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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttatggattatattactacattttattttagtttctttctgttatttctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG

Basic information

species Glycine max
transcript GLYMA20G37190.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37190.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g13530.1 (Oryza sativa), 3'ss of exon 2
-tccttatggattatattactacattttattttagtttctttctgttatttctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
 |    |||    |||| | |  |  |  |   |   | |    |    |  |   ||| | ||   ||| |  |        |     | |    | |||||||| || |  || || || ||||| ||  | ||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||||||
ttttccatgatgcatatcaatttaactcgtgaaacactatgaaagcccatgttttatgtattttgtctttctcattttctttttgctgccatac-ctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG

upper sequence: GLYMA20G37190.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g52490.1 (Oryza sativa), 3'ss of exon 3
tccttatggattata-ttactacattttattttagtttctttctgttatttctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
|| || ||||    | |||     || ||| |  ||      |  | |||      | | |  ||  | |    | ||   | |    || ||| |  |||||||| |||| ||| || || ||||||||  | ||||||||||| ||  | ||||| |||||||||||||| ||||| || ||||||
tcgttgtggagagcaattaactagttgtatctgtgtccagcgccat-attctcctgtatgttgttcctgtaaatttacttcattttgttcctttttgtcagAATGGTCTTGCTACCAAGGTTGAGAAATCTCGCAAGCAAATGAAAGAACGCAAGAACAGAGCTAAGAAGATCCGTGGTGTCAAGAAG

upper sequence: GLYMA20G37190.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G171426_T01 (Zea mays), 3'ss of exon 3
---tccttatggattatattactacattttattttagtttctttctgttatt--tctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
   | |      || |||||      || |||| ||  || |   ||  ||    |||   | |  |   | |  ||||        |    ||| || |  |||||||| |||| |||||| || ||||| ||  | ||||||||||||||| | ||||| || || |||||||| ||||| || ||||||
gcatgcccg-aaatgatattttattgttgtattgtaagttttgattgacatgaacctgatggatgttcactatactgctttt----ttgtgttctgttttgccagAATGGTCTTGCTACTAAGGTTGAGAAGTCCCGCAAGCAAATGAAGGAGCGGAAGAACAGGGCCAAGAAGATCCGTGGTGTCAAGAAG

upper sequence: GLYMA20G37190.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------tccttatggattatattactacattttattttagtttctttctgttatttctgcct--gtttctttgttttgtgctaacaaaactaaaatcttttattg----------------------cagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
                           |   ||    || |  | |||  ||||| | ||| ||  |  || |  ||     |    | |||||   ||    ||      |  |||||  || ||                      |||||||||||||| || ||  | |||||||||||||| || || |||||||| ||||| || || |||||||| ||||| |||||||||
gtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG

upper sequence: GLYMA20G37190.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------------------tccttatggattatattactacattttattttagtttctttctgttatttctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattg-cagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
                                                                                                   ||||    ||| | |  |  ||     ||  | || |  ||   ||  ||     | | |  || |     ||||    |    | | |  ||| |||||||||||||| |||||  | ||||| |||||||| ||||| ||||| || ||||| || || ||||| || ||||| |||||||||
gtaaatgctttttccactcttgtttccattgttatatattgctactcacattgacccgtcttaaatcattactcttgctcattactgtttgtctgaaaattataagctatgtgataagtttcggactttatatcgtattgcacttggtgttctctgcatctttatacttaaacatgctttgtctatgtggttggcagAATGGACTTGACACTAAGATTGAGAAGTCAAGGAAACAAATTAAGGAAAGGAAGAACAGGGCGAAGAAAATCCGTGGTGTTAAGAAG

upper sequence: GLYMA20G37190.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 3'ss of exon 3
--tccttatggattatattactacattttattttagtttctttctgttatttctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
  |    |   || |  |       |||| ||| |  ||   |        |||  ||    | || | || |   |   ||  |    | |||  | |||||||||| | ||||| || || ||||| || |||||||||||||||||||| ||||||||  | |||||| | || || || ||||||
tttttaaaaaaatcacgtcttccttttttctttgaactttaattgccctcctctctctaccccattttcttcttgcattgaatttgc--tgtttggtggcagAATGGATTGGATACCAAGGTCGAGAAGTCTAGGAAGCAAATGAAGGAGAGGAAGAATAGGTCCAAGAAGGTCCGAGGTGTAAAGAAG

upper sequence: GLYMA20G37190.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0151g00900.t01 (Vitis vinifera), 3'ss of exon 3
---tccttatggattatattactac---attttattttagtttctttctgttatttctgcc-tgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
    |  | |  | |   | |  |    || |||| || | ||  || || ||||     | || |||| | | |    || || | |  ||  | | |    |||||||||| | ||||| || || || || |||||||||||||||||||| || ||||| || || |||||| | || ||||| ||||||
acaacaatgtacacttagtgaacaaggaatcttatctt-gctttattttgctattcgaaacatgcttctctttct----ctgaccatagcaacttgtctg--cgcagAATGGATTGGATACCAAGGTGGAAAAGTCAAGGAAGCAAATGAAGGAAAGGAAGAACAGGGCCAAGAAGGTCCGAGGAGTGAAGAAG

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|254315878|gb|GR825687.1|GR825687
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|15337472|gb|BI498128.1|BI498128
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|193647660|gb|FK593573.1|FK593573
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATACAAAGGAAGCAAATGAA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAAT-CAA-GGAAGCAAATGAA
EST: gi|13480907|gb|BG510250.1|BG510250
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCCAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|193377428|gb|FK338810.1|FK338810
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|208106456|gb|GD905573.1|GD905573
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATA
EST: gi|31470717|gb|CD412745.1|CD412745
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCCAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|193696996|gb|FK635310.1|FK635310
EST:     GTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: GTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|209703211|gb|BW673345.1|BW673345
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|7146365|gb|AW508287.1|AW508287
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|13791434|gb|BG654025.1|BG654025
EST:     GTTGAGAATGCCAAGAAGTACGAGCCCAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: GTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|7924600|gb|AW830626.1|AW830626
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|193325398|gb|FK291830.1|FK291830
EST:     TTCAGTTGAGAATGCCAAGTAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATAGGACTTGATACTAA
genomic: TTCAGTTGAGAATGCCAAG-AAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAAT-GGACTTGATACTAA
EST: gi|192303061|gb|FG994179.1|FG994179
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|9983978|gb|BE658086.1|BE658086
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|193390968|gb|FK353752.1|FK353752
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGA
EST: gi|193611659|gb|FK560864.1|FK560864
EST:     ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGG                         AATGGACTTGATACTAAAGTA
genomic: ATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgtgagttatt ... tttattgcagAATGGACTTGATACTAAAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG
                                          tcttttatt  CT-rich tract
                            taacaaaactaaaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttatggattatattactacattttattttagtttctttctgttatttctgcctgtttctttgttttgtgctaacaaaactaaaatcttttattgcagAATGGACTTGATACTAAAGTAGAGAAATCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTTAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
-ccttatg
- - - - - - - - - ctacatt
- - - - - - - - - - - - - - - - - - -ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctaac