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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaatcacaggttccattttgtagtctatttgggtttttttaatcaatggtagatattcagttctcttgtcattacattgattttcaaaattttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATC

Basic information

species Glycine max
transcript GLYMA20G37170.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37170.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 3'ss of exon 12
tcaaatcacaggttccatttt-gtagtctatttgggtttttttaatcaatgg---tagatattcagttctcttgtcattacattgattttcaaaattttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATC
|| ||| | ||||| || || | | ||| | || || || |||| || |||| | | || ||||| || | ||||||| | | |||||||| || |||||||| ||||| |||||||| |||||||| ||||| || ||||| | || ||||||||||||||||||||||
tctaattt---gctccatcttagttgcatgttttcagtcaaacaacaaacaaatataatcattcttttttcttttttcttttttt-ttttctcttccttttcagGTTTTGGTTTTATTCCCATCCTCCCAAGGTTTAGAAGTTACTTGGTCATCTGTTGTCAAAATCGGCCAATCCCTATATCGTGAGGGACCTGGTAAAGATC
















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|15662004|gb|BI699375.1|BI699375
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|120496110|gb|EH224277.1|EH224277
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|209697808|gb|BW663939.1|BW663939
EST:     AGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: AGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|23064255|gb|BU579028.1|BU579028
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTATCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|213602074|gb|DB981924.1|DB981924
EST:     ATACATGCCCTTACCAAATGACGAAATCTA-TGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: ATACATGCCCTTACCAAATGACGAAAT-TATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|120495894|gb|EH224061.1|EH224061
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|214007199|gb|DB986191.1|DB986191
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|23064112|gb|BU578885.1|BU578885
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|209703398|gb|BW676225.1|BW676225
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|254340372|gb|GR858497.1|GR858497
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|208093644|gb|GD896491.1|GD896491
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|10236984|gb|BE805872.1|BE805872
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|120496009|gb|EH224176.1|EH224176
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|151398068|gb|EV267946.1|EV267946
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
EST: gi|22928471|gb|BU545610.1|BU545610
EST:     CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAG                         GTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT
genomic: CATACATGCCCTTACCAAATGACGAAATTATTGCAAGGGTAGCAAAACAGgttggttaac ... attttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggtagatattcagttctcttgtcattacattgattttcaaaattttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATC
                               cattgat  putative branch site (score: 4)
 ttttatt  putative PPT
 tcattacattgatttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaatcacaggttccattttgtagtctatttgggtttttttaatcaatggtagatattcagttctcttgtcattacattgattttcaaaattttattagGTTTTAGCGCTGTTCCCATCATCTCAAGGTTTGGAAGTCACTTGGTCTTCTGTTGTTAAAATTGGTCAATCTTTGTACCGTGAGGGACCTGGTAAAGATC

- -aatcaca
- - - - - - - - - - - - - - - - gggtttt