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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactcagaatgccacaagttaactttgtatctttttaaaaaatttatggatcaaaattatattttcatttggaatactataaaaaaatcaagcaag...

Basic information

species Glycine max
transcript GLYMA19G01470.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01470.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os12g26290.6 (Oryza sativa), 5'ss of exon 7
GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactcagaatgccacaagttaac---tttgtatctttttaaaaaatttatggatcaaa------attatattttcatttggaatactataaaaaaatcaagcaag----------------------------------------------------------------
 |||||| || || ||||| |||||||||||||| || |||||||||||||| ||||| || || ||  | ||  |    || |  ||||| || ||||||| ||  |     |  | ||  ||  |   ||||         ||||||| ||   ||  |       ||||  ||| ||  ||||| | | ||   | |||  ||||                                                                 
AATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaa-attttatttacatct-gcaaattcaaattaattaaattagtgagaatgtgtacaatttacctgatattctgattcttttgtgaag

upper sequence: GLYMA19G01470.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G312997_T01 (Zea mays), 5'ss of exon 6
GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactcagaatgccacaagttaactttgtatctttttaaa-aaatttatggat--caaaattatattttcatttggaa--------tactataaaaaaatcaagcaag------------------------------------------------------
||||||| || || ||||| |||||||||||||| || |||||||||||||| ||||| || || ||| | ||  |    || || ||||| || ||||||| ||  | | | |  | ||  ||    |  ||| | || ||| |||   ||  |       ||||  ||| ||  |||||        |||      ||| ||||  ||                                                       
GATTGGTCACTTCTGCTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTGGAGCTTCTCAAGACTAAGACCATGAGAGCTGGAATGCGCGCAAATTGgtgaggat-atattatctcatttt---ctcatatttgttgaaagaaaacaattaacgctggtattacttttccaagtggaaattttatttacatctgcaaattcaaataaattaattagtgagattgtgtacaaatttacctcatattctaattcttttgtgaag

upper sequence: GLYMA19G01470.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G100724_T01 (Zea mays), 5'ss of exon 4
GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaaga-----------------ctcagaat-gccacaagttaactttgtatctttttaaaaaatttatggatcaaaattatattttcatttg-gaatactataaaaaaatcaagcaag----------------------------------------
||||||| || || | ||| |||||||||||||| || |||||||||||||| ||||| || || ||| | ||  |    |  || ||||  || ||||||| ||                  |||| | | |    |||  |||  |  |   |  ||  |  |||     |  ||||| ||||| ||| ||  ||| | |   ||  |   ||  ||                                        
GATTGGTCACTTCTGTTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTCGAGCTTCTCAAGACTAAGACCATGAGAGATGGAATGCACGCAAATTGgtgaggatatattatctcgttttctcatatttgttgaaagaaaacaattaacactggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaattagtgagattgtgtacaaatttacctcgttctaattcttttgtgaag

upper sequence: GLYMA19G01470.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G01420.1 (Arabidopsis thaliana), 5'ss of exon 6
GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactcagaatgccacaagttaactttgtatctttttaaaaaat----ttatggatcaaaattatattttca---tttggaatactataaaaaaatcaagcaag
|  | ||||||||||| ||| | || ||| |||| ||||| |||||||| ||  |||| || ||||| || ||||||||||| || ||||| || ||||||| |   |    || ||||   ||   ||| |   | | |||  |||    ||| | |   |  ||  ||| | |   ||| ||||| | | |    |         
GGCTAGTGACCTCAGCCGTGGTAGCCAAGATTCACACCATAGATTGGACAGTCCAGCTTCTCAAAACCGACACTTTACTTGCTGGGATGCGAGCAAATTGgtcaatat----ataccactttttttttttttgaatctataatgaatcacgttacgtacagacgttgcattctaacacttttgaatattgtgattttag--------

upper sequence: GLYMA19G01470.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv14s0066g01670.t01 (Vitis vinifera), 5'ss of exon 6
GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactcagaatgccacaag---ttaactttgtatctttttaaaaaatttatggatcaaaattatattttcatttggaa-tactataaaaaaatcaagcaag
|  ||||||| || ||||| ||||||||  |||||||||| ||||||||||| ||||| || ||||| |||||  |||||||||| ||||| ||||||||||||   | | | |  | ||||    || ||   ||  ||  | ||   |  ||||||   ||  |          || || |||||||    |   || |   
GGCTGGTGACTTCTGCTGTAATTGCAAAAATTCATACCATAGATTGGACTGTGGAGCTTCTCAAAACCGATACACTACTTGCAGGAATGCGCGCCAATTGgtaaatattacattttctcaagaatctagctagctaggttactcaat--tcaatggatttgaaaaaaccagaagcatgaaagtactatatggta--taaccttt

upper sequence: GLYMA19G01470.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv14s0066g01690.t01 (Vitis vinifera), 5'ss of exon 7
GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactcagaatgccacaagttaactttgtatctttttaaaaaatttatggatcaaaattatattttcatttggaatactataaaaaaatcaagcaag-----------------------------------------------
|  ||||||| || ||||| |||||||| |||| ||||||||||||||| || ||||| || |||||||||||||||| ||| |  ||||| | |||||||| |   |    || | |  | ||||  |    |||  |||||| ||           ||||| || |  | |||| ||  |  || ||||| || |                                                  
GGCTGGTGACTTCTGCTGTAATTGCAAAAGTTCTTACCATTGATTGGACCGTGGAGCTTCTCAAAACTGATACTTTACATGCTGCAATGCGAGGCAATTGgtgaacattcttattcta--aattaatctc---tctacttaaaacat---------ggaattacatatatacttggcatcttgaaagaaaatgaaactgtgttgtgtcaagaaattttcatttggggttttaaaaatattgtttcag

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|21889807|gb|BQ743020.1|BQ743020
EST:     GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTG                         GTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
genomic: GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactca ... gttttttcagGTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
EST: gi|15663097|gb|BI700468.1|BI700468
EST:     GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTG                         GTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
genomic: GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactca ... gttttttcagGTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
EST: gi|17401371|gb|BM178153.1|BM178153
EST:     GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTG                         GTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
genomic: GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactca ... gttttttcagGTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
EST: gi|37995905|gb|CF807494.1|CF807494
EST:     GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTG                         GTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
genomic: GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactca ... gttttttcagGTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
EST: gi|254336835|gb|GR843014.1|GR843014
EST:     GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTG                         GTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
genomic: GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactca ... gttttttcagGTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
EST: gi|21889538|gb|BQ742751.1|BQ742751
EST:     GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTG                         GTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
genomic: GTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactca ... gttttttcagGTATGGATTATTAGGGAAGAAATTTAAGGATACATTTGGGCATGTTGGTGG
EST: gi|254339407|gb|GR848124.1|GR848124
EST:     TTTACTTGCAGGCATGCGTGCCAATTG                         GTATGGATTATTAGGGCGAGAAATTTAAGGATACATTTGGGCATGTTGGTG
genomic: TTTACTTGCAGGCATGCGTGCCAATTGgtaagactca ... gttttttcagGTATGGATTATTAGGG-AAGAAATTTAAGGATACATTTGGGCATGTTGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACCATTGATTGGACTGTAGAGCTCCTTAAAACTGATACTTTACTTGCAGGCATGCGTGCCAATTGgtaagactcagaatgccacaagttaactttgtatctttttaaaaaatttatggatcaaaattatattttcatttggaatactataaaaaaatcaagcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaaa