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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtcagacacgttttgattcacccaaaatttattgattttgtaaatatggatggatttgggaaaccacgggggtggatgggaaatatttgtgcatggcttgttcatgtgattttttgtttatattatttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG

Basic information

species Glycine max
transcript GLYMA19G45130.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 16
gtactgtcagacacgttttgattcacccaaaatttattgattttgtaaatatggatggatttgggaaaccacgggggtggatgggaaatatttgtgcatggcttgttcatgtgattttttgtttatattatttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG
                                                             |    | | |         ||| ||   || ||  ||       |     || | | |||||  | | || ||   |||||||||||||| ||  ||||||| ||||| |||||||| |||||| ||||   | | |||||| ||||||||||||||||| ||||  || |     |  
------------------------------------------------------------gtaatcatctatatattataatgtgatg-atctgaacaaatgaaatctgaatg-tatattgttcttttaatctgttacagCCGGAGCCAGAGTTTAGACCACCCATGTCTGAAGTGGTGCAAGCATTGGTTGTATTGGTGCAGAGAGCTAACATGAGCAAGAGAACTGTTGGAGTCGGCT

upper sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 15
gtactgtcagacacgttttgattcacccaaaattta-ttgattttgtaaatatggatggatttgggaaaccacgggggtggatgggaaatatttgtgcatggcttgttcatgtgattttttgtttatattatttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG
                                |||| || |  |    | |   ||||||||    |  |       |  | ||         ||   | |   ||||| | |||||||    || |||  ||| |||||||| |||||||| ||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||| || |||||||||||| ||||  ||||||      
------------------------gtaaggtgtttagttaaagtaaagagtgcagatggattcatcatcctgtttcagctgctga--------tggtaaagatctgttc-tctgattttaatattttatcgttttgggcagCCTGAGCCAGAGTTCCGGCCACCAATGTCAGAAGTGGTGCAAGCACTGGTGCGGCTAGTCCAGCGGGCAAACATGAGCAAGAGAACCATTAGTAACGAAC

upper sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S204_22V6.1 (Physcomitrella patens), 3'ss of exon 14
gtactgtcagacacgttttgattcacccaaaatttattgattttgtaaatatggatggatttgggaaaccacgggggtggatgggaaatatttgtgcatggcttgttcatgtgattttt-tgtttatattatttg--gggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG
                                         ||      |   | || |   |  || |  ||| | ||  |        |   |   ||   | ||| | | |   || || || |   || ||  | |||||||||||| || |||||||| |||||||| |||||||| || ||||| ||  | ||  ||||||| || |   ||||||| || | ||          ||
-----------------------------------------ttcaccgcttgagttgaaggagacaagc--cggagttgatttatcttcctcgataattgaagttttcctctaacacttgtggttttgcaatgtgatgtgcagCCGGAGCCCGAGTTCCGACCCCCGATGTCTGAAGTGGTGCAGGCACTTGTAAGGCTGATGCAGCGTGCGAGTCTGAGCAAACGCAGATCGGAGTCCGCTG

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|207693825|gb|GD676352.1|GD676352
EST:     CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAG                         CCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
genomic: CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAGgtactgtcag ... tttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
EST: gi|31466756|gb|CD408784.1|CD408784
EST:     GTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAG                         CCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
genomic: GTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAGgtactgtcag ... tttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
EST: gi|208142401|gb|GD935399.1|GD935399
EST:     CTCTTTGCGTTCAG                         CCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
genomic: CTCTTTGCGTTCAGgtactgtcag ... tttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
EST: gi|31471460|gb|CD413488.1|CD413488
EST:     CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAG                         CCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
genomic: CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAGgtactgtcag ... tttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
EST: gi|207848955|gb|GD820652.1|GD820652
EST:     CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAG                         CCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
genomic: CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAGgtactgtcag ... tttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
EST: gi|209706939|gb|BW683228.1|BW683228
EST:     CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAG                         CCGGAGCCAGAATTCCGACCACCGAT-TCAGAAGTGGTTCAAGCACTGGTG
genomic: CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAGgtactgtcag ... tttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
EST: gi|209698334|gb|BW678065.1|BW678065
EST:     CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAG                         CCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG
genomic: CTGTTAAGTCTCTTTCTCGATTTGCCGATGTTATTGCTCTTTGCGTTCAGgtactgtcag ... tttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatttgtgcatggcttgttcatgtgattttttgtttatattatttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG
                    ttcatgtgattttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtcagacacgttttgattcacccaaaatttattgattttgtaaatatggatggatttgggaaaccacgggggtggatgggaaatatttgtgcatggcttgttcatgtgattttttgtttatattatttggggcagCCGGAGCCAGAATTCCGACCACCGATGTCAGAAGTGGTTCAAGCACTGGTGCGACTAGTGCAGCGAGCTAACATGAGCAAGCGAACATTTAGTAGTAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG