Sequence
atgc intronic sequence ATGC exonic sequencegtagctctgtttcgaattactatcatagtaatgtcttctagttatcacattgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16540.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 3
-gtagctctgtttcgaattactatcatagtaatgtcttctag--------ttatcacattgtctcaaagcttctatttttgttgt-----tgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTT-AATGTCT
| || |||| | | | |||| |||| |||| | | | | ||||| | | || |||||| |||| | | | ||| ||||||||||| || || ||||| || |||| |||||||||||||||||||| | | || |||| || | | || |||||| ||||
attttgtccttttcta--tgtgagcata-taatttcttttggaaagtgtttggttacattattggtgaatttgcatttttattgttttcatacccccttttagTACTATCTGAAGACTGGCACGTGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGT-TCAGTTGAATGAAC
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 3
-----------gtagctctgtttcgaattactatcatagtaatgtcttctagttatcacattgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
| || |||| | | | || || || || | | | || ||| || || | |||| | || | ||| ||||||||||| || || ||||| || |||| |||||||||||||||||||| | | || |||| || | | || | ||||
ttgcttgcacattttctgcttttcttttctgtgttattatatcgttttttggaaagtgtatggtcacattatttattgttttcacatccctcctttttagTACTATCTGAAGACTGGCACATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAAC
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
-----gtagctctgtttcgaattac-tatcata---gta---atgtcttctagttatcacattgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT-
| | || | ||| ||||||| ||| || || | |||| | | |||| | ||| || ||||| | | |||| ||| |||||||||| || |||||||| |||| || |||| ||||||||||||||| |||| ||||| |||| |||||| || | | ||| | |
taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactg-attcccttttttgtgctt-tccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 3
------gtagctctg-tttcgaattactatcatagtaatgtcttctagttatcacatt----gtctcaaagcttct-atttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
| | || | | | || ||||||| | | | || ||||| | | | | | || ||| || ||||| | | |||| ||| |||||||||| || |||||||| |||| || |||| ||||||||||||||| |||| ||||| |||| |||||| || | | ||| | |
ctaattttggtcttgatatagtatatatatcatatatgtatttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgctt-tccagTACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCATGAATATTT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
-----------------------------------gtagctctgtttcgaa--ttactatcatagtaatgtcttctagtta-----tcac--attgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
||| || || | | || |||| | | | | || ||| |||| || ||| || | ||||| || ||||| | |||| |||||||||||||| || |||||||| |||| || ||||| ||||||||||||| | | ||||| |||| |||||| || | | ||| | |
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaag-tgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
----------------------------gtagctctgt-ttcgaattactatcatagta-atgtcttctagttatcacattgtctcaaagcttctat----ttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
| || | | |||| |||| | | | | | || ||| ||||| | | | |||| | ||| | | ||| |||||||||||||| || |||||||| |||| || ||||| ||||||||||||| | | ||||| |||| |||||| || | | ||| | |
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaa-acattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 3
----gtagctctgtttcgaat-tactatcatagtaatgtcttctagttatcacatt----gtctcaaagctt--ctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
| | | || | || ||| | | || | | ||| | || || || || | | ||| || || | | |||| || |||||||||| || ||||| || |||| || |||||||||||||||||||| |||| ||||| |||| |||||| || || | ||| | |
tttaatgtcctcatatcatgtgtaagatctctattttctcatttttttaatatgttctgagttggaagagttgacaaatttgctttgaatggttctccagTACTACTTGAAGACAGGAACTTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctagttatcacattgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
ttctattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagctctgtttcgaattactatcatagtaatgtcttctagttatcacattgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG