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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcaattgtaacatattttagtggccccaatatttgtttacattcttgaaatcaaacatgttacttacttcttgtaacttattgttttcacggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTATTCAGAAATGCAGGTTATGGTGGTAGATGTCTCTAGGAGAAAGATGGAA

Basic information

species Glycine max
transcript GLYMA09G33590.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33590.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G65640.2 (Arabidopsis thaliana), 3'ss of exon 3
gtttgcaattgtaacatatt-ttagtggccccaatatttgtt-tacattcttgaaatcaaacatgttacttacttcttgtaacttattgttttcacggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTATTCAGAAATGCAGGTTATGGTGGTAGATGTCTCTAGGAGA--AAGATGGAA
|| |  | ||   | | | | ||  ||     ||| ||  || || | | ||   |   |  || ||  | | ||        || |||| |  | | | | |||| ||| ||||||||| |||  || |     ||||| ||||| |||||| |||||||||| |||||||||||||| || ||  | ||       | ||| |  
gtatcgatttaatataaagtatttatgcatggaatgttaattatatagtattcgtaatgataatattgatgagtt--------ttgttgtatatatg-tttatagGGAGCTGAGCAGAGAGATTTCATAACATCAGAAGATATAAAACAAGCATTATTCAGAAACGCAGGTTATGGTGGAAGCTGCTTGTAATGAGTCATGATTG--

upper sequence: GLYMA09G33590.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G10570.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttgca-attgtaacatattttagtggccccaatatttgtttacattcttgaaat-caaacatgttacttacttcttgtaacttattgttttcacggtctttagGTAGCA----GAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTATTCAGAAATGCAGGTTATGGTGGTAGATGTCTCTAGGAGAAAGATGGAA
||    | ||| | |||  ||    | |||  | |   ||  |  |    | ||||  | |     || ||| ||  ||| |  |  ||||||    || | || ||||      ||||||||| |     | |    |||||  |  || ||||||||| ||||||| ||||||||||| || |||||||| |||| ||       ||
gtacaaatattattacactttgatttagccttacttggtgcatcgacaaattaaatgtatattctataattattttctgttatattctgtttttttcgtatatatgtagGTTGGTGAGCAGAGATACATGGTTACTTCGGAAGCTACTAAACAAGCACTAATCAGAAACGCAGGTTATGGAGGAAGATGTCTGTAGGGGAGCTTCAAAA

upper sequence: GLYMA09G33590.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g03550.t01 (Vitis vinifera), 3'ss of exon 3
gtttgcaattgtaacatattttagtggccccaatatttgtttacattcttgaaatcaaacatgttacttacttcttgtaacttattgttttcacggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTATTCAGAAATGCAGGTTATGGTGGTAGATGTCTCTAGGAGAAAGATGGAA
|| || |  |  | | || |||  || |  ||    |  ||||||| ||    || || | | | |  |   | ||  ||  |||  ||||  | |   ||||| ||||||||||  ||      | |     ||||| |||||||||||| |||||||||| ||||||||| |     ||||                    
gtatgtatgttcatcttaatttcctgacttcatatctactttacatgct----atgaatcgtctaatctttattttcaaatgtatgttttttgctggtgttagGCAGCAGAGCAGCAAACAATGCTAAATTCTGAAGATATAAAGCAAGCATTATTCAGAAACGCAGGTTATTGAAAACGATG--------------------

upper sequence: GLYMA09G33590.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s1312g00010.t01 (Vitis vinifera), 3'ss of exon 3
gtttgcaattgtaacatattttagtggccccaatatttg-tttacattcttgaaatcaaacatgttacttacttcttgtaacttattgttttcacg-gtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTATTCAGAAATGCAGGTTATGGTGGTAGATGTCTCTAGGAGAAA---GATGGAA-
    | |  |  | || ||||   |   |   ||||||  ||||||| ||| ||||||      |   || |||  | ||  |  |  |  |     || | |||||||  ||||||         |  |     ||||| |||||||||||| |||||||||||||||| ||||| || |||||||| ||| |||||   |||| || 
----gtatgttgatcagatttc--tccactttatatttactttacatgctttaaatcatctgattcgtttgctttctctatttgttcttcatggtatgtatctaggtagTGGAGCAGCAGGCAGAGACTAATTCTGAAGATATAAAGCAAGCATTATTCAGAAATGCAGGCTATGGAGGAAGATGTCTGTAGAAGAAAAGGGATGAAAA

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|193658417|gb|FK605916.1|FK605916
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|193523061|gb|FK481408.1|FK481408
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|193369092|gb|FK338496.1|FK338496
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|193448781|gb|FK414654.1|FK414654
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|16342027|gb|BI967622.1|BI967622
EST:     GTGTGATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|207756191|gb|GD727090.1|GD727090
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|193417937|gb|FK382215.1|FK382215
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAACTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|193696023|gb|FK637491.1|FK637491
EST:     CAGCTTCAATGATTTTTCTAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: CAGCTTCAATGATTTTTC-AATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|193649657|gb|FK596794.1|FK596794
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAAAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|254336206|gb|GR842385.1|GR842385
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|26057443|gb|CA800357.1|CA800357
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|207759479|gb|GD733908.1|GD733908
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCA
EST: gi|254336205|gb|GR842384.1|GR842384
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
EST: gi|193483309|gb|FK451096.1|FK451096
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAAGCAAGCACT
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAA-GCAAGCACT
EST: gi|193417348|gb|FK383824.1|FK383824
EST:     GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAG                         GTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA
genomic: GTGTTATAAGCAGCTTCAATGATTTTTCAATGCAAGCATCTTGCACAGAGgtttgcaatt ... cggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaatcaaacatgttacttacttcttgtaacttattgttttcacggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTATTCAGAAATGCAGGTTATGGTGGTAGATGTCTCTAGGAGAAAGATGGAA
                                       ttttcac  CT-rich tract
                             taacttattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcaattgtaacatattttagtggccccaatatttgtttacattcttgaaatcaaacatgttacttacttcttgtaacttattgttttcacggtctttagGTAGCAGAGCAGAGAAATTGTATGAGCCAGGAAGAGATAAAGCAAGCACTATTCAGAAATGCAGGTTATGGTGGTAGATGTCTCTAGGAGAAAGATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA