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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtccttctctatctttatatacttgtattcctgtttgttttattccccccctcagtttctgtacttagcaatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGGAATGGATACCCTGGCCCGTGGCCTGAGGAATGCTGCCAAGTTGATTGAG

Basic information

species Glycine max
transcript GLYMA17G07380.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 9
gtcagtccttctctatctttatatacttgtattcctgtttgttttattccccccctcag-----tttctgtacttagc-aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGGAATGGATACCCTGGCCCGTGGCCTGAGGAATGCTGCCAAGTTGATTGAG
|| ||  |   |||   || | |   || || |  |   |     |||   ||    |      ||    |  || |   ||   | ||||| |||||||| ||||| || |||||||| ||||| || || |||  ||||||||||||  |||| ||||| ||||| ||||| | |||  |  | |||
gtaagagcgattcttgattcacaatgttttactgtttcatacaaaattaaaccgagaaagaagcttataatgtttggttgattaaacagGCGAAGAGAGAGTACAGACGTGGAAGACTTATTCATTGCTCATATTAGTGGAATGGATACAATGGCTCGTGGACTGAGAAATGCAGTCAAAATCTTGGAG
















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|6725436|gb|AW309835.1|AW309835
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|151410382|gb|EV280197.1|EV280197
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|298173204|gb|HO020188.1|HO020188
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|18693005|gb|BM521853.1|BM521853
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|21887322|gb|BQ740535.1|BQ740535
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|151407803|gb|EV277618.1|EV277618
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTT
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGC-G-GAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTT
EST: gi|5175496|gb|AI759829.1|AI759829
EST:     GGAGGACTAGCACCCAGTGGATTCAACTTCGATGCGATATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|51335738|gb|CO979604.1|CO979604
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|10235983|gb|BE804871.1|BE804871
EST:     GGAAGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGGTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|22525640|gb|BU084451.1|BU084451
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|19934808|gb|BQ079838.1|BQ079838
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|5760217|gb|AI965580.1|AI965580
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|163921552|gb|EH039311.1|EH039311
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|192327522|gb|FK018198.1|FK018198
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|298193926|gb|HO040574.1|HO040574
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|22932991|gb|BU550130.1|BU550130
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
EST: gi|13478586|gb|BG508003.1|BG508003
EST:     GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATT                         GCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG
genomic: GGAGGACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtcagtcctt ... aatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattcctgtttgttttattccccccctcagtttctgtacttagcaatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGGAATGGATACCCTGGCCCGTGGCCTGAGGAATGCTGCCAAGTTGATTGAG
         tttgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtccttctctatctttatatacttgtattcctgtttgttttattccccccctcagtttctgtacttagcaatgttatagGCGGAGAGAGAGCACAGATGTTGAAGACTTGTTCATAGCCCACATTGTTGGAATGGATACCCTGGCCCGTGGCCTGAGGAATGCTGCCAAGTTGATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC