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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaacgtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta...

Basic information

species Glycine max
transcript GLYMA20G24070.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaacgtcgtcgttacgtcatcaattaatgttatttgaatgcag-agactaaaagcggtgacgaagaaaatgttta--
|||||| ||||||||||| |||||||| || || || || ||||| ||||| ||||| |||||||| || |||||| | || || ||||| || ||| |||||  |      |  |   ||| ||| | |  | |   |   | |||| || || |  | | |  ||   | | | ||  | |  | |    | |||  |   
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttgtgaatttgtaaccaacattcat---ttatcattttatttcttctaagggcgccataatcaattctgcaatgttttacatgcatctt

upper sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaacgtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta
||| ||||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||||||||| |||||||||||||||||||||||||| |||| || |||     ||| | |  ||    || || | |   |    |  | |     | |||   || ||       |  | ||       | |       
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctc--gcaatcaca--ctacagacatc-ttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag------

upper sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaac-gtcgtcgtt-acgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaa-aatgttta------------------
 ||||||||||||||||| ||||||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||| ||||||||  ||||| || | | ||| | | |   || ||    |  | |||   |   | ||||      |||| ||  |||     | ||  | || |   ||| | | | |                   
TTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAATGGAGAGAGTGACTCTATTCCTTAACCTGgtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaatt--ctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacag

upper sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaac-gtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta-
 ||||||||||||||||||||||||||||| ||    || ||||| ||||| || ||||| || || || |||||||||||||| ||||| || |||||||||  ||  |   |||    ||||  |      |   |  | |  |||  || |   |  |||  | |  ||   | ||   |     |      |      
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatctcacttttaatcttcatcttctgtttaacacggcaaagatatc--ttcaccgtggttgtgttcctagttcagaactagctcttattccttttccctg

upper sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgta-attctttaaaaattaaaatctgttaacgtcg-tcgttacgtcatcaattaatgttatttgaatgcaga---gactaaaagcggtgacgaagaaaatgttta-------------------------------------------------------------------------------------------------
 || || ||||||||||| |||||||| |||||    || ||||| || || ||||| || |||||||| |||||||||||||| ||||| || |||||||||  | | |    | ||    ||| ||| ||||| |  | ||  |||   |  ||  ||| || |     |      |       || | | |  |   || |                                                                                                  
TTTCGCCGCTATGGGAGTGAACATGGAAACTGCCACTTTCTTCAAACGCGATTTTGAAGAAAATGGATCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatgtacatcttcagttt---tcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggctttcag

upper sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 7
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaacgtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta
 |||||||||||||| || ||||||||||||||||||||||||||  | || |||||||| |||||||| ||||| ||||| ||  | ||| | ||  |||||   | |||   ||| | |  ||  || | |||  ||||  |  ||     | |  |                                         
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgta---cgttatggattgacaa-tgccaatg-cgtttttactcctccatcgtgtttcgtacag-------------------------------------

upper sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 7
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaacgtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta
 |||||||||||||| || ||||||||||||||||||||||||||  | || |||||||| |||||||| ||||| ||||| ||  | ||| | ||  |||||   | |||   ||| | |  ||  || | |||  ||||  |  ||       |  |                                         
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgta---cgttatggattgacaa-tgccaatg-cgtttttactcctccatcgtgcttcgtacag-------------------------------------

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|16279439|gb|BI943437.1|BI943437
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|151411391|gb|EV281202.1|EV281202
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTC
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTC
EST: gi|23729967|gb|BU763089.1|BU763089
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAACGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16279488|gb|BI943462.1|BI943462
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16278548|gb|BI942962.1|BI942962
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|19346883|gb|BM891771.1|BM891771
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
EST: gi|16279486|gb|BI943461.1|BI943461
EST:     ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTG                         GCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattcttt ... tttactgcagGCAAATGATCCTACAATTGAGCGTATTATCACTCCTCGTATTGCTCTTACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaacgtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA