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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccaatatgagtttagttacctttttattggtttaacatttttgcaatgaacaacaataccaaagaggtttttttctttgtgactgaactcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG

Basic information

species Glycine max
transcript GLYMA12G30540.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 16
tgccaatatgagtttagttac--ctttttattgg--tttaacatttttgcaatgaacaaca-ataccaaagaggtttttttctttgtgactgaactcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG
||   |  |    | |  | |  |  | | ||||  || | ||| || |||||      || || |||  ||  |   |   |||     | | ||  |  |||||| ||||||| | ||||||||||| || || ||| ||||||||||||| || ||||||||||| || |||||||| || ||  || | | ||||
tgtgtactttccatcaaatgcaacaatatgttggagttcaccatcttggcaatctgttgcatatgccattgatatcagtagtttt-----tcatcttctaaacagGAGTAACATTTCATTTGTTCGTCTGGATGGAACTCTGAATCAGCAGCAACGGGAAAAAGTAATTAAACAATTCTCAGAGGAAAGCAACATCCTG
















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|193531732|gb|FK493204.1|FK493204
EST:     TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCG                         GAATAACATTCCGTTCGTTCGTCTTGACGGGACTTTGAATCAGCGGACAGC
genomic: TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCGgtaagatttg ... tcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAG-CAGC
EST: gi|193324264|gb|FK292628.1|FK292628
EST:     TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCG                         GAATAACATTCCGTTTGTTCGTCTTGAC
genomic: TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCGgtaagatttg ... tcatgtacagGAATAACATTCCGTTTGTTCGTCTTGAC
EST: gi|207694182|gb|GD674277.1|GD674277
EST:     CTTGCAGATTCCCTTTACTCG                         GAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG
genomic: CTTGCAGATTCCCTTTACTCGgtaagatttg ... tcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG
EST: gi|193666288|gb|FK610597.1|FK610597
EST:     TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCG                         GAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGC
genomic: TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCGgtaagatttg ... tcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGC
EST: gi|208185102|gb|GD984136.1|GD984136
EST:     TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCG                         GAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG
genomic: TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCGgtaagatttg ... tcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG
EST: gi|208307393|gb|GE107071.1|GE107071
EST:     TTCCCTTTACTCG                         GAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG
genomic: TTCCCTTTACTCGgtaagatttg ... tcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG
EST: gi|207771108|gb|GD743871.1|GD743871
EST:     TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCG                         GAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG
genomic: TTCAGCCAGTGGACTGCTTTTCTAGACCTCTTGCAGATTCCCTTTACTCGgtaagatttg ... tcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgaacaacaataccaaagaggtttttttctttgtgactgaactcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG
                        tttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccaatatgagtttagttacctttttattggtttaacatttttgcaatgaacaacaataccaaagaggtttttttctttgtgactgaactcatgtacagGAATAACATTCCGTTTGTTCGTCTTGACGGGACTTTGAATCAGCAGCAGCGAGAAAAAGTAATCAAGCAATTCTCCGAAGACGGCGAAACCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
tgccaat
- - - - - - - - - - - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgaac