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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACGTTGTTTCAGATGCATGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaattctaattcttggaagtaaatgaatttgcataatccattttcattagttgtgtggggtatttaccaaaatagatgaacag

Basic information

species Glycine max
transcript GLYMA02G46230.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46230.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G26850.1 (Arabidopsis thaliana), 5'ss of exon 6
AAACGTTGTTTCAGATGCATGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaattctaattcttggaagtaaatgaatttgcataatccattttcattagttgtgtggggtatttaccaaaatagatgaacag
  |   |||||||||    ||| | || ||||| ||||||||||| ||||||||  |||| |||||||| ||||||| |||  | |   |  | ||||||||| ||  || |  |    ||||| | | |    |||   | |   | ||  || |   |||      | ||   |    | |    |||
TGATACTGTTTCAGACTGCTGTGTTTGCCTTCAAAACAACAACATTCCTTTCAACATTCTCATCTCTGATTGTGGAAGGCAGATCTTCTTAATGCCACAGgtatat--aactaca-ccgttggatgaatacatgttt---tgaattactta-atcaaaagtgaataacagtttgaatgtaaaaattgcag

upper sequence: GLYMA02G46230.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G55120.1 (Arabidopsis thaliana), 5'ss of exon 6
AAACGTTGTTTCAGATGCATGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaattctaattcttggaagtaaatgaatttgcataatccattttcattagttgtgtggggtatttaccaa--aatagatgaacag
| |   ||| ||||| ||||   | |||||||||||||||||||| ||||||||  |||| |||||||||| ||| || | | | |  ||  | || |||||    |||||   |   | |     |||| |||  |  ||| |  | | |||  ||  | |     || ||| | |    | |||   |||
AGATACTGTATCAGACGCATCCGTTTGTCTTCAGAACAACAACATTCCTTTCAACATTCTCATCTCTGACTCTGGCAAACGAATCTTCCTTCTCCCTCAGgt----taaatctcacaacat---tataaacgaaacttgata-ttgactgtcaaaagaagagctttctaattaaccattgtttgatttgcag
















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|27426396|gb|CA937916.1|CA937916
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|120529237|gb|EH257371.1|EH257371
EST:     TCAAGGTTCTTATCTCTGACTGTGGAAAGCAAGGGTATCTGTTACCACAG                         TGTTATCCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|26059382|gb|CA802296.1|CA802296
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|192302058|gb|FG995206.1|FG995206
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|192302057|gb|FG995205.1|FG995205
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGGATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|6916164|gb|AW397694.1|AW397694
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|18725106|gb|BM523593.1|BM523593
EST:     AAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: AAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|11687681|gb|BF595357.1|BF595357
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|16342958|gb|BI968553.1|BI968553
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|24206305|gb|BU965558.1|BU965558
EST:     GCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: GCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|192297939|gb|FG988381.1|FG988381
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
EST: gi|7028171|gb|AW457954.1|AW457954
EST:     TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAG                         TGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC
genomic: TCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaa ... agatgaacagTGTTATGCAGAGAAACAAGCTCTTGGAGAAGTGAATGCTGAGCTTCTTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACGTTGTTTCAGATGCATGTATATGTCTTCAGAACAACAACATACCTTTCAATGTTCTTATCTCTGACTGTGGAAAGCAAGTGTATCTGTTACCACAGgtaaattaaattctaattcttggaagtaaatgaatttgcataatccattttcattagttgtgtggggtatttaccaaaatagatgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG