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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA

Basic information

species Arabidopsis thaliana
transcript AT2G27860.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagctttt-----agttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
||| ||   | | |||   | |   |   |||     ||  | |   ||||   | ||||     |     |   || | |   |  || |||||||| || ||||| ||||| || || ||||| ||||||||  | || ||||||||||| || ||||| || ||||| ||||||||||| |  |||||||
gtatgtcaaccagtccctttctgagaat-aatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
gtaagtgttc--aaatccaagtatataacccaatgctag---tctgtgtat-atatgcaagctt-ttagttaatgcat--ctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
||||||||||     ||   ||    | |   ||  ||    | | || |  || | ||  ||| | ||   |||||     | |    | || |||||||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||| || ||||||||||| |||||||| ||||||||  |  ||||||
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 5
----gtaagtgttcaaatccaag---tatataaccca------atgctagtctgtgtatatatgcaa-gcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
    ||     ||   ||  |     | | ||| |        ||| || ||  | | | |    || | || ||  || |   ||  |  || |  |  ||||||| || ||| | ||||| ||||||||||| ||||||||  |||| ||||| ||||| || || || || |||||||||||||||||| | |||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatatgttactcgatatttttggataatgattctaaatattttctccattccttttctgtagAATCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 5
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatat--gcaagctttt----agttaatgca---tctctatctatcttt-----cagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
|| |||     | |     |||         |   ||| |||  |||| |  ||  |  |||    | ||  | ||   | ||| | |  ||||     ||||||||||| ||  | ||||| ||||||||||| || |||||  | || |||||||| ||| | ||||| || |||||||||||||||||| | |||||||
gtcagttacttacttttgctattgctttttgttgaagtttgttgatattttagccggagttttgaaaatttgttcaaattttctgttttcctttgtctgcagAATCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
-----------------gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaa-gcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
                  | ||  ||    |     | ||||      || |||||  | | | ||   || | || ||  || |   |   | ||| |  |  ||||||| || ||  | ||||| ||||||||||| ||||||||  |||| ||||| ||||| || || || || |||||||||||||| ||| | |||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 5
---------gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
          ||  | | | |     |   | | |    ||  ||| | | || |  |       ||  |  |  |   | |   | | |||  |||||||||||  |  | ||||| ||||||||||| || |||||  | || |||||||| || || ||||| || |||||||||||||||||| |  ||||||
gtcagttacttacttttgctatgttgaagtttttagatgattttagccagagttttgaaaatttgttcaaaattttctgttttcctttgtctg-cagAATCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
|| ||| |||||   |    |||  |   | |  || | | | | | | |   |    | |  |    | | |    | |   |  |||| ||||| |||| |||||| ||||||||||| ||||||||  |||| |||||||| || || ||||| || |||||||||||||| ||| | |||||||
gttagt-ttcaacatctgtcataacatttagtagtattttttttctttttcttactactgatcttgctctttttctcccacaat--agAACCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagcttttagt---taatgcatctctatctatctttc---agAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
|| ||| |||||   |    |||  |     || | |   || | | | | ||   |||| ||   | ||    |||| | | ||   |   |||| ||||| ||||||||||| ||||||||||| ||||||||  |||| |||||||| || || || || || |||||||||||||| ||| | |||||||
gttagt-ttcaacatctgtcataacatggcttgtttggtagtat-ttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ07025 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaa--gcttttagttaatgcat--ctctat--ctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
                  ||||  || |||   |   |||||| ||    || |  | | |||  | | |     || |||  ||  | | |||||  | ||     | |||||||| ||||| || ||||||||| |||||||  | || |||||||||||||| ||||| ||||| || ||  |    ||| 
------------------gtatgcaagccaccacatttctgtggattctagctattggtgttatgtgacgagctactttattacttccgtgcagAACTTGCTCAAGAGCGAGCCTCTGAAGCTCGTCGATGGTGGACAATCACAACGGACGTTCGTCTACATCAAGGATGCCATTGACGCGGTGATGCGTATGG

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ18978 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaa--gcttttagttaatgcat--ctctat--ctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
                  ||||  || |||   |   |||||| |     || |  | | |||  | | |     || |||  ||  | | |||||  | ||     | |||||||| ||||| || ||||||||| |||||||  | || |||||||||||||| ||||| ||||| || ||  |    ||| 
------------------gtatgcaagccaccacatttctgtggagtctagctattgatgttatgtgacgagctactttattacttccgtgcagAACTTGCTCAAGAGCGAGCCTCTAAAGCTCGTCGATGGTGGACAATCACAACGGACGTTCGTCTACATCAAGGATGCCATTGACGCGGTGATGCGTATGG

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|116380179|gb|EG422771.1|EG422771
EST:     TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAAC                         AATCTTCTACGTCGTGAGCCCCTCAAGCTTGTAGATGGTGGAGAATCACAG
genomic: TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
EST: gi|116422972|gb|EG465564.1|EG465564
EST:     TTGATGGTCCTAGAGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAAC                         AATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
genomic: TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
EST: gi|125264093|gb|EL278178.1|EL278178
EST:     TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAAC                         AATCTTCTACG
genomic: TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACG
EST: gi|125209151|gb|EL224105.1|EL224105
EST:     TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAAC                         AATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
genomic: TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
EST: gi|125265866|gb|EL279951.1|EL279951
EST:     CCTGCTTTAGTAAC                         AATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
genomic: CCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
EST: gi|124804521|gb|EH892276.1|EH892276
EST:     GATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAAC                         AATCTTCTACGTCGTGAGCCTCTCAAG
genomic: GATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACGTCGTGAGCCTCTCAAG
EST: gi|116380174|gb|EG422766.1|EG422766
EST:     TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAAC                         AATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
genomic: TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAG
EST: gi|125062039|gb|EL130536.1|EL130536
EST:     TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAAC                         AATCTTCTACGTCGTGAGCCTCT
genomic: TTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttc ... tatctttcagAATCTTCTACGTCGTGAGCCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagtctgtgtatatatgcaagcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
                           agttaat  putative branch site (score: 4)
                                     tctctatctatctttc  putative PPT
                       ttttagttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG