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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaattatttgatagtaatgtctttggaattttctaatgtatgtctacctgaaatatatatccttgtgatttttcag

Basic information

species Glycine max
transcript GLYMA16G06700.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06700.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 3
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgt--aatgctaattatttg-atagtaatgtctttggaattttctaatgtatgtctacctgaaatatatatccttgtgatttttcag
||||||||||||||| ||||| | ||||| |||||||| | ||||||||||| || ||||||||||| ||||| || |||||||||||||| || || || |||| || | | || || || ||| ||| || || | || | || | | | | | || |||
TAAACTCAGTGATCGGCTTCCTGAACCATACTCAAATGAATCGGCTGCTAGGTTCGCCAATGGAGGAGCGTATCCACCGGATCTAAGTCTTGTAACTAAGgtttggtgctctttctctccatttgtatacaattagaaaattc--atctactatgatctaagcaatttggc--tattttcttccag

upper sequence: GLYMA16G06700.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgt-----aatgctaatt-atttgatagtaatgtctttgg-aattttctaatgtatgtctacctgaaatatatatccttgtgatttttcag
|||||||||||| || |||||||||||||||||||||||| ||||||| |||||||||||||| ||||| |||||||| |||||||||||| | || || || ||||| || | || | || ||| | | || || | | | ||| | | | | || || || || |||
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttt--taaatagttttaatgttctg-ccttccag

upper sequence: GLYMA16G06700.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaattatttgatagtaatgtctttggaattttctaatgtatgtctacc--tgaaatatatatccttgtgatttttcag
|| || |||||||||||||||||||| |||||||||||| ||| ||||| ||||||||||||||||| |||||||||||||||||||| | ||||| ||| ||||| | | |||| | | ||| | |||| |||| ||| | |||| | | | || | ||||
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgta---ttaattttgttatagatcccttgatagaagtg---aatggctgtccacccctacaataactgactctttgtcctctcag

upper sequence: GLYMA16G06700.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 4
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaattatttgatagtaatgtctttggaattttctaatgtatgtctacctgaaatatatatc-cttgtgat-ttttcag
|||||||||||||||||||||||||||||||||||||||| ||||||| ||||||||||||||||||||||||||||||||||||| ||| | ||||||||||| || | || | | | |||| || | ||||| || | | |||| | ||| || | |||||||
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAACAAGCTGCTCGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGCCTTATCACCAAAgtaatttctatgttctggtttggcttcttatggagattat--gtctatgt-tatccaagtgatatcttgcttttgttcttttcag

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|254330992|gb|GR842257.1|GR842257
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
EST: gi|192326638|gb|FK018855.1|FK018855
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
EST: gi|192306424|gb|FG997164.1|FG997164
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
EST: gi|192324650|gb|FK018746.1|FK018746
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
EST: gi|254314652|gb|GR829645.1|GR829645
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
EST: gi|151408312|gb|EV278120.1|EV278120
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
EST: gi|151401029|gb|EV270843.1|EV270843
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGT
EST: gi|151408267|gb|EV278075.1|EV278075
EST:     GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAA                         GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGGTTATCG
genomic: GGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaa ... gatttttcagGCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGG-TTATCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgtaatgctaattatttgatagtaatgtctttggaattttctaatgtatgtctacctgaaatatatatccttgtgatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT