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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatagttgtatgataggtcagattccatgttttcagattcactgttttaacaatctaatgttattcaacgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAATGGAAGGAATCTGAATATGGAGGTGGTCAGTCTGTTCCTGTTGGTGGTA

Basic information

species Glycine max
transcript GLYMA12G35990.1
intron # 4
splice site 3'
intron type U2

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|6666291|gb|AW277750.1|AW277750
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254316196|gb|GR827733.1|GR827733
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|193442814|gb|FK404220.1|FK404220
EST:     TTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: TTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|15287746|gb|BI471637.1|BI471637
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254335629|gb|GR847157.1|GR847157
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|15287699|gb|BI471590.1|BI471590
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|193320327|gb|FK286072.1|FK286072
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254347544|gb|GR853793.1|GR853793
EST:     CCATCA-TC-TCAGTCTG-CCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCA-CGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|193345515|gb|FK313682.1|FK313682
EST:     TCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: TCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|193415995|gb|FK376657.1|FK376657
EST:     TTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: TTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254335630|gb|GR847158.1|GR847158
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|6916447|gb|AW397977.1|AW397977
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|19938617|gb|BQ081805.1|BQ081805
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254345254|gb|GR855804.1|GR855804
EST:     GTTTCCAATCTCTACTTCATCTCCCAG                         CTGCT-CACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: GTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|193702495|gb|FK635161.1|FK635161
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCAACCGTAAAGTAC
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCA-CCGTAA-GTAC
EST: gi|58018067|gb|CX704809.1|CX704809
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254345253|gb|GR855803.1|GR855803
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254347543|gb|GR853792.1|GR853792
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAA-CTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|13562944|gb|BG551164.1|BG551164
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|151407584|gb|EV277399.1|EV277399
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAA
EST: gi|254329727|gb|GR839280.1|GR839280
EST:     CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAG                         CTGCTCCACCGTAAGTACAG
genomic: CCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattatag ... acgtgttcagCTGCTCCACCGTAAGTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatgttttcagattcactgttttaacaatctaatgttattcaacgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAATGGAAGGAATCTGAATATGGAGGTGGTCAGTCTGTTCCTGTTGGTGGTA
                      ttttaacaatctaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattatagttgtatgataggtcagattccatgttttcagattcactgttttaacaatctaatgttattcaacgtgttcagCTGCTCCACCGTAAGTACAGCGGAAACTTCTTTGTAGATCTATTGGGAAAATGGAAGGAATCTGAATATGGAGGTGGTCAGTCTGTTCCTGTTGGTGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG