Sequence
atgc intronic sequence ATGC exonic sequence...agatggacgaagataagagaggaatgacagagaatttttttgtagcagctttttcattttctttagagtgatcgttaaggtcaatgctcctcttttgcagGACAGGAAACCCGAGCTAAGATCAGAAGTCATGGCTTTTAGGGATTATCTCCTATCATCAACAGTATCAGACACGCTTGATGTTTGGGAGCTGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71220.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 6
agatggacgaagataagagaggaatgacagagaatttttttgtagcagctttttcattttct-----ttagagtgatcgttaaggtcaa-tgctcctctt---ttgcagGACAGGAAACCCGAGCTAAGATCAGAAGTCATGGCTTTTAGGGATTATCTCCTATCATCAACAGTATCAGACACGCTTGATGTTTGGGAGCTGAAAG
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---------aaaatttcatgacattataaaagtatattcattgcccgaccacaaaattatccagacactagtgttaccaataaatttacctgtttttgtttactcacagGTGCGTAAACCCGAGTTAGCATCTGAGGTCATGGCTTTTCGGGATTATCTATTGTCATCAACTGTATCAGACACACTTGATGTTTGGGAATTAAAGG
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 6
agatggacgaagataagagaggaatgacagagaatttttttgtagcagctttttcattttctttagagtgatcgttaaggtcaa-tgctcctctt---ttgcagGACAGGAAACCCGAGCTAAGATCAGAAGTCATGGCTTTTAGGGATTATCTCCTATCATCAACAGTATCAGACACGCTTGATGTTTGGGAGCTGAAAG
| | | || | || | | | ||| || || || | ||| || | | ||| | | || | | || | ||||| | ||| | ||| ||| ||| || |||||||||||| |||||||||| | |||||||| ||||||||||| |||||||||||||| | || |
--gtatattcatatttatggtgatgtata-atcattgccccacctcaaaattatc-cagacactagtgttaccaataaatttacctgtttttgtttaatcacagGAACGTAAAACTGAGTTAACATCTGAGGTCATGGCTTTTCGGGATTATCTATTGTCATCAACTGTATCAGACACACTTGATGTTTGGGAATTAAAGG
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 5
agatggacgaagataagagaggaatgacagagaatt--tttttgtagcagctttttcattttctttagagtgatcgttaaggtcaatgctcctcttttgcagGACAGGAAACCCGAGCTAAGATCAGAAGTCATGGCTTTTAGGGATTATCTCCTATCATCAACAGTATCAGACACGCTTGATGTTTGGGAGCTGAAAG
|| | | || | || || |||| || || ||| || | | || | | |||| | | | | ||||||| | ||||||||| || ||| || ||||| |||| ||||||||||| | |||||||| |||||||| || |||||||||||||| | || |
gcattttctactctatctgttcgatatcaataaattgacattcatatttaaaattttgttgtttgtacatatgtatttaa--ctgtttgtgtttatgtgcagGAGCGTAAACCCGAGTTAGCATCTGAGATCATGACTTTCAGGGATTATCTATTGTCATCAACTGTATCAGATACACTTGATGTTTGGGAATTAAAGG
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 6
agatggacgaagataagagaggaatgacagagaatttttttgtagcagctttttcattttctttagagtgatcgttaaggtcaatgctcctct---tttgcagGACAGGAAACCCGAGCTAAGATCAGAAGTCATGGCTTTTAGGGATTATCTCCTATCATCAACAGTATCAGACACGCTTGATGTTTGGGAGCTGAAAG
|||| | | | | | | ||||| | || || ||| | | | | | || | | | ||||||| | ||||| ||||| ||| || | ||||||||||||||||||||| | ||||||||| ||||||| || ||||||||||||||||| || |
--ctggatacatagggtgcacccctctctttggtgcttttta-gtccatgttggtgttgtctatcaatttccccccctcactactgtgtttgtcaatatgcagGAACGCAAACCTGAGCTGTCATCTGAGATAATGGCTTTTAGGGATTATCTCTTGTCATCAACAATATCAGATACTCTTGATGTTTGGGAGCTAAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagctttttcattttctttagagtgatcgttaaggtcaatgctcctcttttgcagGACAGGAAACCCGAGCTAAGATCAGAAGTCATGGCTTTTAGGGATTATCTCCTATCATCAACAGTATCAGACACGCTTGATGTTTGGGAGCTGAAAG
tgctcctcttttgc CT-rich tract
ttttcattttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatggacgaagataagagaggaatgacagagaatttttttgtagcagctttttcattttctttagagtgatcgttaaggtcaatgctcctcttttgcagGACAGGAAACCCGAGCTAAGATCAGAAGTCATGGCTTTTAGGGATTATCTCCTATCATCAACAGTATCAGACACGCTTGATGTTTGGGAGCTGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA