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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtttgcacttttacttttcattcagtgttttgttttgctgaaagagatgatgtactgtaagtttgtaacataatcatgttaaatgtggcatcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTACGAGAAGAGACAGGAGTTAATTCAGTAGAAGTGATCGCTGAG

Basic information

species Glycine max
transcript GLYMA10G33990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33990.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g00030.t01 (Vitis vinifera), 3'ss of exon 2
gagtttgcactt--ttacttttcattcagtgttttgttttgctga--aagagatgatgtactgtaagtttgtaacataatcatgttaaatgtggc-atcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTACGAGAAGAGACAGGAGTTAATTCAGTAGAAGTGATCGCTGAG
     |||  ||  | |  | | || ||   |  | ||   ||     | |||| ||||    |  || |       ||   | || ||| ||    |     |||||||||||||||| ||||| ||||| |||||||| || || ||||| |||   |||||||||||||||  ||||| ||| ||  | || |||
-----tgctgttcatcaaatcttatacaacatgatattccccttgttgaaagattatgtttcttttgtatcagtttgaaaagtatttaatatgattgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTAAAGGAAGAGACAGGAGTTGCTTCAGCAGAGGTTCTTGCAGAG
















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|151401156|gb|EV270970.1|EV270970
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCGGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
EST: gi|5770603|gb|AI973777.1|AI973777
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTAAC                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
EST: gi|192294285|gb|FG986374.1|FG986374
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
EST: gi|8282558|gb|BE020119.1|BE020119
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
EST: gi|7926045|gb|AW832071.1|AW832071
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
EST: gi|31466222|gb|CD408250.1|CD408250
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
EST: gi|24135720|gb|BU926230.1|BU926230
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA
EST: gi|151411273|gb|EV281084.1|EV281084
EST:     TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAG                         GGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCGGCTATCAGGGAGTTA
genomic: TTTTCGCGGCTTCGAGGCTCGACATTCCCAATGCTTGGCAAATGCCTCAGgtcagtgatt ... catcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatgatgtactgtaagtttgtaacataatcatgttaaatgtggcatcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTACGAGAAGAGACAGGAGTTAATTCAGTAGAAGTGATCGCTGAG
                   ttgtaac  putative branch site (score: 2)
                                             catctttt  putative PPT
                          ataatcatgttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtttgcacttttacttttcattcagtgttttgttttgctgaaagagatgatgtactgtaagtttgtaacataatcatgttaaatgtggcatcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTACGAGAAGAGACAGGAGTTAATTCAGTAGAAGTGATCGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - -tgcactt
- - - - - - - - - -tcattca
- - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - -gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt