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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTGTGAATACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctccttttacttttgaaacaatttcttagatacagttataaatatattaactaatgtatttttatgtaaacccctattgcag

Basic information

species Glycine max
transcript GLYMA16G25220.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25220.1 (Glycine max), 5'ss of exon 5
lower sequence: AT2G18290.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTTTGTGAATACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctccttttacttttgaaacaatttcttagatacagttataaatatattaactaatgtatttttatg---taaacccctattgcag
| ||||| ||||| || ||||| ||||| ||  | |||||||| || ||||| || || ||||||||  | || ||||||||||||||||| ||| ||||||| |||||| | |    ||    || || | || |    |      ||||  ||   | ||  |||  |||            |||||||
CTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCACCTCAACGGGAGAGATACTCATATCCGCCAGATCAAAGTTTACGGCCCTAGACCgtgcgtctccatctctcctt----cacttacctaaactgtgcacattatatgcta-tgattgcctttgcatgactcttgatttgattgcag

upper sequence: GLYMA16G25220.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 5'ss of exon 5
CCTTTGTGAATACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctc--cttttacttttgaaacaatttcttagatacagttataaatatattaa-ctaatgtatttttatgtaaacccctattgcag
| |||||||| ||||| ||||||||||||||| | |||||||| || || ||||| || |||||||| ||||| |||||||||||||| ||||||| ||||| ||||       ||| | |||      ||    ||  |||| |||     | |||| ||||   || || |||||  |   | ||||||
CTTTTGTGAACACTTTTATGTTGCAAATTGCTATATTGTCAAATCACCTTAATGGGAGAGATACTCATGTGCGCCAGATCAAAGTTTATGGGCCTCCACCgtatgtcagaatccttattcttg------ttcaccagtcacagatatgggattcttaaactaacccatcttgatgtatgcta-tgttgcag
















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|193675569|gb|FK616559.1|FK616559
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
EST: gi|22540274|gb|BU090117.1|BU090117
EST:     ATGGAAAGGATACTCACGTGCGGCAGAATCAA-GTTTACGGGCCTCGACC                         GAACCCTATCCCA-ATCAGCCATTTCAATTTA
genomic: ATGGAAGGGATACTCACGTGCGGCAGA-TCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTA
EST: gi|151404299|gb|EV274109.1|EV274109
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
EST: gi|6846190|gb|AW348480.1|AW348480
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
EST: gi|193521761|gb|FK481214.1|FK481214
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
EST: gi|193482185|gb|FK444476.1|FK444476
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCC
EST: gi|192305678|gb|FG998028.1|FG998028
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTGCGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
EST: gi|4290377|gb|AI438065.1|AI438065
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATNTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
EST: gi|12691440|gb|BG157776.1|BG157776
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
EST: gi|192308814|gb|FG999811.1|FG999811
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctcc ... cctattgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAATTCATCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTTGTGAATACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgtgtctccttttacttttgaaacaatttcttagatacagttataaatatattaactaatgtatttttatgtaaacccctattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA