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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTGTGAACACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctccttttacttttgaaacaatttcttagatacagttataaatgtattaattaatgttttttatgtaaacccctactgcag

Basic information

species Glycine max
transcript GLYMA02G06190.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G06190.2 (Glycine max), 5'ss of exon 6
lower sequence: AT2G18290.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTTTGTGAACACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctccttttacttttgaaacaatttcttagatacagttataaatgtattaattaatgttttttatgtaaacccctactgcag-----
| ||||| || || || ||||| ||||| ||  | |||||||| || ||||| || || ||||||||  | || ||||||||||||||||| ||| |||||||||||||| | |    ||    || || | ||   || ||    | | |||    | ||    |||   | |  |   | |  |      
CTTTTGTCAATACATTTATGTTACAAATAGCCATTTTGTCAAATCACCTCAACGGGAGAGATACTCATATCCGCCAGATCAAAGTTTACGGCCCTAGACCgtgcgtctccatctctcctt----cacttacctaa--actgtgcacattatatgctatgattgcctttgcatgactcttgatttgattgcag

upper sequence: GLYMA02G06190.2 (Glycine max), 5'ss of exon 6
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 5'ss of exon 5
CCTTTGTGAACACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtc----tccttttacttttgaaacaatttcttagatacagttataaatgtattaattaatgttttttatgtaaacccctactgcag
| |||||||||||||| ||||||||||||||| | |||||||| || || ||||| || |||||||| ||||| |||||||||||||| ||||||| |||||  |||    ||||| | ||| |  | || |  |  | ||    || | ||   | |||   |   | || |||||  |   |  |||||
CTTTTGTGAACACTTTTATGTTGCAAATTGCTATATTGTCAAATCACCTTAATGGGAGAGATACTCATGTGCGCCAGATCAAAGTTTATGGGCCTCCACCgtatgtcagaatccttattcttgttcaccagtcacagatatgggattcttaa---actaaccca---tcttgatgtatgcta-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|208106630|gb|GD906055.1|GD906055
EST:     ACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
genomic: ACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctcc ... cctactgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
EST: gi|208229476|gb|GE022880.1|GE022880
EST:     ACGTGCGGCAGTATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
genomic: ACGTGCGGCAG-ATCAAAGTTTACGGGCCTCGACCgtgcgtctcc ... cctactgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
EST: gi|58024926|gb|CX711667.1|CX711667
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctcc ... cctactgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
EST: gi|6848381|gb|AW350671.1|AW350671
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctcc ... cctactgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
EST: gi|192310829|gb|FK000315.1|FK000315
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctcc ... cctactgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
EST: gi|209711477|gb|BW665229.1|BW665229
EST:     AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACC                         GAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC
genomic: AATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctcc ... cctactgcagGAACCCTATCCCACATCAGCCATTCCAATTTACTTCAAGGGAGTTTATCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTTGTGAACACTTTCATGTTGCAAATTGCTGTGTTGTCAAACCATCTCAATGGAAGGGATACTCACGTGCGGCAGATCAAAGTTTACGGGCCTCGACCgtgcgtctccttttacttttgaaacaatttcttagatacagttataaatgtattaattaatgttttttatgtaaacccctactgcag

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