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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctttgtttttcaaacatgcttaatttgtaagaaatgaaatggaaactacaaattgcttgaaagcttgaacttccataaaagttgacggtactc...

Basic information

species Glycine max
transcript GLYMA09G40650.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os11g02830.1 (Oryza sativa), 5'ss of exon 5
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctt-------tgtttttcaaacatgcttaatttgtaagaaatgaa-atggaaactac--------aaattg---cttgaaagcttg--aacttccataaaagttgacggtactc-----------------------------------------------
||||| || || ||||| || ||| |||| ||| ||||||||||||| || || || ||||| || |||||||||||||||||||||||||| ||||||||||    | |       | ||||| ||   | ||| |||| |      |||| |  |  | |||        ||| ||   |  ||||| ||   || |   ||  ||||   | ||                                                   
TTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATATGTGATGACTGgtactctcctcattttatcttttttaagttttcttcattttttttttctgaatagcgttattacccttcatcaaaatgtgaccagaaagtttactaagtgatatgcaagtatgcagtttctgttttgcccttgcaatttcatctgatgtatatatacctattgggcag

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 5'ss of exon 5
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgta-tgtcctt------tgtttttcaaacatgct-taatttgtaagaaatgaaatggaaactacaaattgcttgaaagcttgaacttccataaaagttgacggtactc--------------------------------------------------------------------------
||||| || || ||||| || ||| |||| ||| ||||||||||||| || || || ||||| || ||||||||||||||||||||||| || |||||||||| ||||||       | ||||| |||  | ||  | ||| |    | |    | |  ||     ||          |  |    |   | |||    |  ||   |                                                                          
TTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACACGGGTGATGGGAACATATGGTTATGCTGCCCCTGAATACGTGATGACTGgtactgtcctcgttttatcttttttaaattttctacatttttttctgagtagcgttgttacccttcatcaaaatgtgaccaggttatttgtcaaaaagaaaagtttaccaagtaatatgcaagtatgcagtttctgttttgcccttgcaatttcatctgatgtatatatacctattgggcag

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G007283_T01 (Zea mays), 5'ss of exon 5
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctttgtttttcaaacatgcttaatttgta-agaaatgaaatggaaactacaaattgcttgaaagcttgaacttc-cataaaagttgacggtactc
||||| || || ||||| || ||  |||||||| | ||||||||||| || || || ||||| ||||| ||||||||||||||||||||||| ||||| ||||  | | |   | ||   | ||||||  | | |  |    | | | |  | |  | ||  | |||   |  ||||||||   |  |  ||   |  ||| 
TTTGGCCTGGCAAAAGCTGGCCCTGAAGGTGATCAGACCCATGTATCAACACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcctcactgtttgtatatgcttggtgtctgcatttcttagaagatatcgtctaacagtttgg--gtatgaacttcatgtcgattttccagacactg

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G099754_T04 (Zea mays), 5'ss of exon 5
------------------------TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctttgtttttcaaacatgcttaatttgtaagaaatgaaatggaaactacaaattgcttgaaagcttgaacttccataaaagttgacggtactc
                        ||||| || || ||||  || ||  |||||||| | || ||||| || || || || ||||| ||||| ||||||||||||||||||||||| ||||| ||||                                                                                                 
GATTATACTGCCAAACTGTCTGACTTTggcctcgcaaaagatggccctgaaggtgatcagacgcatgtgtcgacacgggtgatgggaacctacggttatgctgcccctgaatatgtgatgaccggta-------------------------------------------------------------------------------------------------

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G099754_T01 (Zea mays), 5'ss of exon 5
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtc-----ctttgtttttcaaacatgcttaatttgtaagaa----atgaaatggaaactacaaattgcttgaaagcttgaacttccataaaagttgacggtactc
||||| || || ||||  || ||  |||||||| | || ||||| || || || || ||||| ||||| ||||||||||||||||||||||| ||||| ||||  |      | | ||| ||   | ||||||  | | |  |      |    ||||   |  | || || | | |    |||||| |     || ||  |       
TTTGGCCTCGCAAAAGATGGCCCTGAAGGTGATCAGACGCATGTGTCGACACGGGTGATGGGAACCTACGGTTATGCTGCCCCTGAATATGTGATGACCGgtactttcctctcctcgttgtttgtatatgcttggtatttgggtttcttagatgatggcgtcatctaactgttcggata--tgaactccatgttaaatttcc-------

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G01020.1 (Arabidopsis thaliana), 5'ss of exon 4
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctttgtttttcaa--acatgcttaatttgtaagaaatgaaatggaaactacaaattg-cttgaaagcttgaacttccataaaagttgacggtactc
|||||  |||||||||| ||||| || |||||||||||||||||||| || ||||| |||||||| ||||| ||||||||||| |||||||| |||||||||||| |||   |  |  |   | |||  |    |  ||   ||    |   |   | | |    |||||     |   || | ||     ||  |       
TTTGGCTTAGCTAAAGCTGGACCCCAGGGTGATGAAACCCATGTATCAACTCGAGTTATGGGTACTTATGGCTATGCTGCCCCAGAATATGTGATGACTGgtatgacctgcataatatagcgagatgtatcccattcaacttattttcttagatgcatacacaatcttgacgagctatcctgcaatgtcttttttcacgg---

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 5'ss of exon 5
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctttgttt--ttcaaacatgcttaatttgtaagaaatgaaatggaaactacaaattgcttgaaagcttgaact-tccataaaagttgacggtactc
||||| || || ||||| ||||||||||||||||| ||||||||||| || || || ||||||||||||||||||||||| || ||||||||||||||||||| | ||| |  ||  || | |  ||||| |||| | || | |          || |   | ||||  ||  |||   | |  || |   || ||  ||   
TTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTGgtaaggcctcttgttagtttataattgctttatttatcagcattacttcatggcctcctgctagcttataa--ttgctttatttatcagcatt-actttatct

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S31_254V6.1 (Physcomitrella patens), 5'ss of exon 5
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatg-tcctttgtttttcaaacatgcttaatttgtaagaaatgaaatggaaactacaaattgcttg-aaagcttgaacttccataaaagttgacggtactc---------------------------------------------------
||||| ||||| ||||  || ||  |||| ||  |||| || ||||| || || |||||||| |||||||| |||||||||||||| ||||| ||||| ||| || | |||   | ||||  | ||  |  |    ||   ||  |  |     | |  | | || |   |   | | |||  |||      ||    | |                                                    
TTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATGCTGCCCCTGAGTATGTGATGACAGgtgtgattcttccctattcattcgtgtcttttcgaaaatgtattcag-gcgctttgccgagtactcgcggaaacttatcttgtatatgcagcgatctgattttgtgtaggttcttcattcggttgcttcatttaactatgtattgatttgcag

upper sequence: GLYMA09G40650.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S207_2V6.1 (Physcomitrella patens), 5'ss of exon 5
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctttgtttt--tcaaacatgcttaatttgtaagaaatgaaatggaaactacaaattgcttgaaagcttgaacttccataa-aagttgacggtactc
|| || ||||| ||||  |||||  |||| ||  |||| || || || || || || ||||| |||||||| |||||||||||||| ||||| ||||||||| ||  || |       || | ||||  || | || ||    |   | |     | || ||  |||      || |  |   || | || || |    |   
TTCGGGCTAGCGAAAGATGGACCTGAAGGAGACAAAACTCACGTTTCAACACGTGTTATGGGCACCTATGGCTATGCTGCCCCTGAGTATGTGATGACTGgtgtgaactctcccccactctatcatgtctactctgaaaatgctatgacgtcttttccagatcacttttcttttttacgtatgatcataaattcaaatga---

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|208329336|gb|GE128464.1|GE128464
EST:     CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTG                         GCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
genomic: CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctt ... atatggccagGCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
EST: gi|193350738|gb|FK317070.1|FK317070
EST:     CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTG                         GCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
genomic: CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctt ... atatggccagGCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
EST: gi|207753546|gb|GD725972.1|GD725972
EST:     CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTG                         GCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
genomic: CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctt ... atatggccagGCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
EST: gi|208178692|gb|GD977539.1|GD977539
EST:     CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTG                         GCCACCTGACGGCTAGGAGTGACGTCTACAGCTTTGGCGTTGTTCTTTTGG
genomic: CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctt ... atatggccagGCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
EST: gi|208332777|gb|GE130316.1|GE130316
EST:     CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTG                         GCCACCTGACGGCTAGG-GTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG
genomic: CCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctt ... atatggccagGCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCTACCCGAGTCATGGGTACCTATGGTTATGCTGCCCCTGAATATGTAATGACTGgtatgtcctttgtttttcaaacatgcttaatttgtaagaaatgaaatggaaactacaaattgcttgaaagcttgaacttccataaaagttgacggtactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaaa