Sequence
atgc intronic sequence ATGC exonic sequence...ttgttctcaaatgtttaacgtttgcaaacccgaaattgcatttgcatgtactagtgttactttttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16780.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 6
----ttgttctcaaatgtt--taacgtttgcaaacccgaaattgcatttgcatgtactagtgttactttttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
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tttcctggttgataacactggttatggttatatgtttgcaatta-gttcttttattcaaatggaatatttct-tttgtcaatttcacatt----tatttcctgtagTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCGTCTTTTGTCGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACCAAAGCTGCTGATGTCGGAGC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------ttgttctcaaatgtt-taacgtttgcaaacc-cgaaattgcatttgcatgtactagtgttactttttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
|| | | || || | |||||||| | | | || |||| || | | || ||| ||||| | | |||| | |||||||||||| ||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||||||| || || | |||||||| || ||
gtaagtttcttgtacacaatacacctgaaaacacactagattacaatccaacttgtccaccaattatctacttattttattgtttttgcaaattgcaataccattttgttatgtgaaaggaacattattctgct-gctgattcatatgtttt-ttttgtgtgtagTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCCTCTTTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACGAAAGCTGCTGATGTTGGAGC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 6
------ttgttctcaaatgtttaacgtttgcaaacccgaaattgcatttgcatgtactagtgttactttttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
|| | | || | || |||| ||| ||| | | | | | | || | | || || ||| | ||| |||| ||| |||||||||||||||| || |||||||| |||||||| || |||||||| |||||||||||||||||||||||||||| || |||| ||||||||| || ||
tatgacatgatttaaatttttgtccgttctgtcacct---attctctctctccctctctctctaatttgtca--ttgattttttaaaattcttgttttcctt-cagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCTCAGTTGGGTGGTGGAATATACACAAAGGCAGCTGATGTTGGAGC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
ttgttctcaaatgtttaacgtttgcaaacccgaaattgcatttgcatgtactagtgttactttttagcttaatga------tttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
| | || | | || || | | || || | | | | | || || ||||| | | ||||| | |||||||||||||||| || |||||||| |||||||| || |||||||| ||||||| |||||||||||||||||||| || |||| |||||||| || ||
-----tttgaccgtgacatgattttaatttttgt-tcattctctcacctattctctctctctctcaaattggcgatcgatttttgagcattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
ttgttctcaaatgtttaacgtttgcaaa---cccgaaattgcatttgcatgtactagtgttacttt-ttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
| || || | ||| || | | | | ||| | |||| |||||| || ||| | | | ||| ||| || | | | | || | | |||||||||||||||||||||||||||| ||||| || |||||||||||| | ||||||||||||||||||||||||||||| || | ||| ||||| || ||
-tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgt---acttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtactagtgttactttttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
atttgac putative branch site (score: 4)
tttgactttcccattt CT-rich tract
ttacttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttctcaaatgtttaacgtttgcaaacccgaaattgcatttgcatgtactagtgttactttttagcttaatgatttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - tctcaaa
- - - - - - - - - - - - caaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttga