Sequence
atgc intronic sequence ATGC exonic sequencegtaactggatctaaatcctttgacaaatgatcttccctattgcatttgtaggaaaataatattctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgtatgctaacattgcgattggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G37160.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 9
gtaactggatctaaatcctttgacaaatgatcttccctattgcatttgtaggaaaataatattctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaa----tgtatgc--taacattgcgattggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
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------------------------------------------------------aatagtgct-tgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaattcaatgccataatgaaaagtctgctgtaccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G36480.2 (Glycine max), 3'ss of exon 3
-------------------------------------------------gtaactggatctaaatcctttgacaaatgatcttccctattgcatttgtaggaaaata-atattctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgtatgctaaca-ttgcgat--tggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
| | | | || | | | | ||| ||| || | | || | |||| ||| | || || | | | || || |||| | | || || |||| ||| | | ||| | | || | |||| ||||||||||| || ||||||| ||||| |||||||| || |||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||
gttagtcttgtttggttctagtcaattaattaatgaaatcggcatttatggatccgtttcctttttccctagttcacctctttctctagagcttatataaaataatatgtatcttactctagcttgtgattcttc----tgtttttgg--ttaattaatactttgagaatacaatttcacaatcataactctgctttaacagCATGGATGGAAAATATATTTTGACGGGAGGGGAAGATGATTTAGTTCAAGTTTGGAGCATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACATAAC
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 9
------------------------------------gtaactggatctaaatcct-ttgacaaatgatcttccctattgcatttgtagg------aaaataatattctgtg--ttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgta-tgctaacattgcga--ttggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
| ||||| | |||| || | | ||| | || | | | || ||||||| | | || || | || || |||| | | | || || || ||| | ||||| || | || | |||| |||||||||||||| ||||||| || || || ||||| || |||||||| ||||||||||||||||| ||||||||||||||||||||||| |||||
gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctccttta-attcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G33740.1 (Glycine max), 3'ss of exon 8
gtaactggatctaaatcctttgacaaatgatcttccctattgcatttgtaggaaaataatattctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgtatgctaacattgcgattggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
||| | || ||||| | || | | |||| | | | | | | | | ||||| | | || ||| | | || | | || ||||||||||| || ||||||| ||||| |||||||| || |||||||| ||||| ||||||||||| ||||||||||||||||| |||||||| ||
--------------------------------------------ttttgggttaattaatactttgagaatacaatttcataatgatacaacatcaaacccttatc-ccactttgttatt-cataataataactc---tgctttaatagCATGGATGGAAAATATATTTTGACGGGAGGGGAAGATGATTTAGTTCAAGTTTGGAGCATGGAAGATCGCAAGGTTGTGGCATGGGGCGAGGGACATAAC
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 8
gtaactggatctaaatcctttgacaaatgatcttccctattgcatttgtaggaaaataatat--tctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgtatgcta-acattgcgattggcctga-cagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
| || |||| | | | || || ||| ||| | | ||| | | | | || | |||| || ||| || |||| ||| |||||||||| || |||||||||||||||| ||||| | |||||||| ||||||||||||||||| |||||||||||||||||||||||||||||
-----------------------------------------------------acatgatatcatttcttctagttctttttccttttgtaaaatattattactccctttgaaaagagagtggtataatagacaacaaaatgatgctgaacagCGTGGATGGAAAATATATTTTGACTGGAGGTGAGGATGATCTAGTTCAAGTTTGGAGTATGGAAGATCGGAAGGTTGTGGCATGGGGTGAGGGACACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagcatgcgttgttaatttgtaaatgtatgctaacattgcgattggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
tgctaac putative branch site (score: 1)
ttaatttgtaaatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactggatctaaatcctttgacaaatgatcttccctattgcatttgtaggaaaataatattctgtgttaattttttctccctcaagttgcttttagcatgcgttgttaatttgtaaatgtatgctaacattgcgattggcctgacagTATGGATGGAAAGTACCTTTTGACTGGAGGTGAAGATGACTTGGTTCAAGTGTGGAGTATGGAAGATCGAAAGGTTGTGGCATGGGGTGAGGGACACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA