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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagcaaaaggctcttctctttagccaaatttggatttgtagctgtgtgaaattaagactgcaaacaacttccaataacttaattcatctgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG

Basic information

species Glycine max
transcript GLYMA19G34360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G02590.1 (Arabidopsis thaliana), 3'ss of exon 4
---------aaaagcaaaaggctcttctctttagccaaatttggatttgtagctgtgtgaaattaagactgcaaacaacttccaataacttaattcatctgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTAACTGACATCCCATT---ATCATCAGTCGAG
         ||||| |||||  | || | | ||   || |||       | |  |||  |  |||  |||   ||  |  ||   |    |   ||| ||   |   ||||||||||||||||  |||| |||||||||||||| || || ||||| || ||||| || ||  |   ||||||||| |||
tgctcatctaaaagtaaaagctttttttatatatataatttt-----catggg-gtg-aagcttatcactttcaatgatatctgtttctctttgtcaact--ttggtagGTTTTGAGCATGAGCCGACTTGGTGGAGCCGGTGCGGTTGCTCCACTTGTTACTGATATGCCTCTTTCATCATCAGTTGAG

upper sequence: GLYMA19G34360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0141g00220.t01 (Vitis vinifera), 3'ss of exon 4
aaaagcaaaaggctcttctctttagccaaatttggatttgtagctgtgtgaaat-taagactgcaaacaacttccaataact--taattcatctgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG
| | | || |||  || |    ||  |   ||   |||   |  | |  ||||| |   ||| ||      | || || |||  || |   |        ||||| ||||||||||||||| |||| ||||| |||||||| |||||||| ||||| ||||| |||||| |||||||||||
acagggaatagggactacc---taaacttgttcccattctcatttttcggaaatcttcaacttcatttttttcccgattactgatattctgttcattaaccagGTCTTGAGCATGAGTAGATTGGGCGGAGCTGGTGCAGTTGCACCACTTGTAACAGACATTCCATTAGCATCAGTCGAG
















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|254317152|gb|GR826097.1|GR826097
EST:     TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAG                         GTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
genomic: TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAGgtaaaatgca ... tgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
EST: gi|254322969|gb|GR835684.1|GR835684
EST:     TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAG                         GTTTTGAGCATGAGTAGACTGG-TGGAGCCG-TGCAGTG-CAC-ACTGGTA
genomic: TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAGgtaaaatgca ... tgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
EST: gi|19453220|gb|BM954630.1|BM954630
EST:     TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAG                         GTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
genomic: TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAGgtaaaatgca ... tgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
EST: gi|21677257|gb|BQ629608.1|BQ629608
EST:     TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAG                         GTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
genomic: TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAGgtaaaatgca ... tgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
EST: gi|21888332|gb|BQ741545.1|BQ741545
EST:     TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAG                         GTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA
genomic: TGTTAGATGAAATTGTGGATTATGTCAAGTTCTTAAGGCTTCAAGTGAAGgtaaaatgca ... tgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgaaattaagactgcaaacaacttccaataacttaattcatctgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG
                                       ttcatctgcctttc  CT-rich tract
                             aataacttaattcat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagcaaaaggctcttctctttagccaaatttggatttgtagctgtgtgaaattaagactgcaaacaacttccaataacttaattcatctgcctttcagGTTTTGAGCATGAGTAGACTGGGTGGAGCCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG

- aagcaaaa
- - - - - - - - - - - - gccaaat
- - - - - - - - - - - - - - - - - - - -gtagctg
- - - - - - - - - - - - - - - - - - - - - - - - -gaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaac