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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTGCATTGTCTCCTTGTGCTACAACACTCCCGGTCTTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatcaatggcctatgattatttaaagtgatatgttatttgttggtaaaacggtgtcagtgattatcaataataaaaattctgatgttgaccttaa...

Basic information

species Glycine max
transcript GLYMA14G04600.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04600.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g17020.1 (Oryza sativa), 5'ss of exon 2
TTCCTGCATTGTCTCCTTGTGCTACAACACTCCCGGTCTTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatcaatggcc--tatgattatttaaagtgatatgttatttgttggtaaaacggtgtcagtgattatcaataataaaaattctgatgttgaccttaa
| |||||||| || || ||||| ||||| || || || |||||||||||||| ||||| || ||||||||| | ||||| ||||| || || || || ||||    | |  |  ||  | |  | | ||  | || | |||| | |   |   ||    |  |  |  || |   ||         |  ||  |||      
TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttccactgttttcagttgcattgct-tgttttctaccgaacaataaattgctatacttttttttatagccgcaacacattatgaaagag-

upper sequence: GLYMA14G04600.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G21070.1 (Arabidopsis thaliana), 5'ss of exon 2
TTCCTGCATTGTCTCCTTGTGCTACAACACTCCCGGTCTTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatcaatggcctatgattatttaaagt-gatatgttatttgttggtaaaacggtgtcagtgattatcaataataaaaattctgatgtt-gaccttaa-----------------------------
|||||||||| ||||||||||| ||||| |||||||| || || |||||||||||||||   ||||||||||| || ||||||||||| || || |||||||   | | | |    | |  ||  | | | | | || |   | | ||| ||            ||   || |   || |   | |    |   || | ||                              
TTCCTGCATTATCTCCTTGTGCAACAACTCTCCCGGTTTTCCTCGCTGTTGGAAATTCCAAGTCCATGATGGTTCTCGCCATCATAGTTCTGCTCTTCAGgtgagactaagtctattgtttttggtcacatttgttacgccttctcttgatatcgtcaatcttatggcaattagatatgattttacaagggaaagaacatatgtttgaaatgattggtattctttgggcag

upper sequence: GLYMA14G04600.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 2
TTCCTGCATTGTCTCCTTGTGCTACAACACTCCCGGTCTTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatcaatggcctatgattatttaaagtgatatgttatttgttggtaaaacggtgtca-gtgattatcaataataaaaattctgatgttgaccttaa
|||| || ||||| |||||||| || ||||| || || |||||||| ||||| ||||| || ||||||||||||||||| || ||||| || || |||||||||  ||     |  |||    || ||| |  || | |  ||  ||| |  |   || ||  |  | |     ||  ||| ||      |   | ||   
TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgc-atttttctttccttgattcacttgtttcttgacacttcttctagcaaacatagaacagagcatctgtg

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|20814260|gb|BQ298738.1|BQ298738
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGTGGTCAT
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
EST: gi|151413044|gb|EV282852.1|EV282852
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTTATGGGGCCA
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTT-ATGGGGCCA
EST: gi|151395627|gb|EV265504.1|EV265504
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
EST: gi|151405668|gb|EV275482.1|EV275482
EST:     GAAATTCCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CAACAATAACTGTGATGACTTC
genomic: GAAATTCC-TCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCA-CAATAACTGTGATGACTTC
EST: gi|298193663|gb|HO040311.1|HO040311
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGC
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGC
EST: gi|192326157|gb|FK016964.1|FK016964
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
EST: gi|17021827|gb|BM092861.1|BM092861
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGG
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGG
EST: gi|51337160|gb|CO981026.1|CO981026
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
EST: gi|22525658|gb|BU084469.1|BU084469
EST:     GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAG                         CACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG
genomic: GGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatca ... gcatttacagCACAATAACTGTGATGACTTCGCTAGTAGCGTTGTCATTTTATGGGGCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTGCATTGTCTCCTTGTGCTACAACACTCCCGGTCTTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatcaatggcctatgattatttaaagtgatatgttatttgttggtaaaacggtgtcagtgattatcaataataaaaattctgatgttgaccttaa

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