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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCCTGGAACTGCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtatttacaggacaactttggttgaaccaggcattcttataatgtttaatcacaactggttttaccatgcaaaagttgtttccttatgtttgtgaa...

Basic information

species Glycine max
transcript GLYMA10G32850.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32850.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G130034_T02 (Zea mays), 5'ss of exon 9
GTATCCTGGAACTGCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtatttacaggacaactttggttgaaccaggcattcttataatgtttaatcacaactggttttaccatgca-aaagttgtttccttatgtttgtgaa
|||| ||| |  | ||||| ||||||||||| |||||||| |||||||| ||||||||||||||| ||    |||        |    |  ||| |   ||  |  |  |    ||       || |||| | |   | |||||  |    |  |   ||    
GTATTCTGCAGTTACATCCAGGAGCAATCAATAGCATCCCAAGCAAATCACACCTAGAAATTGgtatgagcctac-------ttcctttcaaacaaaatatgatagttctcaggaaaatatgatgattttccaactaataaagtcatggtatccttgatgcag-

upper sequence: GLYMA10G32850.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G43600.1 (Arabidopsis thaliana), 5'ss of exon 9
GTATCCTGGAACTGCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtatttacaggaca--actttggttgaaccaggcattcttataa--------tgtttaatcacaactggttttaccatgcaaaagttgtttccttatgtttgtgaa------------------------------------------
|||| ||||| || |||||||| |||||||||||||| || |||||||| || || ||||| |||   |  |||     ||  ||      | |   ||  | |||  |||        || || |||  | ||   || |  | ||  |   |  | |  | | ||| ||                                            
GTATTCTGGAGCTACATCCTGGGGCAATCAACAGCATTCCAAGCAAATCCCATCTTGAAATCGgtaattccttatgtttcattacacatactaatagagaaagtctggtaaatataacgtgctttatctgagct--cttgaggaagctgagagtagtcctatttttttttggtttgatcgttggactaagttctttttcttgtgttctttcaaag

upper sequence: GLYMA10G32850.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 9
GTATCCTGGAACTGCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtg----tatttacaggacaactttggttgaaccaggcattcttataatgtttaatcacaactggttttaccatgcaaaagttgtttccttatgtttgtgaa
|||| ||||| |||||||||||||||||||||||||| || |||||||| || |||||||||||| ||    | |||||   | || |||    | || ||  |   |||   ||  ||  ||  |  |  |||  | |        ||     | | |  |  | |
GTATTCTGGAGCTGCATCCTGGAGCAATCAACAGCATTCCAAGCAAATCACATCTAGAAATTGgtatggttctttttactaaataagttttccaggacaagctacagttac--tgagtagcca--atggtgtttgtcctcatggttctgccatatgaaggcttagta

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|14011696|gb|BG726618.1|BG726618
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|17963753|gb|BM270498.1|BM270498
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|208079463|gb|GD877639.1|GD877639
EST:     ATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTA
genomic: ATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATT-
EST: gi|208291691|gb|GE090265.1|GE090265
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|6133980|gb|AW132430.1|AW132430
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|208302703|gb|GE099992.1|GE099992
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|209728924|gb|BW654991.1|BW654991
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|10255068|gb|BE822834.1|BE822834
EST:     AGCATCCCCAGCAAATCTCANNNAGAAATTG                         ANNNAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: AGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|208256912|gb|GE057489.1|GE057489
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|192296643|gb|FG991211.1|FG991211
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAA
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAA
EST: gi|19345779|gb|BM890659.1|BM890659
EST:     CCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: CCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|6667618|gb|AW279069.1|AW279069
EST:     GCATGCTGGAGCAATCAGCAGCATCCGCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGA
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGA
EST: gi|298164165|gb|HO013810.1|HO013810
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|193614589|gb|FK565133.1|FK565133
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACGCAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
EST: gi|192306704|gb|FG998858.1|FG998858
EST:     GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTG                         ACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC
genomic: GCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtattt ... attgttacagACACAAGAGACATTGATGAGGAAAGAAGAAATAAAGTGGTTGAGAAAATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCCTGGAACTGCATCCTGGAGCAATCAACAGCATCCCCAGCAAATCTCACCTAGAAATTGgtgtgtatttacaggacaactttggttgaaccaggcattcttataatgtttaatcacaactggttttaccatgcaaaagttgtttccttatgtttgtgaa

- - - - - - - - - - GGAGCA