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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatgacactcataatatgcaaaccccccttggctttcgcacaaaatctcctttctttattaattaaattcaattcaattatatatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTTCACAAG

Basic information

species Glycine max
transcript GLYMA01G03940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G60060.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gtactatgacactcataatatgcaaaccccccttggctttcgcacaaa-atctcctttctttattaattaaattcaattca------attatata-------tctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTTCACAAG
      | ||   |  || ||| |||    ||     ||    |  |||  |  ||    ||   || | || |    ||  || |      |||| ||        | ||||||||||| ||  | ||| ||||  ||||||||||||| || ||||||||||||||||||
gtatatttctccaaatcttatattatatgtacataatttcatatatgcatgatcatacatttaacttgtaaaattgtgtctctttatatatgattacatgaaaatgttttttcagACCATTGCCTTGATTTCTGTTCGAGAAGGTGTTGTCCAGTTAGGAGCTGTTCACAAG

upper sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0026g00350.t01 (Vitis vinifera), 3'ss of exon 5
gtactatgacactcataatatgcaaaccccccttggctt--tcgcacaaaatctcctttctttattaattaaattcaattcaattatatatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTTCACAAG
    |||| || |   | || |||   |  ||   | ||  | |    | |  | ||||| |           ||  ||||||    | || || |||||||| || || ||||| || |||||||||||  ||||||| |||||||||||||||
---gtatggcattagaattaagcatcacatccaaagattgatagttagagacgtgctttcct---------ggtttgattcaa----acattttgcagACCATTGCGCTGATTGCAGTTAGAGAAGGTGTCATTCAATTGGGAGCTGTTCACAAG
















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|207836733|gb|GD807038.1|GD807038
EST:     CACCCTAGGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAG                         -CCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
genomic: CACCCTAGGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAGgtactatgac ... tatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
EST: gi|193414491|gb|FK377463.1|FK377463
EST:     CACCCTAGGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAG                         ACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
genomic: CACCCTAGGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAGgtactatgac ... tatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
EST: gi|12689978|gb|BG156314.1|BG156314
EST:     CACCCTATGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAG                         ACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTACGAGCTGTT
genomic: CACCCTAGGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAGgtactatgac ... tatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
EST: gi|193722485|gb|FK662579.1|FK662579
EST:     ACTT-GGAAGCCCAGTTCCTGTCTGGTATAAAG                         ACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
genomic: ACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAGgtactatgac ... tatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
EST: gi|207683745|gb|GD665048.1|GD665048
EST:     AAGCCCAGTTCCTGTCTGGTATAAAG                         ACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
genomic: AAGCCCAGTTCCTGTCTGGTATAAAGgtactatgac ... tatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTT
EST: gi|16348841|gb|BI974436.1|BI974436
EST:     CACCCTAGGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAG                         ACCATAGCTCTTATTGCTGTA
genomic: CACCCTAGGACTTGGGAAGCCCAGTTCCTGTCTGGTATAAAGgtactatgac ... tatctttcagACCATAGCTCTTATTGCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacaaaatctcctttctttattaattaaattcaattcaattatatatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTTCACAAG
                   tattaat  putative branch site (score: 2)
                                             tatctttc  putative PPT
             tttctttattaattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatgacactcataatatgcaaaccccccttggctttcgcacaaaatctcctttctttattaattaaattcaattcaattatatatctttcagACCATAGCTCTTATTGCTGTAAGAGAAGGTGTTGTTCAATTAGGAGCTGTTCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT