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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaatcatactccatttttttgcacacttagttgtattatttgtttaccatgcttcatgaatctagagttgcttcagatttaccaaatgatctaatatttccagttcatttgctttctattatgtgaattaattaagtgtgatctaatgattaacaattctgaatttggtttgatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGCCGTGCATGTTTTTCTGCCAAGAATGCTGCAAAGTGTGCCTTTGTGTTCC

Basic information

species Glycine max
transcript GLYMA06G20830.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G20830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g06210.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtaatcatactccatttttttgcacacttagttgtattatttgtttaccatgcttcatgaatctagagttgcttcagatttaccaaatgatctaatatttccagttcatttgctttctattatgtgaattaattaagtgtga--tctaatgatta---acaattctgaatttggtttgatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGCCGTGCATGTTTTTCTGCCAAGAATGCTGCAAAGTGTGCCTTTGTGTTCC
                                                                                         | | |     | |||   |  ||||||   ||| | |||  |  |||| ||  ||||  ||| ||||| |   |   || |     ||| || |   | |||| ||||| ||  ||||||| || ||||||||| |||| ||||||||||| || |||||||||||||| ||| | |||||      |||||| ||||| ||
-----------------------------------------------------------------------------------------actaaaactgtgttttt-gagcatttgaactct-tgatggaacataataaatggtgaattctgatgatcatttatgtttttttccctgggttaaatgagcagAATGCCCATCACAATGCACGAGGAGATGTAGCAAGACGCAGTACCACAAACCATGCATGTTTTTCTGTCAAAAGTGCTGTGCCAAGTGCCTGTGTGTACC
















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|9203736|gb|BE329960.1|BE329960
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|9264571|gb|BE352718.1|BE352718
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|9819913|gb|BE555356.1|BE555356
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|23052700|gb|BU577192.1|BU577192
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|9899967|gb|BE608935.1|BE608935
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|9899961|gb|BE608929.1|BE608929
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|120532624|gb|EH260757.1|EH260757
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|192294802|gb|FG987491.1|FG987491
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTTGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|11688767|gb|BF596443.1|BF596443
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|21677414|gb|BQ629765.1|BQ629765
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|151405122|gb|EV274936.1|EV274936
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|9259419|gb|BE347566.1|BE347566
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|192303149|gb|FG997725.1|FG997725
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|8403032|gb|BE058666.1|BE058666
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|9203371|gb|BE329657.1|BE329657
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|192303148|gb|FG997724.1|FG997724
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|21887742|gb|BQ740955.1|BQ740955
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|6726886|gb|AW311166.1|AW311166
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|16346227|gb|BI971822.1|BI971822
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|7796343|gb|AW781740.1|AW781740
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|11412475|gb|BF424486.1|BF424486
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|151403238|gb|EV273048.1|EV273048
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|192299215|gb|FG988673.1|FG988673
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|33388516|gb|CA851723.1|CA851723
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|15815568|gb|BI787843.1|BI787843
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
EST: gi|22522146|gb|BU080957.1|BU080957
EST:     AGGAGTTATGGACCTGGGAGTCTAAAGACCTCAC                         AGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC
genomic: AGGAGTTATGGACCTGGGAGTCTAAAGACCTCACgtgagtaatc ... gatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaattaagtgtgatctaatgattaacaattctgaatttggtttgatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGCCGTGCATGTTTTTCTGCCAAGAATGCTGCAAAGTGTGCCTTTGTGTTCC
                 taatgattaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaatcatactccatttttttgcacacttagttgtattatttgtttaccatgcttcatgaatctagagttgcttcagatttaccaaatgatctaatatttccagttcatttgctttctattatgtgaattaattaagtgtgatctaatgattaacaattctgaatttggtttgatatatcagAGTGCCCTTCTGAATGCACAAGAAGATGTAGCCAGACACAGTACCACAAGCCGTGCATGTTTTTCTGCCAAGAATGCTGCAAAGTGTGCCTTTGTGTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG