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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccctgcaaaaattggtttcttctgaatctgtatattgacaatgaatcttgtggttgtgacatctagctgaagttaggttaggcttagcattact...

Basic information

species Arabidopsis thaliana
transcript AT2G20530.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 3
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccctgcaaaaattggtttcttctgaat--ctgtatattgacaatg-aatcttgtggttgtgacatctagctgaagttaggttaggcttagcattact
||| ||  |  || | || | |||| |  ||| |||||||||||| ||||||||||| ||||||||||| || ||||| || |||||| ||||||||||||||| |   || | |||    ||     ||  |  || | || || || || | |  | ||||| |||        | | | | | |     | || |     
TGGTGGAATTGGTTTGTATGCTGCTGCTAACAGTCTCTACAATGTTGATGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaattgaaaatgttttgctatttactg-cattgcagtgctttggttatgattgtggtgttatgcttgatgtttttcagaagag--

upper sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 2
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccctgc---aaaaattggtttcttctgaat--ctgtatattgacaatgaatcttgtggttgt-gacatctagctgaagttaggttaggcttagcattact
||| ||  |  || | || |  ||| |  ||| ||||||||| || || |||||||| ||||||||||| || ||||| || |||||| ||||||||||||||| |   ||    |||||    ||      |  |  |||| || || || || |     || |  | |  |    | |    ||  |  || ||| |       
TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactg-cattggagtgcttgatgattgttactcggttatgattgtggcagtctttgtg-----

upper sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G11670.2 (Glycine max), 5'ss of exon 2
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccct--gcaaaaattggtttcttctgaatctgtatattgacaatgaatcttgtggttgtgacatctagctgaagttaggttaggcttagcat-tact-
||| |||||   | | || || ||| |  |||   | |||||||| || ||||||||||||||||||||||| || ||  |||| ||| ||||||| ||||||| ||| |   | |  | || |   |     || | | || ||  |||| | ||||       | | | |   | || ||  |||    |  | || |||| 
TGGTGGGCTTGTTGTATATGGGGCTGCAAACAGCTTGTACAATGTTGAGGGAGGTCATCGAGCCATTGTCTTCAATCGTGTTGTCGGTGTCAAAGATAAGgttattccattgtccatgactgttgaatgaatgatttttttaatg-taatgcaacttgcaac---gccttttgcatcaactttagttgaagtctgtatgtactc

upper sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G01850.1 (Glycine max), 5'ss of exon 1
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtcc-----ctgcaaaaattggtttcttctgaatctgtatattgacaatgaatcttgtggttgtgacatctagctgaagttaggttaggcttagcattact
||| |||||   | |||| || ||| |  |||   | |||||||| || ||||||||||||||||||||||| || ||  |||| ||| |||| || ||||||| |||     |    |   ||   |   |      || ||  || ||    ||   | |     | |  | ||| ||||||  |        |   |     
TGGTGGGCTTGTTGTTTATGGGGCTGCAAACAGCTTGTACAATGTTGAGGGAGGTCATCGAGCCATTGTCTTCAATCGTGTTGTCGGTGTCAAGGATAAGgttattccattgtccatgactgttaaatgaatgatttcctttaatttaacttgcaactctttttgcatcatctttagttgaagtctgtactcaaatgaaa-----

upper sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccctgcaaaaattggtttcttctgaatctgtatattgacaatgaatcttgtggttgtgacatctagctgaagttaggttaggcttagcattact------
||| |||||  || | || || ||||   ||| ||| |||||||| || ||||||||||| |||||||| ||||| ||  | |||||| |||| |||||||||      | |     |||||||||  || || ||     ||| |||  ||    |  || |    |||   |  |      || || | |    |  |      
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttcc---ccttggtttct--tgcatatgagacctga-aatccattaaattatttttgtctctgcttatatggttttttgggtaattgcttttagattt

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|86023968|gb|DR319721.1|DR319721
EST:     GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAG                         GTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
genomic: GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccct ... gattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
EST: gi|86023978|gb|DR319731.1|DR319731
EST:     GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAG                         GTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
genomic: GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccct ... gattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
EST: gi|164105096|gb|EL968154.1|EL968154
EST:     TGTTGGTATCAAAGACAAG                         GTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
genomic: TGTTGGTATCAAAGACAAGgttagtccct ... gattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
EST: gi|86023959|gb|DR319712.1|DR319712
EST:     GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAG                         GTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
genomic: GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccct ... gattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
EST: gi|163976073|gb|EL970734.1|EL970734
EST:     TCAAAG-CAAG                         GTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
genomic: TCAAAGACAAGgttagtccct ... gattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
EST: gi|86023969|gb|DR319722.1|DR319722
EST:     GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAG                         GTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
genomic: GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccct ... gattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
EST: gi|47828978|gb|CK118662.1|CK118662
EST:     GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAG                         GTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC
genomic: GAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccct ... gattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccctgcaaaaattggtttcttctgaatctgtatattgacaatgaatcttgtggttgtgacatctagctgaagttaggttaggcttagcattact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaatgaa