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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttataatgttttgcaaaacttttgttgttgttgctggtaatgatggtaatcctttttctttacttaaccccattggctttggttgagtcactgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGAGAGCTTCAG

Basic information

species Glycine max
transcript GLYMA20G30120.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00800.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------ttataatgttttgcaaaacttttgttgttgttgctggtaatgatggtaatcctttttctttacttaaccccat--tggctttggttgagtca-ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGAGAGCTTCAG
                                                                       |  |||| | ||| |  | ||| | ||    |  || |  |    |  |      |||| |  ||  ||   |  |  ||||| ||   | | || ||| ||||||||||| ||| ||||||| || ||||||| |||||| ||||| |||| ||||||||| 
gtaatctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaat-tattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAAGAGCTTCAA
















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|298185172|gb|HO030385.1|HO030385
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGG
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGG
EST: gi|192311913|gb|FK004222.1|FK004222
EST:     AATTGGGGTCGTTGCTTTGTTGGTTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
genomic: AATTGGGGTCGTTGCTTTGTTGG-TTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
EST: gi|15204816|gb|BI427584.1|BI427584
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
EST: gi|151402645|gb|EV272458.1|EV272458
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
EST: gi|192334065|gb|FK026222.1|FK026222
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
EST: gi|19348858|gb|BM893390.1|BM893390
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
EST: gi|208321091|gb|GE123862.1|GE123862
EST:     TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGC
genomic: TAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGC
EST: gi|192311912|gb|FK004221.1|FK004221
EST:     AATTGGGGTCGTTGCTTTGTTGGTTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
genomic: AATTGGGGTCGTTGCTTTGTTGG-TTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
EST: gi|298179287|gb|HO027758.1|HO027758
EST:     GTTGGTTTTTGGCCCTAAAGGTCTTGCTGAG                         GTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA
genomic: GTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttga ... ctgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcctttttctttacttaaccccattggctttggttgagtcactgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGAGAGCTTCAG
                acttaac  putative branch site (score: 3)
       tttttctttacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttataatgttttgcaaaacttttgttgttgttgctggtaatgatggtaatcctttttctttacttaaccccattggctttggttgagtcactgaatacagGTTGCTCGAAATCTGGGAAAAACATTGCGTGCATTTCAACCCACCATTAGAGAGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - tgttttg
- - - - - - -caaaact
- - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - -gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctttgg