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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccagtaaagaaacattatcaaatgccttagttggtaaagagtattgcatttgcatgttactgtgatgactgggagtgtaactgggattattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTCAAAAGCGGCCTTAAGGGAGGAGTGCACATTGTTAAGACTGACCAGGTTG

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 2
tttccagtaaagaaacattatcaaatgccttagttggtaaagagtattgcatttgcatgttactgtgatgactgggagtgtaactgggattattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTCAAAAGCGGCCTTAAGGGAGGAGTGCACATTGTTAAGACTGACCAGGTTG
           | ||  | |   |  |  |   ||  |||    ||||    ||   ||||       |||    |||||| | |    |  |  | |||||||| |||||||| || ||||| || || ||| ||||| | ||||| ||||| || || |||||||| || || |||||||||||   |||  ||| ||
-----------gtaaattcagtgagggattcgattc-taatctctatta---ttagttgttgtctaattga--aagagtgtcattttcgt-gtgatacagTTGGTTGTTAAGAGCCAGATTTTGGCTGGTGGAAGAGGTCTTGGAACATTCAAGAGTGGTCTTAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 2
tttccagtaaagaaacattatcaaatgccttagttggtaaagagtattgcatttgcatgttactgtgatgactgggagtgtaactgggattattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTCAAAAGCGGCCTTAAGGGAGGAGTGCACATTGTTAAGACTGACCAGGTTG
|    | |||      | | |    |   ||   |  |  | | |    ||    |    || || ||  |  |  |   |||||  |||| | |||||||||||||| || || |||||| | || || || ||||| |||||||| |||||||| || |||||||| ||||| |||||||||||||||||||||||||
tgaagattaatatttaagtttttgttcatttcccttctctaaatttcctcagcaaccaaataatgggaaaaaagcaatgctaactttgattctggtgcagTTGGTGGTAAAAAGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTG
















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|298172859|gb|HO019843.1|HO019843
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGACGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|298184950|gb|HO030163.1|HO030163
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGGG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|298176586|gb|HO023173.1|HO023173
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|61241640|gb|DN591031.1|DN591031
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|19347335|gb|BM892215.1|BM892215
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|209712883|gb|BW679160.1|BW679160
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|192308759|gb|FG999784.1|FG999784
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|151397308|gb|EV267181.1|EV267181
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|4260145|gb|AI416641.1|AI416641
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
EST: gi|151409274|gb|EV279082.1|EV279082
EST:     TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAG                         TTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC
genomic: TTGAAGAGGCCAGAAAGGTCATCAAGGACCTTTTCCCTAATGAAAATGAGgtaacctatg ... tattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcatttgcatgttactgtgatgactgggagtgtaactgggattattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTCAAAAGCGGCCTTAAGGGAGGAGTGCACATTGTTAAGACTGACCAGGTTG
                                gtgtaac  putative branch site (score: 3)
                                           attattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccagtaaagaaacattatcaaatgccttagttggtaaagagtattgcatttgcatgttactgtgatgactgggagtgtaactgggattattgtgcagTTGGTGGTTAAGAGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTCAAAAGCGGCCTTAAGGGAGGAGTGCACATTGTTAAGACTGACCAGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - aaagaaa
- - - - - - - - - - - -aatgcct
- - - - - - - - - - - - - - - - gttggta
- - - - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggagtg