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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA

Basic information

species Glycine max
transcript GLYMA13G19500.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA
                                                                    | |  ||  ||    | || || | |    |  |   | ||  |   | | ||      ||  |  |||  |   |  | || |  ||  ||||| |||  |||||||||||| ||||| || |||||||||||||||||||| | |||||||||||||||||||||||| || || ||||| || |||||||
-------------------------------------------------------------------gtttggcttcattccaacatttacaaa---gtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaa--cagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA

upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA
                                                                                  | |   |   ||   | | |  |     ||   |||      |||  |  |||     | |  |   | |   || ||||| |||  |||||| ||||| ||||| ||||||||||||||||||||||| | ||||||||| ||||||||||| || || || ||||| ||||||||||
---------------------------------------------------------------------------------gtttg-gtccctactca-acaagtgcgctttcttcagaatgaatgaaca--gattctaaagtggtaa-ggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA

upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA
                                                                            || ||||  | |  ||  | |  ||||   ||  | ||  |||      ||||    |        |  || || |  |||  ||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||| | |||||||| || ||||  |||||||| || || ||| | ||||| |
--------------------------------------------------------------------------gttagatattca-acgtacttgt-catattagtacttataaaagtaacagagattga-aactagaagctctttctgcttgaat--agGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA

upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 6
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA
                                                                                  || | | | ||    | |||||| |    |    | | ||| | |   ||||  ||   || |   |||| ||   ||||| ||||||||||||||||||||||| || ||||||||||||||||||||  | || |||| ||||||||| ||||| ||||| |||||||| ||||| |
---------------------------------------------------------------------------------gtagaaaaagatgacaagatatatttcctctcccaattacttctaaaccttgaattaatcttgaccttgattaa-cacagGGAGAGAAAGATGACAAGATAATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGA

upper sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaa--ttgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA
                             |  || | || |   | |  |   |||| |  |     |          | |||  ||  || |    |||| | |   ||  ||    | |  |  ||  |  |||||   ||||  |||| |  |  |  |||| ||||| ||||||||||| || |||||||||||||| ||||| |||||||| || | ||| || ||||| ||| |||||||||| ||  | || ||||
-----------------------------gtgagggactat---tatgccgtactctttgacggaaaccaaactagcttgtattgat-catgttctcatat-tgttcgtacctaatcatccactatat-gtaaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAA

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|298184004|gb|HO029217.1|HO029217
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCC
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCC
EST: gi|192330021|gb|FK020837.1|FK020837
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|19346407|gb|BM891287.1|BM891287
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|37996937|gb|CF808526.1|CF808526
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|6133848|gb|AW132241.1|AW132241
EST:     GTTGCTTTCTTCGGGCCANAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|9565429|gb|BE474938.1|BE474938
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAC                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGCGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|7587913|gb|AW703719.1|AW703719
EST:     GTTGCTATCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAA                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|208302025|gb|GE097505.1|GE097505
EST:     TTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: TTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|192324146|gb|FK017877.1|FK017877
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|213593665|gb|DB971687.1|DB971687
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|209719745|gb|BW672120.1|BW672120
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|17154018|gb|BM143951.1|BM143951
EST:     GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAG                         GGGGAGAAAGATGACCAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCTATTGGTCTCATGCCTATGATTGATCAGgtatattaga ... tcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA
                                 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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattagacattccctttttccacaaagcaagagcctctctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatttagcagttcttttgattattgatctaccattaattgtgatcaaattcagGGTGAGAAAGATGACAAGATAATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA