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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtatgcattcttttgtttttttttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA

Basic information

species Glycine max
transcript GLYMA17G37540.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 3
-----ggtatgcattctt-ttgtttttttttcaatct-tgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaac-------attgactgtgagat-tataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
        || |||| |  || | |||| | ||||   |   |||||  |||    ||   ||     |||| |||  || | |  |  ||        ||  ||||  |  | | |    | |||| |||||||||||| |||||||||||||| ||||| |||||||| || |||||||| || || || || 
gtatgccgatccattttcattatcttttctccaattgatagcttgtttgttttgtatc---aaacctgttttcatgttcattttgaagaaattttttaaataaactgcaatttgtgttgtttgcagGCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 4
ggtatgc--attcttttgtttttttttcaatct---tgat---ttgttcttttcaattcttaaag--agcattttaatgcacaatgt------ccaagaacattgactgtgagattata---aaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
 ||||||  | || |||| || |   |  || |   ||||   |||   | |     || ||     |  ||||   | | |  | |      ||    ||| |   |   |  | |||      | ||||  ||||||||||| |||||||| |||||  |||| |||||||||||||| || ||  | || || || 
-gtatgcccactcctttgcttctcggtttatttagttgatatcttggcttctctgcctcctagtaccaaaatttaggttccctgtattttcccccttccacaatagtttgaatttcatatttgtttgcagGCTAATCCAGACTACAAGGGTGTCTGCCACATTGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 4
ggtatgcattcttttgtttttttttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
                    | |     | |  |||  |||| ||    |        |||||   ||| |    ||  ||     ||   | ||      | |  |  |||  ||||| ||||| || ||||||||||||||||| ||||| || ||||||||||| ||||| ||||| 
-------------------gtatgatggtttgaattgattctgttttgctt-------gcattcggatgaa----gtttaatgcttttttgtttgtttcactcatctgtagGCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 4
ggtatgcattcttt----tgtttttt-tttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagatt-----ataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
 |||||    ||||    |||||  | ||| | | |  |   | |    |   ||  ||||  |  || | ||      |     |  |||| || ||| |  ||     ||  | | ||||| || ||||| ||||| ||||| ||||||||||| ||||| || ||||||||||| ||||||||||| 
-gtatgatgcctttcaggtgtttcatgttttagtttccaaccgctaaactatcttgctaaaagg--ttatcatctgtccttgtttatcacatggaatgtaaagtttgcttattgactgcagGTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 4
ggtatgcattcttttgtttttt---tttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagatt-----ataaa-atacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
 ||||||  ||| | || |||    ||| | | |  |     |    |  |||  | ||| |  | | | |  |   |     |   || ||| ||| |  ||     || |  || ||||  ||||| || || || ||||| ||||||||||||||||| || ||||||||||| ||||||||||| 
-gtatgc-ctctctggtctttcatgttttagtttccaaccactgaactatattgctgaag-gtgtatca-tctattcttgtttattgcactgaatgtaaactttacgtatgagcatgcagGCCAATCCGGATTACAAAGGTGTATGCCATGTTGCCCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 4
ggtatgcattcttttgtttttttttca-atcttgat-ttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaat----acaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
       ||| | |        |  || ||   |   || || | ||| ||||| |         || || | ||  ||  ||     || |   | |  || |  ||      ||||  |||||||| || ||||| ||||||||||| || ||||| ||||| || |||||| | |||||||| 
-------attatgtaaaacggatcacacatggaggcattattttcttctattctca--------cttgatacgcacagt--aattgatttaatgctaattttgtcgaacttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 3
ggtatgcattcttttgtttttttttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
                                                | | |     |  |||  |||       | |     |  | ||   |     ||   || |||| |||||| ||||| |||||||||||||| ||||| |||||||| |||||||| ||  | || || || 
-----------------------------------------------gtacgtttgcggtgtttgtatgtg----attctgtcgctctaacccgg-----atttgatgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 1
ggtatgcattcttttgtttttttttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
                                                | | |     |  |||    | ||    | |     |  | ||   |     ||   || |||| |||||| ||||| |||||||||||||| ||||| ||||||||||||||||| || || || || || 
-----------------------------------------------gtacgtttgcggtgttt----gtacgtgattcggtcgctctaacccgg-----atttgatgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAG

upper sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 3
ggtatgcattcttttgtttttttttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA-
                                                | | |     |  |||    | ||    | |     |  | ||   |     ||   || ||||  ||||| ||||| |||||||||||||| ||||| |||||||| |||||||| ||  | || || || 
-----------------------------------------------gtacgtttgcggtgttt----gtacgtgattctgtcgctctaacccgg-----atttgatgcagGCGAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAG

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|15813786|gb|BI786061.1|BI786061
EST:     GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAA                         GGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAATG
genomic: GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAAggtatgcatt ... ataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
EST: gi|9204483|gb|BE330707.1|BE330707
EST:     GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAA                         GGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
genomic: GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAAggtatgcatt ... ataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
EST: gi|120492530|gb|EH220697.1|EH220697
EST:     GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAA                         GGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
genomic: GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAAggtatgcatt ... ataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
EST: gi|151403004|gb|EV272817.1|EV272817
EST:     GTACTTTTATGATATTAAGGATCTCAGTAATTTTAA                         GGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
genomic: GTACTTTTATGATATTAAGGATCTCAGTAATTTTAAggtatgcatt ... ataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
EST: gi|120492830|gb|EH220997.1|EH220997
EST:     GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAA                         GGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG
genomic: GAGCAGAATATCAAGTACTTTTATGATATTAAGGATCTCAGTAATTTTAAggtatgcatt ... ataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA
                             cattgac  putative branch site (score: 3)
                                      tgagattataaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatgcattcttttgtttttttttcaatcttgatttgttcttttcaattcttaaagagcattttaatgcacaatgtccaagaacattgactgtgagattataaaatacaGGTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCCCTTGCTCAGGAAGGTCATTGTAGGCCTGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA