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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaggttccattttgtagtctatttgggtttttttaatcaatggtagatattcagttctcttgtcattacattgattttcaaaattttattaggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATCCATATAG

Basic information

species Glycine max
transcript GLYMA20G37170.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37170.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 12
----acaggttccatttt-gtagtctatttgggtttttttaatcaatgg---tagatattcagttctcttgtcattacattgattttcaaaattttattaggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATCCATATAG
    |   | ||||| || || |  | |||    |     ||  ||      ||   ||||  || |||| |   |   ||  |||||      || | ||||||| |   | |||||||| || |||||||| ||||| |||||||| |||||||| ||||| || |||||  | || ||||||||||||||||||||||       
tctaatttgctccatcttagttgcatgttttcagtcaaacaacaaacaaatataatcattcttttttcttttttct-ttttttttttctcttccttttcagGTTTTGGTTTTATTCCCATCCTCCCAAGGTTTAGAAGTTACTTGGTCATCTGTTGTCAAAATCGGCCAATCCCTATATCGTGAGGGACCTGGTAAAGATC-------
















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|10236984|gb|BE805872.1|BE805872
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTT---Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|120496009|gb|EH224176.1|EH224176
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|213602074|gb|DB981924.1|DB981924
EST:     CCCTTACCAAATGACGAAATCTA-TGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGATGTT
genomic: CCCTTACCAAATGACGAAAT-TATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|214007199|gb|DB986191.1|DB986191
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|254340372|gb|GR858497.1|GR858497
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|23064112|gb|BU578885.1|BU578885
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|15662004|gb|BI699375.1|BI699375
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|208093644|gb|GD896491.1|GD896491
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|151398068|gb|EV267946.1|EV267946
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|209703398|gb|BW676225.1|BW676225
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|120495894|gb|EH224061.1|EH224061
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|23064255|gb|BU579028.1|BU579028
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAT                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
EST: gi|120496110|gb|EH224277.1|EH224277
EST:     GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGGTTTTAG                         CGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT
genomic: GCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGG--TT-Ggttaacgaat ... taggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatattcagttctcttgtcattacattgattttcaaaattttattaggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATCCATATAG
                        cattgat  putative branch site (score: 4)
                                       ttttatt  putative PPT
                    attacattgattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaggttccattttgtagtctatttgggtttttttaatcaatggtagatattcagttctcttgtcattacattgattttcaaaattttattaggttttagCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATCCATATAG

- - - - - - - - - - - - -gggtttt