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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaactttgtcaatcggactttctcattgcgttattggttattacttcactaaactcttattttaatcttcatcctttctgcttaacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAG

Basic information

species Glycine max
transcript GLYMA08G34280.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 11
-------------gttaactttgtcaatcggactttctcattgcgttattggttattacttcactaaactcttattttaatcttcatcctttctgcttaacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAG
             | | | |||     |  | | || |   |  || | || | |  |  || |||      || ||||||  | | | |  |      | ||| |||| ||||||||||| || |  || |   |||||||||||||||||||||| ||||| |||||| || | || ||||||
gtcttttgaagatgcttatttttattctttgcccttgtgtatatgtcaatg-taaagatgtcgctacttgtataatttaattat-accttggcc-----attttcagGATGAAAGAGAGCTCAAGAAGCAGAAAAGGAAGCAGTCTAATCGGGAATCAGCACGTAGATCCCGGCTGCGCAAGCAG

upper sequence: GLYMA08G34280.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv02s0012g02250.t01 (Vitis vinifera), 3'ss of exon 10
-gttaactttgtcaatcggactttctcattgcgttattggttattacttcactaa-actcttattttaatcttcatc-ctttctgcttaactt---ttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAG
 |  | ||| |    |     |||||  |   |||  || ||||| | | | ||  | | ||  | |  | ||   | ||||   ||||  ||   | |||| |||||||||||||||||||| ||  | |||||||| || ||||| ||||| ||| |||||||||| || ||||||
tgacaccttcgggcctttttttttcttttaatgttcatgcttattcccttattattattgttgctattttatttgacactttgaacttactttgattcagGATGAAAGAGAGCTTAAAAGACAGAGAAGAAAGCAGTCGAACCGGGAGTCTGCTCGCCGATCCAGGTTGCGTAAGCAG
















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|10252377|gb|BE820143.1|BE820143
EST:     ATCACGAGATGGTGTTCAGTCACAAGTNNNGCTGCAN                         GACGAAAGAGAGCTTAAAAGACAAAGGCGGAANNAGNCTAATCGGGAANCT
genomic: ATCACGAGATGGTGTTCAGTCACAAGTTTGGCTGCAGgttaactttg ... taacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCT
EST: gi|21676139|gb|BQ628490.1|BQ628490
EST:     TGATTGCTGCTGGATCACGAGATGGTGTTCAGTCACAAGTTTGGCTGCAG                         GACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCT
genomic: TGATTGCTGCTGGATCACGAGATGGTGTTCAGTCACAAGTTTGGCTGCAGgttaactttg ... taacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCT
EST: gi|51335529|gb|CO979395.1|CO979395
EST:     TGATTGCTGCTGGATCACGAGATGGTGTTCAGTCACAAGTTTGGCTGCAG                         GACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCT
genomic: TGATTGCTGCTGGATCACGAGATGGTGTTCAGTCACAAGTTTGGCTGCAGgttaactttg ... taacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattacttcactaaactcttattttaatcttcatcctttctgcttaacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAG
                            tcttcatcctttctgc  CT-rich tract
            taaactcttattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaactttgtcaatcggactttctcattgcgttattggttattacttcactaaactcttattttaatcttcatcctttctgcttaacttttagGACGAAAGAGAGCTTAAAAGACAAAGGCGGAAGCAGTCTAATCGGGAATCTGCACGCAGATCCAGGTTACGGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT