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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttatattcttacatgtataccactcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG

Basic information

species Glycine max
transcript GLYMA11G09790.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 4
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 5
tagttatattcttacatgtataccactcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttaca--agAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG
      || |   | || |    |  | |  || ||  || |  ||  |       ||  |   | |  | | | | | |  ||| || | ||  | |  ||| |||||| |||||||| || ||| |||||||||| |||||  | |||||||||||||| || || |||||||||||||| |||||||||||||| ||||
-----gtaattcgatattt---tcttttggtttttgtttgtttctcgtc-----tgtgcttataattcctcaat-tcacttctttactctgctggatattagAGAGGAGCCATGTCACCGAGAGAAGTATGTGAAGGGTTAGGCTTATTTGATCTCAAGAACAGGAAATGGCACATACAAGGTACTTGTGCTCTTCGTGGAG

upper sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 4
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
tagttatattcttacatgtatacca-ctcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG
            || | ||  |    ||| || | | | | || |   |      | |           | ||||  |   |  | | | |   || || || |||||| ||||| ||  | ||| ||||||||||  | ||  |  ||||||||||||| || || ||||| ||||||||||| ||||||||||  ||||
-----------gtaaaagttcataggctctagctttcc-ttatttcatattttttcgttctcatttaccaaaattcgtctgaactctttatgaatttca-gAGAGGAGCCATGTCTCCTCGAGAAGTATGTGAAGGGCTTGGCTTACTTGATCTCAAGAACAGGAAATGGCATATACAAGGCACATGTGCTCTTCAAGGAG

upper sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
tagttatattctt-acatgtataccactcgagttctgcatgatcttccacaaaagcatgactgcca-gttataattgttaatatttttcttttcttta--caagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG
     | |  | | ||||    |  | |   | | ||| |    ||  |  |     |   ||  |   | | || ||||||  |||   |||||       ||||||| |||||| | |||| |||| ||||||||||||||||||||| ||||||||||||  |||| ||||| |||||||| ||||| |||||   |||||
---acacagccatgacattgtgataattgttgatttgctttga-tttgattagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG

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|58016117|gb|CX702859.1|CX702859
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|23729125|gb|BU762647.1|BU762647
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGTCTTCAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|192303487|gb|FG995921.1|FG995921
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|192334432|gb|FK024447.1|FK024447
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|58015262|gb|CX702004.1|CX702004
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|14259783|gb|BG882691.1|BG882691
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|31459239|gb|CD401267.1|CD401267
EST:     CCAACAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|58014737|gb|CX701479.1|CX701479
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCT-                         ---GGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
EST: gi|21479719|gb|BQ576402.1|BQ576402
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         AAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacaaaagcatgactgccagttataattgttaatatttttcttttctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG
                            tgttaat  putative branch site (score: 3)
                                  tatttttcttttcttt  CT-rich tract
                   agttataattgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttatattcttacatgtataccactcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttacaagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG

- - - - - - - catgtat
- - - - - - - - - - - ccactcg
- - - - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - -ccacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccagt