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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagcttttttttttaattacttgtcaatgattttggtacttgggtttactcagatttgtggtttatatgattgttctttagtagaaattgagtagatg...

Basic information

species Glycine max
transcript GLYMA09G04830.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04830.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G472231_T01 (Zea mays), 5'ss of exon 2
GAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagcttttttttttaattacttgtcaatgattttggtacttgggtttactcagatttgtggtttatatgattgttctttagtagaaattgagtagatg--
|||||| ||| | ||||||| ||| | |||||| | ||||||||||||||||| ||||  || || ||||| ||||| |||||||| || || || || |||||   | || |   ||   ||| |        |   || || |   |       |  |    || |  | ||| | | ||||   |  ||  |   |   
GAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctcttctcccaaccccttatgggaaccctccttaattagtactgaatgattgcgcaagttgt--ggttggtgtctagtctgatatgcttgcgttgt

upper sequence: GLYMA09G04830.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G15930.1 (Arabidopsis thaliana), 5'ss of exon 2
GAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctt-----ttttttttaattacttgtcaatgattttggtacttgggtttactcagatttgtggtttatatgattgttctttagtagaaattgagtagatg
|||||||||| ||||||||| ||  | || ||| | |||||||||||||| || ||||  |||||  | |||||||||||||| |||||||| || |||||| || |      | |  ||   ||| ||     | |   ||| | ||   |  |   | | || |   |||    || ||  |||  ||| || |   |     
GAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCAACTTTGgttagttccctcctctccttcgcttaatttctccttaaggtggcatttt--tcgatgaaaagttctcagttagggaatagtgatttcttagtaagtatatct---

upper sequence: GLYMA09G04830.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 5'ss of exon 2
GAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagcttttttttttaattacttgtca-atgattttggtacttgggtttactcagatttgtggtttatatgattgttctttagtagaaattgagtagatg-----
|||||  ||| |||||||||| || |||||||| | || ||||||||||||||||||| ||||||||| || ||||||||||| || ||||| ||||| |||||   ||    |||||| | || ||  || || |  ||| |     || ||    |   | | |||  ||||   ||    || |   ||  || | |      
GAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAATTTCGgtaa---ttcccgtttaatcatttttcttataatatatgtaatatcaatttct--actggatagattaattgatgaatcagcggtggtg-ttctgttgttacatat

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|58023785|gb|CX710526.1|CX710526
EST:     CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
genomic: CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctttt ... ctttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
EST: gi|193482152|gb|FK445689.1|FK445689
EST:     GATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTTAATTTTG                         GCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGAT
genomic: GATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGT-AATTTTGgtaagctttt ... ctttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGAT
EST: gi|298182056|gb|HO026231.1|HO026231
EST:     CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
genomic: CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctttt ... ctttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
EST: gi|254320944|gb|GR827393.1|GR827393
EST:     CGATAAGAGGCATGGACCCCCTTGGCATTGCATCGTTGGTCGTAATTTTG                         GCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTTTATTTGGATC
genomic: CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctttt ... ctttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
EST: gi|208335922|gb|GE134707.1|GE134707
EST:     CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         -CTCATATGTGACTCATGAAACAAA
genomic: CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctttt ... ctttttgcagGCTCATATGTGACTCATGAAACAAA
EST: gi|209727889|gb|BW663401.1|BW663401
EST:     CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
genomic: CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctttt ... ctttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
EST: gi|254320943|gb|GR827392.1|GR827392
EST:     CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTG                         GCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC
genomic: CGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagctttt ... ctttttgcagGCTCATATGTGACTCATGAAACAAACCACTTTGTTTATTTCTATTTGGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTAATTTTGgtaagcttttttttttaattacttgtcaatgattttggtacttgggtttactcagatttgtggtttatatgattgttctttagtagaaattgagtagatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA