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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA

Basic information

species Glycine max
transcript GLYMA10G05130.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttg--attattgatcaaccattaattgtgatgaaatt-----cagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
                                      |   || ||  |   |    ||  ||  ||    || | ||| ||     |||  ||| | |  ||     ||||| |||  |||||| ||||| ||||| ||||||||||||||||||||||| | ||||||||| |||||||||||||| || |||||||| ||||||||||
------------------------------------gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaa-gtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
   | |    |  | ||    |  ||||||    |||      || || |  || | |     | |||  |||  ||| |     ||  ||    ||||   ||||| |||  |||||||||||| ||||| || |||||||||||||||||||| | ||||||||||||||||||||| || || |||||||| || |||||||
--gtttggcttcattccaacatttacaaagtcc-agcgaaatgctattctgatcccca-----tgtttctatt-ctgaccccatgtttgtt----tgaa---cagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
    ||||||||||           ||| | |     ||     | ||  |   | ||  |||      ||||    |  |     |  || || |  |||  ||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||| | |||||||| || ||||  || ||||| ||||| ||| | ||||| |
----gttagatatt-----------caacgta-----cttgtcatattagtacttataaaagtaacagagattga-aactagaagctctttctgcttgaat--agGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 6
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagtt-cttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
                            || || ||           | ||  ||||  || || ||| | |   ||||   |   || |   |||| ||   ||||| ||||||||||||||||||||||| || ||||||||||||||||||||  | || |||| ||||||||| || || ||||| |||||||| ||||| |
--------------------------gtagaaaaagatgacaagatatatttcctctcccaattacttctaaaccttgaattaatcttgaccttgattaa-cacagGGAGAGAAAGATGACAAGATAATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGA

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
------gtatgttagatattccctttttccacaaagcaag--agcctctctctctttttctctctagcagttctt--ttgattatt-----------gatcaaccattaa--ttgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
      |  | |||     | |  |||  |  ||| |||   ||| | | |   |  |  ||||     |||| |   | || ||             ||| |   ||||  |||| | ||  |  |||| ||||| ||||||||||| || |||||||||||||| ||||| |||||||| || | ||| || ||||| ||  ||||||| || ||  | || ||||
gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAA

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|13480494|gb|BG509837.1|BG509837
EST:     GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|209704319|gb|BW683551.1|BW683551
EST:     TATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: TATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|151397331|gb|EV267204.1|EV267204
EST:     GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|31561493|gb|CD487331.1|CD487331
EST:     GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATTATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|58020419|gb|CX707161.1|CX707161
EST:     GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|22931726|gb|BU548865.1|BU548865
EST:     CGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCNNTCTGTGCTGATGATCCTGAGTAT
genomic: CGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|192317150|gb|FK009765.1|FK009765
EST:     GTTGCTTTCTACGGACCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|192331411|gb|FK022716.1|FK022716
EST:     GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|192302348|gb|FG996658.1|FG996658
EST:     GTTGC-TTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|13479092|gb|BG508435.1|BG508435
EST:     GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTACGGGCCAAAGCTATTGGACTCATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|31305438|gb|CD390641.1|CD390641
EST:     CATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: CATGCCTATGATTGATCAGgtatgttaga ... tgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA
                                 cattaat  putative branch site (score: 3)
            ttcttttgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttagatattccctttttccacaaagcaagagcctctctctctttttctctctagcagttcttttgattattgatcaaccattaattgtgatgaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA