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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGTTGTTGGAAACCGTTTTCCAGGCTACTTGGAGTATCCGGGAGTAGGATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaatatcactcatgataatcttgctgtttgaaaggaaatatttgttaatttgtctgttgtatgaaattatgggcttttgaatttgttgtttat...

Basic information

species Glycine max
transcript GLYMA08G26180.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 9
TTCAGTTGTTGGAAACCGTTTTCCAGGCTACTTGGAGTATCCGGGAGTAGGATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgta-------tgacgaatatcactcatgataatcttgctgtttgaaaggaaatatttgttaatttgtctgttgtatgaaattatgggcttttgaatttgttgtttat
||||| || | ||| | || | | || | ||| || || | |||||| || || | | ||||||||||||||||||||| ||||||||| || | || || ||||| || || | | ||| || |||| ||||| || | | |
TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttcttgttaagtacatcttatgatgtgtttcatgaattattccgaattccgattcatttatctgta--attgtctaacag---------------------

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G107867_T04 (Zea mays), 5'ss of exon 8
TTCAGTTGTTGGAAACCGTTTTCCAGGCTACTTGGAGTATCCGGGAGTAGGATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaatatcactcatgataatct-tgctgtttgaaaggaaatatttgttaatttgtctgttgtatgaaattatgggcttttgaatttgttgtttat
||| | | | || | ||||||| | || || | || | | ||| | | | ||||||||||| |||||||| ||||| |||||||||| | ||| |||| || | | ||| || | | | || || | || || | |
TTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGCCATATTATCCTGTTGAAAGAAAATGGGCGCTTGGACTTCAGgtat--tggatactgttcattttactttactttgtatggcctagcacttgtattgatgtatcacttaaccaacag--------------------------

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 9
TTCAGTTGTTGGAAACCGTTTTCCAGGCTACTTGGAGTATCCGGGAGTAGGATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaatatcactcatgataatcttgctgtttgaaaggaaatatttgttaatttgtctgttgtatgaaattatggg-cttttgaatttgttgtttat-
| || |||||| | || |||||||| || |||| |||| ||| | || | || |||||||| | ||| ||||||||||| |||||||||||||| ||| | | | | || | || | ||| ||| | | | | | | | || | | || ||| | | | |
TGGAGCTGTTGGGCAGCGGTTTCCAGGATATGTGGATTATCAAGGAATGGGTTTAAGAACCCAGTTCCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAGgttagactctagtgatt--ttatcttgttctcatgtgacttatggtatgaggtggaaagccaaaatgcggcagctgtgagacagttcaatgtagggatcaac

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|208183688|gb|GD984122.1|GD984122
EST:     GCAACAGTTCCCTGTTGAAAGGAAGTGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|208318672|gb|GE112917.1|GE112917
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|207775418|gb|GD746849.1|GD746849
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|51335928|gb|CO979794.1|CO979794
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|24205208|gb|BU964461.1|BU964461
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|207827077|gb|GD799894.1|GD799894
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|9819566|gb|BE555079.1|BE555079
EST:     GATCGANGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAGAGCTTTGCGA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|23734193|gb|BU765320.1|BU765320
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|14009024|gb|BG725628.1|BG725628
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|193563472|gb|FK521361.1|FK521361
EST:     ATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: ATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|209726301|gb|BW659614.1|BW659614
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAA
EST: gi|193644137|gb|FK592486.1|FK592486
EST:     GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAG                         TCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTG
genomic: GATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaa ... cttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGTTGTTGGAAACCGTTTTCCAGGCTACTTGGAGTATCCGGGAGTAGGATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgacgaatatcactcatgataatcttgctgtttgaaaggaaatatttgttaatttgtctgttgtatgaaattatgggcttttgaatttgttgtttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggaaa