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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttctctctctcttccccaattttttttgttaattttaaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag

Basic information

species Glycine max
transcript GLYMA18G17590.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G121942_T03 (Zea mays), 5'ss of exon 3
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttct-ctctctcttccccaattttttttgttaattttaaaactatt--tattaatcttttttttcttttgcgtgggtgtgtgtctgcag
||||| |||||||| ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   ||||||| ||| | ||  ||| | |    |||    |  |  ||| ||  ||   ||   |  | |  ||| ||| ||| |     |              
GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaagatgctactaaattataagacatcaatgcttaattttgtttccttatttacag--------------

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 3
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttct-ctctctcttccccaattttttttgttaattttaaaactatttat--taatcttttttttcttttgcgtgggtgtgtgtctgcag
      |||||||| ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   ||||||| ||| | ||  ||| | |    |||    |  |  ||| ||  ||   ||  ||  | |  ||| ||| ||| |     |              
-----CGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaagatgctactaaattataagacatcaatgcttaattttgtttccttatttacag--------------

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttct-ctctctcttccccaattttttttgttaattt---taaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag
||||| ||||| || ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   ||||||| |||   ||  ||| | |    ||| |  | ||  | | ||   | | | ||    ||||| ||||  || |||   |                 
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaattatatgacattaccgcttaatgttttccttatttacag-----------------

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttctctctctcttccccaattttttttgttaattttaaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag
|| ||||||||||||||||| ||||||||||| |||||||| ||||| || |||||||| || || ||||| ||||||| |||||||| ||| || |     | ||       |||||  |   |||  ||||    || | ||  | ||     |||||  ||  | |||||  |   
GCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATTgtaagtatttttcactttttgtttggatttttcag--gattccaaaa----ttgtgaacttattgaaaattttgaatgtttttgtgttag---

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttctctctctct--tccccaattttttttgttaatt-ttaaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag
|| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| || |||||||||||||  |||||||||||||  | |   | |  |   ||| ||||| | |  ||| ||   | |   || |||| | |    |   ||     |||            
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag--------

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttctctctctcttccccaattttttttgttaattttaaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag
|| |||||||||||||| || || || ||||| |||||||| ||||| ||||||||||||||||| |||||||| ||||| ||||||| |||   || |   | |     |  |||  |||| |   ||  |  |||   ||  ||||| ||   |||   ||   | |||||  ||||
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattatttt-----agatttggttgtcatcattttatttataggtttttctttcttagatttgatgt---tttgtgtgggcag

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|151408566|gb|EV278374.1|EV278374
EST:     CATCCCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|208250862|gb|GE046499.1|GE046499
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|208163873|gb|GD963639.1|GD963639
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCA
EST: gi|208283758|gb|GE088996.1|GE088996
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATT
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATT
EST: gi|42722515|gb|CK768414.1|CK768414
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|193395678|gb|FK362231.1|FK362231
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGA-TTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|26046065|gb|CA783407.1|CA783407
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|193636233|gb|FK580756.1|FK580756
EST:     ATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: ATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|31465662|gb|CD407690.1|CD407690
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|192326871|gb|FK015128.1|FK015128
EST:     CATCTCCAAGCCGAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|193466054|gb|FK429781.1|FK429781
EST:     ATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: ATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|19453331|gb|BM954741.1|BM954741
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|193587621|gb|FK542656.1|FK542656
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCGTGCTGGTTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|193363862|gb|FK329668.1|FK329668
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|208135400|gb|GD937925.1|GD937925
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|193329922|gb|FK294528.1|FK294528
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|13790432|gb|BG653023.1|BG653023
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|298166319|gb|HO009290.1|HO009290
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGGTT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|208079178|gb|GD873140.1|GD873140
EST:     CATCTCCAAGCCAAGTATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|193452514|gb|FK417534.1|FK417534
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|8283605|gb|BE021164.1|BE021164
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
EST: gi|13478641|gb|BG508037.1|BG508037
EST:     CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT                         TGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA
genomic: CATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttc ... gtgtctgcagTGAGTGGGCAGTGAACATTCAACGTGATAGCTATGCATCATATATTGGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttctctctctcttccccaattttttttgttaattttaaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT