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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaagtacaatttacttgcacaaatgtaaaaaggatagagagcaaaaattggaaagttttattaactgacgaatttgtttattactatgtgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAAGTGATAAAAATGCATGACACAAAGAGCCTATGTTTGAGGGCACTTGCTA

Basic information

species Glycine max
transcript GLYMA02G42290.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42290.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0067g00330.t01 (Vitis vinifera), 3'ss of exon 7
attaagtacaatttacttgcacaaatgtaaaaaggatagagagcaaaaattggaaagttttattaactgacgaatttgtttattactatgtgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAAGTGATAAAAATGCATGACACAAAGAGCCTATGTTTGAGGGCACTTGCTA
      |  |  ||  ||   | | ||   | |  ||  |    | |  |||   |  ||  |||  |       |   |||||    ||||  |  |||||||| || |||||||||||||| |||||  ||||||||||||||||||| ||| |     ||||||| ||||||||| ||||||| |||||||| ||| 
---gtctctatattctttctcccattgcccatactattta----acatcttgctcaaattggttatata------tatcttattgtcctgtgtgttgcagTTCATTACATTTGGATTTGCTTGTACACCCCTGTATTTTGTGTGGGAGAAGGTGGTGGGGGTGCATGATACAAAGAGCATATGTTTAAGGGCACTCGCTC

upper sequence: GLYMA02G42290.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18760 (Selaginella moellendorffii), 3'ss of exon 6
attaagtacaatttacttgcacaaatgtaaaaaggatagagagcaaaaattggaaagttttattaactgacgaatttgtttattactatgtgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAAGTGATAAAAATGCATGACACAAAGAGCCTATGTTTGAGGGCACTTGCTA
                          |||| || |||    | | |  ||     |  ||  ||  |||  ||  |    |  | | || ||  |  ||||| || || ||||||||||||||||| || ||||| || |||||||||||  | ||     | |||   |     ||  |     |  | |||  |||  
--------------------------gtaagaaagat---catcgatgatctatgatcttcgttc-ctg--gagctaaact--tcccat-tgtctcgcagTTTATTACGTTTGGATTTGCTTGCACGCCCTTGTACTTCGTGTGGGAGAAGATAATTGGCGTCCATAGAAGTCCAAGGTTCCTACTTCGAGCAGCTGCCC
















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|193647640|gb|FK589689.1|FK589689
EST:     GCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAG                         TTCATCACTTTTGGATTTGCTTGCACACCATCGTATTTTGTGTGGGAGAAA
genomic: GCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAGgtccatatac ... tgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAA
EST: gi|13789895|gb|BG652486.1|BG652486
EST:     CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAG                         TTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTTGGGTGGGAGAA
genomic: CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAGgtccatatac ... tgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTT-GTGTGGGAGAA
EST: gi|298192347|gb|HO036429.1|HO036429
EST:     CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAG                         TTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAA
genomic: CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAGgtccatatac ... tgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAA
EST: gi|151394389|gb|EV264260.1|EV264260
EST:     CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAG                         TTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAA
genomic: CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAGgtccatatac ... tgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAA
EST: gi|18733933|gb|BM527893.1|BM527893
EST:     CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAG                         TTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAA
genomic: CCCGCTCTGGTTGGCGCGATACCGCTGTCATCTTAATGCTCATTCATCAGgtccatatac ... tgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattggaaagttttattaactgacgaatttgtttattactatgtgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAAGTGATAAAAATGCATGACACAAAGAGCCTATGTTTGAGGGCACTTGCTA
                           aatttgtttattacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaagtacaatttacttgcacaaatgtaaaaaggatagagagcaaaaattggaaagttttattaactgacgaatttgtttattactatgtgaatgacagTTCATCACTTTTGGATTTGCTTGCACACCATTGTATTTTGTGTGGGAGAAAGTGATAAAAATGCATGACACAAAGAGCCTATGTTTGAGGGCACTTGCTA

- - - - - - - -cttgcac
- - - - - - - - - - - - - - aaaaagga
- - - - - - - - - - - - - - - - - - - - -agcaaaaa