Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattcattaacaaaattgtagtccaagtactactatgttgttttaatcttcttttctgttttgaagtgcttactattggatccattttctctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAAACTACAGTAGAGTTGCCAATTATGCACCAGCTTATGCAATGAATGATGA

Basic information

species Glycine max
transcript GLYMA12G09680.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09680.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G22360.1 (Arabidopsis thaliana), 3'ss of exon 1
-----cattcattaacaaaattgtagtccaagtactactatgttgttttaatcttcttttctgttttgaagtgcttactattggatccattttctctt---tatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAAACTACAGTAGAGTTGCCAATTATGCACCAGCTTATGCAATGAATGATGA
      |||  | |        | |    ||   ||  || |  | |||| ||||  |   || ||   |||  |||   || |||   ||     ||   | | |||||||  |||| || ||||| |||||||| || || ||||| || |||||||||||  | | ||| ||  || |||| |||||||||||||||||||||||
gtaagtatttttcactttctccgaatcgtaatctctcttaagaagatttagtctttgtaattgattctgagt-tttatgttttgatgtgttggtgattggattttcagGGAGGGTTCCATTTTCGTATTTGGAAGAGATTCATATGAGATTCATGAAAAACTATGGCAAAGTGGCTCATAATGCTCCAGCTTATGCAATGAATGATGA

upper sequence: GLYMA12G09680.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S231_34V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------cattcattaacaaaattgtagtcc-aagtactact-atgttgtt----ttaatcttcttttctgttttgaagtgcttactattggatccattttctctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAAACTACAGTAGAGTTGCCAATTATGCACCAGCTTATGCAATGAATGATGA
                                                                                         | ||  |   |  | | | | ||  |||| | | |  || |||     | |||      || | || |    |  ||  ||||   | | | ||   ||| |||||| || ||||||||||| ||  | || |||||||| ||||||||||||||||||||  |||  || || | |  |||   ||| ||||||||||| || ||
gtaagatattttccttgccgtttacgatttgattcttcctcatattatgcaaaccttaggggttttgcagtttatttcaactttgattgcttttttaggcggagtagaattcagaagttcgaatcgtgctgtcaaactaaatgagtgcttatattattttttattttttattattttcttattggatttttccagGAAGGATTCCTTTCTCATATCTTGAGGATATCCACATGAGGTTTATGAAAAACTATGGTAAGGTGGCAAGTACTGCCTTAGCATATGCAATGAACGACGA

upper sequence: GLYMA12G09680.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S52_233V6.1 (Physcomitrella patens), 3'ss of exon 3
--cattcattaacaaaattgtagtccaagtactactatgttgttttaatcttcttttctgttttgaagtgctt-actattggatccattttctctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAAACTACAGTAGAGTTGCCAATTATGCACCAGCTTATGCAATGAATGATGA
  |  |    |   |  |      ||||    |   |   |   | |     | |       |  || || || |    ||  |  |||||  ||     |||| ||||| |||||| | ||  | || |||||||| ||||||||||||||||||||| | | ||| || |     ||    || ||  |||||||||| ||
ggctctggacacttagttcagctcccaaaggttcaaaccctaaatgacgtgacataatgagatcaaattgattcagcgatgattttatttttcctg---acagGAAGAATCCCTTTCGCATATCTTGAGGATATCCACATGAGGTTTATGAAAAACTACGGAAAAGTGGCAAGCACAGCCTTGGCGTACACAATGAATGACGA

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|58019488|gb|CX706230.1|CX706230
EST:     CCGATCGGATGGCATCACNTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|6566232|gb|AW233913.1|AW233913
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|298191166|gb|HO038645.1|HO038645
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|19270002|gb|BM886258.1|BM886258
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|16996834|gb|BM086206.1|BM086206
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|20811964|gb|BQ296442.1|BQ296442
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|22523664|gb|BU082475.1|BU082475
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|58016376|gb|CX703118.1|CX703118
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|193525042|gb|FK479721.1|FK479721
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCCTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|4291345|gb|AI441748.1|AI441748
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|5607011|gb|AI901109.1|AI901109
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|213593201|gb|DB966082.1|DB966082
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|16348428|gb|BI974023.1|BI974023
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|208122723|gb|GD922729.1|GD922729
EST:     CCGATCGGATGGCGTCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|207730353|gb|GD708809.1|GD708809
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGAC-C-TTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|213598752|gb|DB964290.1|DB964290
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|15813797|gb|BI786072.1|BI786072
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|208171062|gb|GD969317.1|GD969317
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA
EST: gi|7591035|gb|AW706776.1|AW706776
EST:     CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTNTATGAAAA
genomic: CCGATCGGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcttttctgttttgaagtgcttactattggatccattttctctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAAACTACAGTAGAGTTGCCAATTATGCACCAGCTTATGCAATGAATGATGA
                     tgcttac  putative branch site (score: 2)
                                   tccattttctctttat  putative PPT
                        ttactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattcattaacaaaattgtagtccaagtactactatgttgttttaatcttcttttctgttttgaagtgcttactattggatccattttctctttatccagGGAGAATTCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAAAACTACAGTAGAGTTGCCAATTATGCACCAGCTTATGCAATGAATGATGA

cattcat
- - - - aacaaaa
- - - - - - - - - - - -caagtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttac