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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaaaattgctgtgactttgttatattttattgttttaagatctttgggattttcattcttgtagataaaattcctaatgctaagttaccttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTTCAAAATTATTCTAGGGAAAGAAGAAGCAAGCGTTCGAAGCGGAAGCGTG

Basic information

species Glycine max
transcript GLYMA11G14960.1
intron # 10
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|31460075|gb|CD402103.1|CD402103
EST:     CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAG                         GGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
genomic: CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAGgtaagtatta ... cttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
EST: gi|22929510|gb|BU546649.1|BU546649
EST:     CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAG                         GGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
genomic: CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAGgtaagtatta ... cttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
EST: gi|209708317|gb|BW683907.1|BW683907
EST:     CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAG                         GGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
genomic: CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAGgtaagtatta ... cttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
EST: gi|20448388|gb|BQ252512.1|BQ252512
EST:     CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAG                         GGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
genomic: CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAGgtaagtatta ... cttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
EST: gi|7926014|gb|AW832040.1|AW832040
EST:     CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAG                         GGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
genomic: CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAGgtaagtatta ... cttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
EST: gi|16104820|gb|BI892560.1|BI892560
EST:     CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAG                         GGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
genomic: CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAGgtaagtatta ... cttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
EST: gi|16105954|gb|BI893694.1|BI893694
EST:     CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAG                         GGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT
genomic: CTTCTGTGTCTGCTTCTGATGATGGCTCGGATACAGAAAGTGACAATAAGgtaagtatta ... cttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggattttcattcttgtagataaaattcctaatgctaagttaccttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTTCAAAATTATTCTAGGGAAAGAAGAAGCAAGCGTTCGAAGCGGAAGCGTG
                            tcctaat  putative branch site (score: 2)
                                         ttacctt  putative PPT
               ttgtagataaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaaaattgctgtgactttgttatattttattgttttaagatctttgggattttcattcttgtagataaaattcctaatgctaagttaccttgttacagGGACAGGAAGATGCAGAAGAAGCATATGCTTCTAAAGTTGGCGAAGAGGTTCAAAATTATTCTAGGGAAAGAAGAAGCAAGCGTTCGAAGCGGAAGCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
aagaaaa
- - - -ttgctgt
- - - - - - - gactttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgc