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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcag

Basic information

species Glycine max
transcript GLYMA05G07020.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 4
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaat-gagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcag
||||||||| ||||||||||| ||||| |||||||||||   ||||||  | ||||||||||| || ||||| || || || || |||||| | || || ||||| |    || |    | | |  |  || |  |   ||||  ||  | |||     |   |||       | |  | |||
TAAACTCAGCGATCGCTTTCCACAGCCTTATGCAAATGAGCAAGCAGCCCGATTTGCTAATGGTGGCGCCTACCCGCCGGACCTTAGTCTTATCACAAAGgtaattgcagttaatggtgttgcattgctttgatgtggcctttcactgat-tatggcttactgtttgcattgcattcatccag

upper sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 3
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtgtagtctgctagta---acgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcag
|||||||||||||||  ||||  | |||||  |||||||| | || |||||||| || ||||||||||| ||||| || |||||||||||||| || || ||   | |     |||     |    |     |||||   |   |  ||  |||    |||  |||||  |  ||  | || |||
TAAACTCAGTGATCGGCTTCCTGAACCATACTCAAATGAATCGGCTGCTAGGTTCGCCAATGGAGGAGCGTATCCACCGGATCTAAGTCTTGTAACTAAGgtttggtgctctttctctccatttgtatacaattagaaaattcat--ctactatgatctaagcaatttggctattt-tcttccag

upper sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgt--aatgagtgtagtctgct--agt--aacgtctttagattttcttttgcttttatatcataaataattttaccctta-atgtttcag
|||||||||||| || ||||| |||||||||||||||||| |||| || |||||||||||||| ||||| |||||||| |||||||||||| | || || ||    ||    || | | ||  |    ||| ||| |||     ||| || |||| | |  |||||| |||||   ||     || |||
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtag-caaacttgtg-ttttgtgttttaaatagttttaatgttctgccttccag

upper sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcag
 || || |||||||| ||||| ||||| ||||||||||||  ||||||||| ||||||||||||||||| ||||||||||||||||||||  | ||||| ||| | | | |  |    |||   | |   ||||  |   |     |  |   |   ||||| |    | ||    | ||||
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgtta---tagatcccttgatagaagtgaatggctgtccacccctacaataactgactctttgtcctctcag

upper sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 4
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtgtagtctgctagtaacgtctt-tagattttcttttgcttttatatcataaataattttacccttaatgttt-cag
||||||||||||||| ||||| ||||||||||||||||||  ||| ||| ||||||||||||||||||| ||||||||||||||||| ||| | |||||||||||   | |  |||| |  |  | |||| | ||  || | |   | ||||   |   ||| | || |  ||  | ||| |||
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAACAAGCTGCTCGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGCCTTATCACCAAAgtaatttctatgttctggtt-tggcttcttatggagattatgtctatgttatccaagtgata-tcttgcttttgttcttttcag

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|15285987|gb|BI469878.1|BI469878
EST:     GGTTTGCTAATGGAGGATTCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
EST: gi|16343642|gb|BI969237.1|BI969237
EST:     AATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: AATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
EST: gi|58018184|gb|CX704926.1|CX704926
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
EST: gi|8670252|gb|BE191359.1|BE191359
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtg ... aatgtttcagGCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgagtgtagtctgctagtaacgtctttagattttcttttgcttttatatcataaataattttacccttaatgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG