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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaaataacaaaaggtatatatatatatatatatatatatatatatatatatattaaatcattaattgagtaattaactaatgtggttgcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGGCAGGACCAGAGAAGCACCAAGCAGTGGCACTGAGATCAGACTCAGACCT

Basic information

species Glycine max
transcript GLYMA15G20550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G20550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G33220.1 (Arabidopsis thaliana), 3'ss of exon 3
---ttaaaaataacaaaaggtatatatatatatatatatatatatatatatatatatattaaatcattaattgagtaattaactaatgtggttgcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGGCAGGACCAGAGAAGCACCAAGCAGTGGCACTGAGATCAGACTCAGACCT
    ||| | |  | |   ||  ||  || | |  ||| | |  | | | |   | | |||| ||  |||| |  |    |  |  ||       |  | |||| || || || ||||||||| ||||| |||| || || ||||||||||| ||||| ||||||||||| || || || ||||||||||||||||| |||||
gtaataagattttctagttgttaattcatgttttgata-acaattgttttttcttttcttaattc--taatggttttgaaacattgtgacacaaaaatttcagCGGTAAGCGGAAGAGGATTCTTAGCAAGAGATATAACGTTCCAGAACACAGCAGGGCCAGAGAAGCATCAGGCGGTAGCACTGAGATCAGACTCTGACCT

upper sequence: GLYMA15G20550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G43270.1 (Arabidopsis thaliana), 3'ss of exon 2
ttaaaaataacaaaaggtatatatatata-tatatatatatatatatatatatatattaaatcattaattgag-taattaactaat-gtggttgcatgtg-cagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGGCAGGACCAGAGAAGCACCAAGCAGTGGCACTGAGATCAGACTCAGACCT
              | ||  | || |||| ||| | |       ||| | |   | |   |  ||||||  || | || || |  |  |      || || |||||||||| || |||||||| || ||||| || || |||||||| ||||| |||||||| || || |||||||| || ||| |  |||| ||  | || ||
------------gtaagtccaaatttataatatctttcacctagtattttttgttttcttactattaatgaagattatgaattggttataaaactatttggcagCTGTGAGCGGTAGAGGATTTATTGCACGCGATATCACCTTCCAAAACACAGCAGGACCGGAAAAACACCAAGCGGTCGCAATCCGATCCGATACGGATCT

upper sequence: GLYMA15G20550.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g01900.t01 (Vitis vinifera), 3'ss of exon 3
---ttaaaaataacaaaaggtatatatatatatatatatatatatatatatatatatattaaatcattaattgagtaattaactaatgtggttgcatg---tgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGGCAGGACCAGAGAAGCACCAAGCAGTGGCACTGAGATCAGACTCAGACCT
   || |  ||  ||||||      | | || | |    |  ||   |   |  |  | | || |  ||||  |||  ||||||||| |||    |||   ||||||||| |  |||| |||||| || ||| ||||||| || ||  ||||||||||||||||||||||||||||||| || ||| |||| || || ||||||||
aagtttaggatg-caaaagactaggaaaaatctctgcccaactaccaaccaagctggagtcaacc--taat--agtt-ttaactaatttggcataatggaatgcagCTGTTAAGGGCAAAGGATTTATTGCAAGAGACATGACATTTGAGAACACGGCAGGACCAGAGAAGCACCAAGCGGTAGCATTGAGGTCCGATTCAGACCT

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|207835500|gb|GD808185.1|GD808185
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAGGATTCATAGCACG
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACG
EST: gi|208076736|gb|GD877331.1|GD877331
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAGGATTCA
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATTCA
EST: gi|298180723|gb|HO022162.1|HO022162
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGG
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGG
EST: gi|27446106|gb|CA953229.1|CA953229
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGG
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGG
EST: gi|11688658|gb|BF596334.1|BF596334
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAAGAATCATAGCTCGAGACATTACCTTCCAGAACACTG
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGG
EST: gi|208259170|gb|GE052466.1|GE052466
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAGGATTCAT
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATTCAT
EST: gi|193411115|gb|FK376780.1|FK376780
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAGGATT
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATT
EST: gi|193348515|gb|FK315589.1|FK315589
EST:     TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTG                         CTGTGAGTGGCAGAGGATT
genomic: TAACAGAAGTTTCATTGATGGTTGGACCACGTTCCGGTCAGCTACTTTTGgtaagaacac ... gcatgtgcagCTGTGAGTGGCAGAGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatatattaaatcattaattgagtaattaactaatgtggttgcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGGCAGGACCAGAGAAGCACCAAGCAGTGGCACTGAGATCAGACTCAGACCT
                                aactaat  putative branch site (score: 2)
     atatattaaatcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaaataacaaaaggtatatatatatatatatatatatatatatatatatatattaaatcattaattgagtaattaactaatgtggttgcatgtgcagCTGTGAGTGGCAGAGGATTCATAGCACGAGACATTACCTTCCAGAACACGGCAGGACCAGAGAAGCACCAAGCAGTGGCACTGAGATCAGACTCAGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtt