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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctccattctttaatcactgtgctttcaggttatctcttatttacttttctctgttcaaaacaaattttgacag

Basic information

species Glycine max
transcript GLYMA12G34820.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G34820.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g57150.1 (Oryza sativa), 5'ss of exon 2
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgt-----atatctccattctt-taatcactgtgcttt--caggttatctcttatttacttttctctgttcaaaacaaattttgacag-------------
 |||||||| |  || || |||||||| || ||||  || || ||||| || ||||| |||||||| ||||| ||||| ||||| |||||||||||||||||     | ||||   | |||  |||  |    ||||  |      |  || |  | | | |   | |         ||| ||  ||             
CAAGGAGCTCCGCTCCTACGAGAAGGAGGTGGAGAAGGAGGCGGCCAAGACTGCTGACATGAAGGAGAAAGGCGCCGACCCCTACGATCTCAAGCAACAGgtgaagaagatctttgtgcttgcaattgcaagcctttttcccccctttactaacctgcctgttaatttgtctgcattattctggtagtaaattgcaagtg

upper sequence: GLYMA12G34820.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G30410.1 (Arabidopsis thaliana), 5'ss of exon 2
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatat-ctccattctttaa-tcactgtgctttcaggtt---atctcttatttacttttctctgttcaaaacaaattttgacag------------------------------------------------
||| ||||| || ||||||||||| ||||||||||||||||| || || || |||||||||||||| ||||| || |||||||| || || || ||||||||| |   | |||| ||||  || ||||  |   || ||   | | | | |||  |  ||    |  | || |   | ||                                                    
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatttcattgtttatctctctgtattcgaagattcggagcccgtctttgttcgtcagaatctagaa-atgctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag

upper sequence: GLYMA12G34820.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0021g01180.t01 (Vitis vinifera), 5'ss of exon 2
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatc---------tccattctttaatcactgtgct----ttcaggttatctcttatttacttttctctg-ttcaaaacaaattttgacag-------
 |||||| | ||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||||| || ||||| || || ||||| || || ||||||||||  |         | |||| |  ||  |   |  |    ||   ||||| | |  |    || | | || |||     || | || |          
TAAGGAGTTCCATTCCTATGAGAAAGAGGTTGAAAGAGAAGCTGCAAAAACTGCGGATATGAAGGAGAAGGGAGCTGACCCTTATGACCTTAAACAACAGgtatgcccaggtccttttcattttccaaatagcatcatgaaattggtgttatatatcttaaggttatgtttggttcctggaaagtattaagtaaaaaaaa

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|9564281|gb|BE473790.1|BE473790
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GANAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|15287556|gb|BI471447.1|BI471447
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|7042468|gb|AW472362.1|AW472362
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|192327965|gb|FK023826.1|FK023826
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|7285517|gb|AW598004.1|AW598004
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|31475472|gb|CD417500.1|CD417500
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|192304981|gb|FG996113.1|FG996113
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGACCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|213603291|gb|DB981948.1|DB981948
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|10238770|gb|BE807658.1|BE807658
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|192333924|gb|FK024737.1|FK024737
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|33387458|gb|CA850665.1|CA850665
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|21286136|gb|BQ474007.1|BQ474007
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|254336864|gb|GR843043.1|GR843043
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|13791202|gb|BG653793.1|BG653793
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|192332178|gb|FK023827.1|FK023827
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|151406447|gb|EV276262.1|EV276262
EST:     CTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|10255581|gb|BE823347.1|BE823347
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|192333115|gb|FK026444.1|FK026444
EST:     CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAG                         GAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctcc ... attttgacagGAAAATGTCTTGGCTGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGAAGGAAAAAGGAGCCGATCCCTATGATCTCAAGCAACAGgtatatctccattctttaatcactgtgctttcaggttatctcttatttacttttctctgttcaaaacaaattttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA