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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatattaggtggtccttacaaaattgccactgcagaacatgttccttagcttttattgaaattaacctttttcgttgttttctaatgatttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAATCTAGGGGATGAAAAGTTAGCTACAGATGGATTTCAAGAAGCCATAGATT

Basic information

species Glycine max
transcript GLYMA04G15130.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G15130.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 6
----caaatattaggtggtccttacaaaattgccactgcagaacatgttccttagcttttattgaaattaacctttttcgttgttttctaatgatttattt-tagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAATCTAGGGGATGAAAAGTTAGCTACAGATGGATTTCAAGAAGCCATAGATT
    | ||    |  | |   | | |  ||   |   |        | ||| ||     ||    || |  | | ||   ||   ||  |||  ||| | | |||||  | ||| | ||    |||||||| ||||||||||||||||| |||||||| ||  | ||||     ||    || || ||| | ||||| ||    |
tcagccaaggccatcttgctttca-aggataagcttagggctctcagatccgtaa----tacctgaagtgccatattattttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT
















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|213614371|gb|DB966973.1|DB966973
EST:     TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAG                         GTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
genomic: TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAGgttggttatt ... tttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
EST: gi|120530995|gb|EH259128.1|EH259128
EST:     TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAG                         GTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
genomic: TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAGgttggttatt ... tttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
EST: gi|58017733|gb|CX704475.1|CX704475
EST:     TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAG                         GTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
genomic: TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAGgttggttatt ... tttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
EST: gi|105632896|gb|DW246569.1|DW246569
EST:     TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAG                         GTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
genomic: TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAGgttggttatt ... tttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
EST: gi|58014381|gb|CX701123.1|CX701123
EST:     TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAG                         GTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT
genomic: TGAATGTTCGACGTGATGCTGTCAAGCACAATTCAAACGTTCCATCCCAGgttggttatt ... tttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttagcttttattgaaattaacctttttcgttgttttctaatgatttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAATCTAGGGGATGAAAAGTTAGCTACAGATGGATTTCAAGAAGCCATAGATT
                                    ttctaat  putative branch site (score: 2)
                                             tttatttt  putative PPT
                               ttgttttctaatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatattaggtggtccttacaaaattgccactgcagaacatgttccttagcttttattgaaattaacctttttcgttgttttctaatgatttattttagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAATCTAGGGGATGAAAAGTTAGCTACAGATGGATTTCAAGAAGCCATAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - -ccttaca
- - - - - - - - - - - - - - -cactgca
- - - - - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaattaa