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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttcttttattggtaatgattgtttgctaatgaaatgtccccatgctttctcctagtacgggattaagatttgttcagcttcttctgcaaatag...

Basic information

species Glycine max
transcript GLYMA08G23990.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 15
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgtt-cttttattggtaatgattgtttgctaatgaaatgtccccatgcttt--ctcctagtacgggattaagatttgttcagcttcttctg-caaatag-------------------------------------------------------------------
|||  | ||||| ||| |||||||||||||||| ||  | ||||||||||| || ||||| ||  |||| ||||| || || |||||||||||||| |||||   | || ||  ||||  |  | |||   |   ||| |||   |   ||| ||   |   |  | |   |||| | ||   || || | ||||| ||   ||                                                                   
TGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttgctcatattttttttcatttacttgcaataaaa-accatgatgtttcaacctttttttctttattatg-ttgcctcggcattttctggcaggcagcatggtaatgactaaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcag

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 12
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttctt--ttattggtaatgattgtttgc------taatgaaatgtccccatgctttctcctag---tacgggattaagatttgttcagcttcttc-tgcaaatag-----------------------------------------------------
|||  ||||||||||| | |||||||||||||| ||  | ||||||||||| || ||||| ||  |||| ||||| || || || ||||||||||| |||||  |  ||  |  | ||   |     ||  ||||      ||     ||||    |   ||| ||||     |  || |||   || | ||    | |  | | |||||                                                       
TGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtcatgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcag

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 16
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 16
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgtt-cttttattggtaatgattgtttgctaatgaaatgtccccatgctttctcctagtacgggattaagatttgttcagcttcttctgcaaatag
 ||| | || |||||| | || ||||||||||| |||||||| |||||||||||  | || ||  |||| |||||||| || || ||||||||||| ||||| ||| |  ||| |  | ||| | | | | |  |   |  |       |  |||    |    ||   | ||   ||||    | ||   |   ||    
GGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTGTCCAGgtatgtatcacttatccttgta-taagtatctattgtggtgaccaatgaactcttgtctcagcaaccctaatacattttgaaggggttgaacgataatctt

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 16
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgtt--ctttta----ttggtaatgattgtttgctaatgaaatgtccccatgctttctcctagtacgggattaagatttgttcagcttcttctgcaaatag
 ||| | |||||||| |||| ||| || |||||||| || || ||||||||||||||||| || |||||||| ||||||||||| ||||||||||| ||||  ||| ||  |  | |    |    ||   ||  || ||  | |  ||   ||||     | || |   |     | ||  | | |  |    |  || |     
GGAATCTTTTTATGAACAATATGACCCTGATTTTATTAATATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTTAATGAAATTGTCCAGgcatgtttttcccctcaaacttctagaagactttgtttctcttcacctgaaaccat--caccaccaacctccattatgagcatggctttggaattcatgtag----

upper sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttcttttattggtaatgattgtttgcta---------atgaaatgtccccatgctttctcctagtacgggattaagatttgttcagcttcttctgcaaatag
 ||| | ||||||||||||| ||||||||||||||||||||| ||||||||||||||||| || |||||||| ||||||||||| ||||||||||| || || ||| ||| |   | | |  |  || | |  ||         |||| ||        ||  | ||| | ||  |    ||||  || |      |||  |   |   
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttccca-tagtgttccaagacatgata-----cttgggagga---

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|298182032|gb|HO026207.1|HO026207
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|192305531|gb|FG998315.1|FG998315
EST:     CCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: CCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|57575332|gb|CX548307.1|CX548307
EST:     GGCTCGTG-AGTTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: GGCTCGTGAAG-TTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|7639458|gb|AW733780.1|AW733780
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|13787440|gb|BG650032.1|BG650032
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|58024853|gb|CX711594.1|CX711594
EST:     AGGCTCGTG-AGTTCTGCAAAGGGAAGATGACCTGAATGAAATGGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|192324960|gb|FK015411.1|FK015411
EST:     AGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|21676820|gb|BQ629171.1|BQ629171
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|12691488|gb|BG157824.1|BG157824
EST:     CCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: CCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|7042485|gb|AW472379.1|AW472379
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|58023444|gb|CX710185.1|CX710185
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|6724341|gb|AW308740.1|AW308740
EST:     TGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: TGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|192309103|gb|FG999386.1|FG999386
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|26268400|gb|CA819463.1|CA819463
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
EST: gi|57575633|gb|CX548608.1|CX548608
EST:     AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACTTGAATGAAATTGTTCAG                         CTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT
genomic: AGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttc ... tttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttcttttattggtaatgattgtttgctaatgaaatgtccccatgctttctcctagtacgggattaagatttgttcagcttcttctgcaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctcc