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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcttgtatatctaagtccaatacttttaatgtcatgtttggccaagattgtagtaagttcttgaagagcattcactaagttgattgttgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG

Basic information

species Glycine max
transcript GLYMA20G22090.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G02200.1 (Arabidopsis thaliana), 3'ss of exon 5
aactcttgtatatctaagtccaatacttttaa-tgtcatgtttggccaagattgtagtaagttcttgaagagcattcactaagttgattgttg-tgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG
       ||||    | ||  | |   |||   | || |||   | ||    | |  ||  ||      ||   |  || | |   ||  |   | ||| ||||||||||| | |||||||| || ||  ||||| |||| |||||||| |||||||| |   | || || ||||| |||||||||||||| |||||| |  
-------gtatcataatgtgaattggatttgtctttcttgtcctgacactgctcttttatatttgattggaatttcaacgatggcaatcttaaatcttgcagTGTGATTTATTGGACTTGCCAGCCGTAGCACAATTGGAAAAGGATGCTAAATATGCACCTGTTTACCAACTTCTGAAGATTTTTCTTACTCAGAGGTTAA

upper sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 5
aactcttgtatatctaagtccaatacttttaatgtcatgtttggccaagattgtag--taagttctt-gaagagcattcactaagttgattgttgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG
   |     |  | | | ||   |  ||||    |||   |||   |  ||| | |  |  || |   ||| |  | |  ||   ||  | ||||| ||  |||||||| | || ||  ||||||| ||   |||| ||||||| || || ||||||||  || | ||||||||||| ||||||||||| || |||||||| |
---tgcaccacctgttattctctttattttttcttcagtcttgattataattttgggttgggtgcccagaaaattaattcctttttttttggttgtatttcagTGTGATCTGCTGGATATGCCTGCAGTAGGACAATTGGAGAAAGACGCTAAATATGCATTGGTCTATCAGCTTCTGAAGATTTTTCTCACTCAGAGGCTTG
















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|8827521|gb|BE211251.1|BE211251
EST:     AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
EST: gi|208170220|gb|GD966571.1|GD966571
EST:     AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
EST: gi|5342719|gb|AI795003.1|AI795003
EST:     GAGGGCACCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: GAGGGCACCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
EST: gi|15337560|gb|BI498216.1|BI498216
EST:     AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
EST: gi|23734414|gb|BU765436.1|BU765436
EST:     AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
EST: gi|15286594|gb|BI470485.1|BI470485
EST:     GGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: GGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
EST: gi|19453133|gb|BM954543.1|BM954543
EST:     CCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: CCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
EST: gi|192294162|gb|FG986251.1|FG986251
EST:     AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAG                         TGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA
genomic: AGGCTGCACGTGCAATTGTGGAATTTGTGAGGGCACCTGACGTATTTCAGgtaccttatc ... tgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagattgtagtaagttcttgaagagcattcactaagttgattgttgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG
                                   agttgat  putative branch site (score: 5)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactcttgtatatctaagtccaatacttttaatgtcatgtttggccaagattgtagtaagttcttgaagagcattcactaagttgattgttgtgttgtagTGTGATTTACTAGACTTGCCTGCTGTTACACAACTGGAGAAGGATGCCAAATATGCTCTGTTATATCAGCTTCTTAAGATTTTTCTTACCCAGAGGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattca