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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttctcacaaactttagtgaacgaacaaacagttgctactgtattttgatgaagatgagaggaatgctcaagaatgaaatcgatgctgacctttttttgtgtgccatgagcag

Basic information

species Arabidopsis thaliana
transcript AT1G09430.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09430.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 5'ss of exon 9
TGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttctcacaaactttagtgaacgaacaaacagttgctactgtattttgatgaagatgagaggaatgctcaagaatgaaatcgatgctgacctttttttgtgtgccatgagcag
||| || |||||  |||||||||| |||||||| || || || || ||||||||||| || ||||| ||||  || |||||||||||  ||||||| ||||     ||       | | ||  |       ||| || |  | ||| | ||   || ||         |||  |||   ||   ||   |  || |    ||     |    || ||||
TGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTCGAGCTTTAAGAGAGAAGgcaagtttcgattggatcgttgttctgtccccaaccactc-ccact-tgttgccattaa---------aatcttcatccatcttat---tattgtctggcttccaaatctggtg-gcag

upper sequence: AT1G09430.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 12
TGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttctcacaaactttagtgaacgaacaaacagttgctactgtattttgatgaagatgagaggaatgctcaagaatgaaatcgatgctgacctttttttgtgtgccatgagcag
||| || || ||  ||||| |  |  | || ||||||||||| || ||||||||||| ||||| ||||||||||| |||||||||||  |  | ||||||||   ||| |    | | || ||  |     |  ||  |||| | | | |||| |  ||  || | | ||   |       |   ||  | | |                         
TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttccctg-agatttgagctacttttc--acttttgcgaatct-ttttaaaaaatgtg-gtgtaacattttcattcgttttctgttcag-------------------------
















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|125126783|gb|EL171850.1|EL171850
EST:     TGATGTGGCAGCTTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAG                         GAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGG
genomic: TGATGTGGCAGC-TACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGG
EST: gi|86087110|gb|DR382869.1|DR382869
EST:     CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGYTAAGAGAAAAG                         GAAMCAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA
genomic: CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA
EST: gi|125270367|gb|EL284452.1|EL284452
EST:     TGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAAGAAAAG                         GAAACAAGATTGAAAGCATCAA
genomic: TGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGA-GAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCATCAA
EST: gi|116442520|gb|EG485112.1|EG485112
EST:     CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAG                         GAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA
genomic: CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA
EST: gi|125003657|gb|EL075926.1|EL075926
EST:     CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAG                         GAAACAAGATTGAAAGCATACAAGAATGCACATTTACGTAAGGAGAG
genomic: CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCAT-CAAGAATGCACATTTACGTAAGGAGAG
EST: gi|124786849|gb|EH876528.1|EH876528
EST:     CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAG                         GAAACAAGATTGAAAGCATCAA
genomic: CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCATCAA
EST: gi|116442521|gb|EG485113.1|EG485113
EST:     CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAG                         GAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA
genomic: CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA
EST: gi|86078164|gb|DR373921.1|DR373921
EST:     CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAG                         GAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA
genomic: CTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttc ... ccatgagcagGAAACAAGATTGAAAGCATCAAGAATGCACATTTACGTAAGGAGAGGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTCGAGCGCTAAGAGAAAAGgtgctctttctcacaaactttagtgaacgaacaaacagttgctactgtattttgatgaagatgagaggaatgctcaagaatgaaatcgatgctgacctttttttgtgtgccatgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA