomic: GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggatt ... ttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGG
EST: gi|14990248|gb|BI315921.1|BI315921
EST:     GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG                         CAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGGAGTACTGANGCTACAAC
genomic: GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggatt ... ttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAAC
EST: gi|298194583|gb|HO043055.1|HO043055
EST:     GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG                         CAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAAC
genomic: GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggatt ... ttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAAC
EST: gi|19936100|gb|BQ080722.1|BQ080722
EST:     TGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG                         CAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAAC
genomic: TGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggatt ... ttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAAC
EST: gi|254342009|gb|GR853146.1|GR853146
EST:     GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG                         CAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAAC
genomic: GAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggatt ... ttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggttctgttattcttgagcctgcatcttactattttgtttcatttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAACTTTGGAAGCCAGTAAAAATCCAATGAG
                                       tttcattt  CT-rich tract
                                tattttgtttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgggattaaaacttaatctatatgtggttctgttattcttgagcctgcatcttactattttgtttcatttgattccagCAATCTATTCCGTGTGTTTGGTTGTGTTCCTGGAAGTACTGAGGCTACAACTTTGGAAGCCAGTAAAAATCCAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG