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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtactaggtcacggattgtattagatacttcttttatccaacttatcttcattgtttgttgagttttctatgattccgttgcctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG

Basic information

species Arabidopsis thaliana
transcript AT3G51130.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51130.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------gtttgtactaggtcacggattgtatta--gatacttcttttatccaacttatcttcattgtttgttgagtttt--ctatgattccgttgcct------catgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG
                                                                                                |||  |||||  |   |  |||  ||   ||  || || || |   | || | |  |   |   ||   ||||  ||    |||   | | |      ||||||||| ||  ||||  |||||||||||||||||||||| |||||||| || |||||||| |||||||| |||||||||
gtttgtcgcatatgatttatggcttaacttactgtcatttatgttttctattattgtttgaacttgcactagcaattgactgtctgcttcgggcaggttactactatctgttgctttgcctttgtgaggctcctgttgttttattt-tttgaaagatgcatttgtttttatcttgagttcttctacttaatgcacatgcagGAACCCCTGAAGTTGGATGTTGTTATTAGCTTTCCTGATCATGGCTTCCATCTTCGCTTTGATCCGTGGTCTCAG

upper sequence: AT3G51130.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G37380.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------gtttgtac---taggtcacggattgtattagata--cttcttttatcca-acttatcttcattgtttgttgagttttctatgattccgttgcct-------catgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG
                                                                ||| ||   ||  | || |  ||  | |   |   | ||  ||||      | |     || ||| || ||   |   ||| | | |   ||       ||||||||| ||  ||||  ||||| |||||||||||||||| |||||||| || |||||||| || ||||| |||||||||
gtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG

upper sequence: AT3G51130.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 2
-------gtttgtactaggtcacggattgtattagatacttcttttatccaacttatcttcattgtttgttgagttttctatgattccgttgcctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG
        ||  |  || || |       | |     | | ||      ||  | |   || ||| |  |  |   |   |    |  |     | || ||||| || || || |||||| | || |||||||||||||||||||| ||||||||||| |||||||| ||||| |||
gtgtcatcttattgttaagt-atcttgcatttccagcattgctaaggggcatatcaggatc-ttgctactgaaacatctcactgatatgacaatttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG

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|164091284|gb|ES091510.1|ES091510
EST:     GTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: GTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040772|gb|DR336527.1|DR336527
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040774|gb|DR336529.1|DR336529
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040770|gb|DR336525.1|DR336525
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040779|gb|DR336534.1|DR336534
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTSAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|124739796|gb|EH830958.1|EH830958
EST:     TCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: TCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040778|gb|DR336533.1|DR336533
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040777|gb|DR336532.1|DR336532
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040776|gb|DR336531.1|DR336531
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040775|gb|DR336530.1|DR336530
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040771|gb|DR336526.1|DR336526
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
EST: gi|86040773|gb|DR336528.1|DR336528
EST:     AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAG                         GATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT
genomic: AGCAGCAGCCTAACATATATGATGTTGTTCATGTTAAATACTACGACGAGgtttgtacta ... cctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaacttatcttcattgtttgttgagttttctatgattccgttgcctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG
                                          ttgcctc  CT-rich tract
                           ttttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtactaggtcacggattgtattagatacttcttttatccaacttatcttcattgtttgttgagttttctatgattccgttgcctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA