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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggtttcttcacctttagttttgccattgaaaaagtaccttattagtctctgctgttaccaaatgatctggacatgattatatcagtaaatgaa...

Basic information

species Arabidopsis thaliana
transcript AT4G39460.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39460.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G15150.1 (Glycine max), 5'ss of exon 5
GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggtttct---tcacctttagtttt--gccattgaaaaagtaccttattagtctctgctgttaccaaatgatctggacatgattatatcagtaaatgaa
||| || |||||||||||||||||||| ||||| | |||||||||| |||||| ||  |||||||| ||  |||| ||  || ||||  |||| |||   ||  |   | | | ||| | |   |   |||    |    | | ||||    ||    |   |       | |  |  ||||||  |  |  |   
GGCATCTGCTTTATTTGTTGGAGTTTATGAACCTATAAAGCAGAAATTGCTGAGGATATTTCCTGAACACCTAAGTGCTTTTACTCATTTGgtaagatacttcttagataaacattaatatgaagatgttggtgtaaatgcatgttaggaattgaaagt--taggaagattagttagaattataataagatct---

upper sequence: AT4G39460.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G31870.1 (Glycine max), 5'ss of exon 6
GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggtttcttcacctttagttttgccattgaaaaagtaccttattagtctctgctgttaccaaatgatctggaca--tgattatatcagtaaatgaa---
||| || |||||||||||||||||||| ||||| | |||||||||| |||||| |   |||||||| ||  | || ||  || ||||| |||| |||   ||  |  |   | |   |||  ||  | | | |    ||  | |   || |   |    ||  |  |||    |  ||| |    |||    |   
GGCATCTGCTTTATTTGTTGGAGTTTATGAACCTATAAAGCAGAAATTGCTGAGGGTATTTCCTGAACACCTGAGTGCTTTTACTCACTTGgtaagatacttcttata---taaacattgatatgaagatattggtgta--aattcatgttaagaattgatagttaggaagattagttagaattataataagatct
















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|86037549|gb|DR333304.1|DR333304
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|86037535|gb|DR333290.1|DR333290
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|152038462|gb|AV823633.2|AV823633
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|86037538|gb|DR333293.1|DR333293
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|86037548|gb|DR333303.1|DR333303
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|125206195|gb|EL221149.1|EL221149
EST:     GCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: GCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|86037553|gb|DR333308.1|DR333308
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGAACTTGCTGCATCTCTGATTCGAGT
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGA-CTTGCTGCATCTCTGATTCGAGT
EST: gi|86037534|gb|DR333289.1|DR333289
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|86037555|gb|DR333310.1|DR333310
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|86037540|gb|DR333295.1|DR333295
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCTACA
EST: gi|86037544|gb|DR333299.1|DR333299
EST:     AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG                         ACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCT
genomic: AGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggt ... caaattgcagACTGCAGGGGCCATCGGTGGACTTGCTGCATCTCTGATTCGAGTGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTGgtgagagggtttcttcacctttagttttgccattgaaaaagtaccttattagtctctgctgttaccaaatgatctggacatgattatatcagtaaatgaa

- - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaag