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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattcttacatgtataccactcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttacaagaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAGATGG

Basic information

species Glycine max
transcript GLYMA11G09790.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 5
tatattcttacatgtataccactcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttaca--agaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAGATGG
  || |   | || |    |  | |  || ||  || |  ||  |       ||  |   | |  | | | | | |  ||| || | ||  | |  ||| |||||| |||||||| || ||| |||||||||| |||||  | |||||||||||||| || || |||||||||||||| |||||||||||||| ||||    
-gtaattcgatattt---tcttttggtttttgtttgtttctcgtc-----tgtgcttataattcctcaat-tcacttctttactctgctggatattagAGAGGAGCCATGTCACCGAGAGAAGTATGTGAAGGGTTAGGCTTATTTGATCTCAAGAACAGGAAATGGCACATACAAGGTACTTGTGCTCTTCGTGGAG----

upper sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
tatattcttacatgtatacca-ctcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttacaagaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAGATGG
        || | ||  |    ||| || | | | | || |   |      | |           | ||||  |   |  | | | |   || || || |||||| ||||| ||  | ||| ||||||||||  | ||  |  ||||||||||||| || || ||||| ||||||||||| ||||||||||  ||||    
-------gtaaaagttcataggctctagcttt-ccttatttcatattttttcgttctcatttaccaaaattcgtctgaactctttatgaatttca-gAGAGGAGCCATGTCTCCTCGAGAAGTATGTGAAGGGCTTGGCTTACTTGATCTCAAGAACAGGAAATGGCATATACAAGGCACATGTGCTCTTCAAGGAG----

upper sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
-tatattctt-acatgtataccactcgagttctgcatgatcttccacaaaagcatgactgcca-gttataattgttaatatttttcttttcttta--caagaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAGATGG
  | |  | | ||||    |  | |   | | ||| |    ||  |  |     |   ||  |   | | || ||||||  |||   |||||       ||||||| |||||| | |||| |||| ||||||||||||||||||||| ||||||||||||  |||| ||||| |||||||| ||||| |||||   |||||    
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|58014737|gb|CX701479.1|CX701479
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         GAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCA
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCA
EST: gi|192303487|gb|FG995921.1|FG995921
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGAAAG                      
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCT----Ggtatgtcttt ... tacaaga
EST: gi|31459239|gb|CD401267.1|CD401267
EST:     CCAACAAACAGGACCTGAAAG                      
genomic: CCAACAAACAGGACCT----Ggtatgtcttt ... tacaaga
EST: gi|151397286|gb|EV267159.1|EV267159
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|151397286|gb|EV267159.1|EV267159
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|151397286|gb|EV267159.1|EV267159
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|151397286|gb|EV267159.1|EV267159
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|14259783|gb|BG882691.1|BG882691
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGAAAG                      
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCT----Ggtatgtcttt ... tacaaga
EST: gi|58016117|gb|CX702859.1|CX702859
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGAAAG                      
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCT----Ggtatgtcttt ... tacaaga
EST: gi|58015262|gb|CX702004.1|CX702004
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGAAAG                      
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCT----Ggtatgtcttt ... tacaaga
EST: gi|23729125|gb|BU762647.1|BU762647
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGTCTTCAAACAGGACCTGAAAG                      
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCT----Ggtatgtcttt ... tacaaga
EST: gi|151405888|gb|EV275703.1|EV275703
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|151405888|gb|EV275703.1|EV275703
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|151405888|gb|EV275703.1|EV275703
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|151405888|gb|EV275703.1|EV275703
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|192334432|gb|FK024447.1|FK024447
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|192334432|gb|FK024447.1|FK024447
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|192334432|gb|FK024447.1|FK024447
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|192334432|gb|FK024447.1|FK024447
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTG                         A
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGgtatgtcttt ... tacaagaaag-
EST: gi|21479719|gb|BQ576402.1|BQ576402
EST:     CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCTGAAAG                      
genomic: CATTTATGCTCCACAGTATCATCTTGGTGTTTGCCAACAAACAGGACCT----Ggtatgtcttt ... tacaaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagcatgactgccagttataattgttaatatttttcttttctttacaagaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAGATGG
                        tgttaat  putative branch site (score: 3)
                              tatttttcttttcttt  CT-rich tract
                 ttataattgttaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatattcttacatgtataccactcgagttctgcatgatcttccacaaaagcatgactgccagttataattgttaatatttttcttttctttacaagaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - catgtat
- - - - - - - - - ccactcg
- - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - -ccacaaa
- - - - - - - - - - - - - - - - - - - - - - - - -gcatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccagt