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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg...

Basic information

species Glycine max
transcript GLYMA13G16570.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg
 ||||| |||||  | ||||| || || |  || ||   |||||||||||||||  | ||||| |||||||||||||| ||||| ||||| |||||||||||  || | |  ||  | |    |  | | |    |   |  |||    | |||   ||  | || |   | | ||||    |  || || |        
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgt--ttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgac-ttggttttgtgttgttttctggtgaatttgcag-------

upper sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttt-tacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg
 ||||| ||| ||   || ||||| ||||   | ||  ||||||||||||||||  | ||||| |||||||||||||| ||||| ||||| ||||| ||||||        |||     |   | ||||   || | ||| |  |  || |   | || |||| || |  || |||||| |                    
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatct-cactggtttctgggttttttcag-------------------

upper sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg
 |||||  || | |||||||| || || |   | |||   ||||| ||||||||  | ||||| |||||||||||||| || || ||||| |||||||||||    |    ||||||      |  |  ||||  || | | |   |   |||     || ||||      | |||     |||  | ||| |       
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataattt----gatttctctgtcag------

upper sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 3
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaattttt-ttgttgttttttacaagtaatacctacacttgtctacgg-atttttttaaattgatgtgtaaacgttcg--
 ||||| |||||||| |||||||| ||||  || ||| |||| || |||||||| |||||||| || ||||||||||| || |||||||| |||||||||||  ||    ||| ||   | | |  ||| || ||||| |   ||    |  | |  | |  |   || |   ||| |||| |    ||| ||| | | |    
ATTTGACATGCTGCGAAGACAGTCCCTTCGTCCTGATTACATTAAAATGTTTGTGTTGGATGAAGCAGATGAAATGCTCTCTCGAGGTTTCAAGGATCAGgtcatt----cttaaaccctaaatccattcttattgttttcacttttgtggcaaaatttccatcaactgcaatattcttttgacagtatgagtatatgatgcat

upper sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 3
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgtttttt-acaagtaatacctacacttgtctacggattt-ttttaaattgatgtgtaaacgttcg
||  || ||| |||||||  |  |||| |   | ||   |||||||   |||||  |||||||||| ||||| |||||||| || || ||||||||||||||| |     |  |  ||    |       ||   |         |   |        |    ||| |  |  | | |||| |     | ||  || |   |
GTACGACATGTTGCGCAGGAACGCACTGCGCGCGGACTCCATCAAGTGCTTTGTGCTGGATGAGGCCGATGAGATGCTTTCTCGGGGGTTTAAGGATCAGgtattccgttcggtg-ttggagcagggggattgcatcacgcagggatgggcgtctttcaagtctgtttgtgcctctgttttgagccagtctg-gaatgaggg

upper sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg
 |  ||||||||  |  | |   | || | ||| ||  ||||||||||||||||  |||| ||||| || || ||||| ||||| ||||| ||||| ||||||   |  |    ||      ||| ||        ||  | |  |  ||    |  |                                          
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataaccaccctgcctgtgccttgtgtgtcgcag-----------------------------------------

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|6964144|gb|AW432837.1|AW432837
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTNTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
EST: gi|193324903|gb|FK288101.1|FK288101
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAG
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAG
EST: gi|17964246|gb|BM270984.1|BM270984
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
EST: gi|19348482|gb|BM893023.1|BM893023
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
EST: gi|16347593|gb|BI973188.1|BI973188
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGTTATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
EST: gi|5606752|gb|AI900850.1|AI900850
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
EST: gi|10847701|gb|BF070341.1|BF070341
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
EST: gi|12772500|gb|BG237427.1|BG237427
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
EST: gi|193329010|gb|FK293014.1|FK293014
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAG
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAG
EST: gi|193421303|gb|FK391450.1|FK391450
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAG
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAG
EST: gi|17400847|gb|BM177629.1|BM177629
EST:     TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAG                         ATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC
genomic: TTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttca ... ttgttatcagATCTACGATATATTTCAGCTGCTGCCATCTAAGATTCAAGTGGGAGTTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT