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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactgtagtctgctagtaatgtttttagattttctattgcttttatatcggaaataattttacccttaatatttcag

Basic information

species Glycine max
transcript GLYMA19G22530.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 4
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactgt-agtctgctagtaatgtttttagattttctattgcttttatatcggaaataattttacccttaatatttcag
||||||||| ||||||||||| ||||| |||||||||||   ||||||  | ||||||||||| || ||||| || || || || |||||| | || || |||||  | || | |    | | | || ||| |  |   || |  ||  | ||| |   |   |||       | |  | |||
TAAACTCAGCGATCGCTTTCCACAGCCTTATGCAAATGAGCAAGCAGCCCGATTTGCTAATGGTGGCGCCTACCCGCCGGACCTTAGTCTTATCACAAAGgtaattgcagttaatggtgttgcattgctttgatgtggcctttcactgat-tatggcttactgtttgcattgcattcatccag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 4
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 3
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgt--aatgactgtagtctgctagta-atgtttttagattttctattgcttttatatcggaaataattttacccttaatatttcag
|||||||||||||||  ||||  | |||||  |||||||| | || |||||||| || ||||||||||| ||||| || |||||||||||||| || || ||    ||    |  ||| |   |  ||    |||||   |  ||  ||  |||     ||  |||||  |  ||  | || |||
TAAACTCAGTGATCGGCTTCCTGAACCATACTCAAATGAATCGGCTGCTAGGTTCGCCAATGGAGGAGCGTATCCACCGGATCTAAGTCTTGTAACTAAGgtttggtgctctttctctccatttgtatacaattagaaaattcat--ctactatgatctaagcaatttggctattt-tcttccag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 4
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgt--aatgactgtagtctgctagtaatg--tttttagattttctattgcttttatatcggaaataattttaccctta-atatttcag
|||||||||||| || ||||| |||||||||||||||||| |||| || |||||||||||||| ||||| |||||||| |||||||||||| | || || ||    ||    || | | ||   | ||    | |  |       |   |||| | |   ||||| |||||   ||     || |||
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgccttccag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactgtagtctgctagtaatgtttttagattttctattgct-tttatatcggaaataattttacccttaatatttcag
 || || |||||||| ||||| ||||| ||||||||||||  ||||||||| ||||||||||||||||| ||||||||||||||||||||  | ||||| ||| | | | |  |    |||     ||  ||||  |   || ||| |  |   |   ||||| |    | ||    | ||||
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtattaattttgtta---tagatcccttgatagaagtga-atggctgtccacccctacaataactgactctttgtcctctcag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 4
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactgtagtctgctagtaatgtttttagattttctattgcttttatatcggaaataattttacccttaatattt-cag
||||||||||||||| ||||| ||||||||||||||||||  ||| ||| ||||||||||||||||||| ||||||||||||||||| ||| | |||||||||||  || |  |||| |     |  || | ||  || | |   | ||||    |  ||| | || |  ||  | ||| |||
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAACAAGCTGCTCGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGCCTTATCACCAAAgtaatttctatgttctggtttggcttcttatggagattatgtctatgttatccaagtgata-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|192295297|gb|FG985951.1|FG985951
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|21888018|gb|BQ741231.1|BQ741231
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|21595027|gb|BQ610344.1|BQ610344
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|13479755|gb|BG509098.1|BG509098
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|17401890|gb|BM178672.1|BM178672
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|192323087|gb|FK017373.1|FK017373
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|151402509|gb|EV272322.1|EV272322
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|192306980|gb|FG999985.1|FG999985
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
EST: gi|14008807|gb|BG725411.1|BG725411
EST:     GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactg ... aatatttcagGCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgactgtagtctgctagtaatgtttttagattttctattgcttttatatcggaaataattttacccttaatatttcag

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