Sequence
atgc intronic sequence ATGC exonic sequencegtatttactcaaatccttgattaaatttttgtttatccagcttcaatatgccatgctcagtttgtgtaactcaagatgtgatgtttctttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60100.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60100.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
-----gtatttactcaaatc---cttgattaaatttttgtttatccagcttcaatatgccatgctcagtttgtgtaactcaagatgtg-atgtttc--tttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA
||| || | || || | ||| ||| | |||||| |||||| | |||| || ||||| | || |||||||||||| ||||||||||||| | | ||||||||||||||||| || ||||| ||||||||| | |||||||| ||| | | ||| ||||| || ||
gtaagcggcataccaaagttatactctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
upper sequence: AT5G60100.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G15580.1 (Glycine max), 3'ss of exon 3
---------gtatttac-tcaaatccttgattaaatttttgtttatccagcttcaatatgccatgctcagtttgtgtaactcaagatgtg-atgtttc--tttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA
||| | | | | || | ||||||| || ||| | |||||| |||||| | |||| || ||||| | || |||||||||||| ||||||||||||| | | ||||||||||||||||| || || || ||||||||| | |||||||| ||| | | ||| ||||| || ||
gtaagtggcgtaccaaagttatactttttactaaatttaagtatat--attttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatgcatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGCGCAGTTGATTTTTTAGTGAAACCAATTCGGAGGAATGAACTTAAAAA
upper sequence: AT5G60100.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
----gtatttactcaaatccttgatt-------aaatttttg-tttatccagct-tcaatatgccatgctcagtttgtgtaactcaagatgtgatgtttctttt-tgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA
|||| | | || ||| |||||| | |||| || ||| | | | | | | || | ||| | | |||| || |||||||||||| ||||||||||||| | | |||||||||||| |||| || ||||| ||||||||| | |||||||| ||| ||||||| ||||| || ||
gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAAMapped 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|116481392|gb|EG523984.1|EG523984EST: GCTGTCCAAGATTATGAGCCATAAGACACTTAAGAACATCCCCGTCATAA TGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATG
genomic: GCTGTCCAAGATTATGAGCCATAAGACACTTAAGAACATCCCCGTCATAAgtatttactc ... ctttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATG
EST:
gi|125296155|gb|EL310240.1|EL310240EST: GCTGTCCAAGATTATGAGCCATAAGACACTTAAGAACATCCCCGTCATAA TGATGTCATCACATGATTCTATGGTTCTGGTCT
genomic: GCTGTCCAAGATTATGAGCCATAAGACACTTAAGAACATCCCCGTCATAAgtatttactc ... ctttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaatatgccatgctcagtttgtgtaactcaagatgtgatgtttctttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA
gtgtaac putative branch site (score: 3)
tgtttcttttt putative PPT
tttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttactcaaatccttgattaaatttttgtttatccagcttcaatatgccatgctcagtttgtgtaactcaagatgtgatgtttctttttgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA