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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgactgatcttctctatattcttattgatgtgcccttaaatcttatttttcttttctttttcatttgtatatttaagttgcatgtttgccattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG

Basic information

species Glycine max
transcript GLYMA04G06250.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 7
ctgactgatcttctctatattcttatt---gatgtgccctta-aatcttatttttcttttctttttcatttgtatatttaagttgcatgtttgccattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG
 |   ||||    ||  ||  |  |||   ||   |    || |||   | ||| |    |||  |   | ||  | | |  | ||||   ||  |  || ||||| ||||||||||| ||||| || |||||||| ||||| || ||||| || || ||||| ||||| ||||| |||
ttacttgatacaatcattacccacattttagactagtttctagaatggcactttacaaaacttcct---tcgttcactcat-tagcataaatggaaaatttcagGAGGAAAAAGTTGATAGCTCTCTCGAGTTTCTCATTCTTGCAAGTGATGGTCTCTGGGACGTTGTATCTAACGAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 7
ctgactgatcttctctatattcttattgatgtgcccttaaatcttatttttcttttctttttcatttgtatatttaagttgcatgtttgccatt-ttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG
 ||  | |  ||      ||||||     | | ||   |   |  |  |||||      |      |   || || | | |||| |||   |   |||||||| |||||  ||||||||||||| ||||||||||| || |||||||| || || |||||||||||| | ||||||
-tgctttagatttatgtcattctttgccttctccctccattccaaaactttctgcagaatcagcactaattaatttactggcatttttctgaaaattgcagGAGGAAAAGATTGACAGCTCCCTCGAGTTTCTTATCCTTGCCAGTGATGGACTGTGGGATGTTGTCACAAATGAG
















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|192313213|gb|FK003333.1|FK003333
EST:     TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
EST: gi|120491569|gb|EH219736.1|EH219736
EST:     TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GGAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
EST: gi|254334939|gb|GR844724.1|GR844724
EST:     TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
EST: gi|209722646|gb|BW654653.1|BW654653
EST:     TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
EST: gi|11412749|gb|BF424760.1|BF424760
EST:     TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAGAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTG
EST: gi|192313214|gb|FK003334.1|FK003334
EST:     TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
EST: gi|120492227|gb|EH220394.1|EH220394
EST:     GACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GGAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
genomic: GACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGG
EST: gi|209722645|gb|BW654652.1|BW654652
EST:     TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG                         GAAGAAAA-GTTGACAGCTCCCTTGAGTTTCNTTAT-CTGGCCAGTGACGG
genomic: TTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtctac ... cattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTC-TTATTCTGGCCAGTGACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcttttctttttcatttgtatatttaagttgcatgtttgccattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG
                                            ccatttt  CT-rich tract
       ttttctttttcatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgactgatcttctctatattcttattgatgtgcccttaaatcttatttttcttttctttttcatttgtatatttaagttgcatgtttgccattttgcagGAAGAAAAAGTTGACAGCTCCCTTGAGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG

ctgactg
- - - - - - - - - - - - - - - -tgccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt