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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaagtgccaaattcaaagttgttaaaaaacattttttttgtttgctattaccttgttatgcactgattgtaactaactatatatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT

Basic information

species Glycine max
transcript GLYMA08G10200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G10200.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G34590.1 (Arabidopsis thaliana), 3'ss of exon 3
acaagtgccaaattcaaagttgttaaaaaacattttttttgtttgctattaccttgttatgcactg-attgtaac-taactatatatgcattttattttt--agGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT
     |   |  |    |  |  |   | | ||      |  || |   ||   | ||||||  |       | | |||  |||  |  |||| | || |  || ||||| ||  | ||||| ||||| || |  |||||| | |||||||| ||||| || |||||   ||||||||||||||| ||||||||||| || || 
---gctcttatctctgtatgttctgtgagatataaaacctacttccatgtaaggt-ttatgccttttgccacagcataagcataactaaatttaacttgtgcagACATGAGCTATTACTTTTCGAGGCTCTTCAAGAAGGTCTAGAAGAAGAGATGGACAGAGATCCACATGTATGTGTCATGGGTGAAGATGTAGGCCATTAC

upper sequence: GLYMA08G10200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0043g00720.t01 (Vitis vinifera), 3'ss of exon 3
acaagtgccaaattcaaagttg--ttaaaaaacattttttttgtttgctattaccttgttatgcactgattgtaactaactatatatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT
|  | | | |   ||    | |  || | ||   || || || |   ||   |  ||| ||      |||| ||   ||||  || ||  || | |  | |||||||| ||||| || ||||| ||||| || |||||  |||||||||||||||| || |||||  | ||||| || ||||| ||||| || || ||||||
attattactattctcttgttcgcattcataattgttgttcttatg-acttcaatattgctaattgaggatt-tagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT

upper sequence: GLYMA08G10200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g03770.t01 (Vitis vinifera), 3'ss of exon 4
acaagtgccaaattcaaagttgttaaaaaacattttt-tttgtttgctattaccttg---ttatgcactgattgtaactaactatatatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT
    | | | |||||    || | |   |  |      ||  || ||| | | |       |    ||   | || |     | |   ||  || | |  | |||||||| ||||| || ||||| ||||| || |||||  |||||||||||||||| || |||||    ||||| || ||||| |||||||| || ||||||
----gagtctaattcttttttttcattgattaggccaattcattggctttcatcagaaatctcaaaacaagtagtgatgctattttcctgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGACAGAGATCCCCTAGTATGCGTAATGGGTGAAGATGTGGGCCACTAT

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|21255776|gb|BQ452664.1|BQ452664
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
EST: gi|16348357|gb|BI973952.1|BI973952
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
EST: gi|20075922|gb|BQ094705.1|BQ094705
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
EST: gi|120492745|gb|EH220912.1|EH220912
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
EST: gi|207827812|gb|GD797507.1|GD797507
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGTAGGCCCTACGTGAAGGTTTGGAAGAAGAAA
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTG-AGGCCCTACGTGAAGGTTTGGAAGAAGAAA
EST: gi|192298121|gb|FG991401.1|FG991401
EST:     GCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAA
genomic: GCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAA
EST: gi|207804211|gb|GD775830.1|GD775830
EST:     ACAAAGGAAGGCCGTCCTCCGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCT--GCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
EST: gi|22523607|gb|BU082418.1|BU082418
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
EST: gi|21677852|gb|BQ630203.1|BQ630203
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTT
EST: gi|20448253|gb|BQ252377.1|BQ252377
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
EST: gi|7925286|gb|AW831312.1|AW831312
EST:     ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGG                         GCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT
genomic: ACAAAGGAAGGCCGTCCTGCGGCTTCTACATCAAAATCTGGgtatgtctca ... ttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattaccttgttatgcactgattgtaactaactatatatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT
                          aactaac  putative branch site (score: 1)
                                           ttttattttt  putative PPT
                         taactaactatatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaagtgccaaattcaaagttgttaaaaaacattttttttgtttgctattaccttgttatgcactgattgtaactaactatatatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
-caagtgc
- - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcat