Sequence
atgc intronic sequence ATGC exonic sequencegttagcttttctttttatctattacaaaatatgtgtaactttatcttgtgacgaattatagttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08440.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 6
gttagcttttctttttatctattacaaaatatgtgtaactttatcttgtgacgaattatagttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
| ||| ||| |||| | | | ||| | || | || | ||| | ||| |||| | || |||||||| || || || |||||||| | ||||||||||||||||||||| | || ||||||||||| || ||||| |||||||| || || ||||||||||
------------------------------gtaagta-ttttgtcttatcaggtattgaaaaatctcttggagtacaacacc-attttacaatgcatctgtttt-------cagGCATTCGATCAGCAGCAACAAGATTTGGTTGATGCTGCATCAAAAGCTTTATCCTACAGACAAGACATTATTGAAGAAAATATCCGTCTGACATATGCCT
upper sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
gttagcttttctttttatctattacaaaatatgtgtaactttatcttgtgacgaattatagttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
|| || || |||| ||| | ||| ||| || |||| || || | | | | | |||| | | || | ||| | || |||||||||| || || |||||||| | ||||||| |||||||||||| | || || |||||||| || ||||||||||| || || || |||||||
gtaggccatttctttt---tatcataaactattagtcacttgga---gtaactagtgagtatatcatattatctcaa------aaaaaaaaatctttc--------------agGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
upper sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 5
gttagcttttctttttatctattacaaaatatgtgtaacttt--atcttgtgacgaattatagttactt----attctgtta--accacttagggggtaatttat---ctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
| | |||||| ||| || | | || || || | |||| | || | ||| | | || | | | ||| | | | |||| | |||| || || | ||||||||||| || || || ||||| || |||||||||||||| |||||| | || |||||||| || || || || ||||| || || || |||||||| |
-----gtaaacattttatttatgacgcatcaagtactaccttggagtttgtaaaaaaaaactactaccttagagtcatggcactatgatttaagtgtttatttttttcctttttttgtggggcagGCATTTGATCAGCAGCAGCAAGATCTGGTTGATGCTGCATCGAAAGCTTTGTCCTACAGACAGGATATTATCGAAGAAAACATCCGTCTTACATATGCAT
upper sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
------gttagcttttctttttatctattacaaaatatgtgtaac-tttatcttgtgacgaattatagttacttattctgttaaccacttagg-gggtaatttatctttcttgttg-tgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
| | |||| || |||| || |||| | | | | | | ||| | ||| | | |||| ||| | | | ||| | || | | | ||| || |||| ||||| || || ||||| |||||||| |||||||||||||||||| | || ||| ||||||| || ||||| ||||||||||| || |||||||| |
gtatgcatgaaattttgttgaaatct-ttgtgaaattccttaagcatcttttgtgttttgcatttttcct-tatatttggttgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
upper sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
------gttagcttttctttttatctattacaaaatatgtgtaac-tttatcttgtgacgaattatagttacttattctgttaaccacttagg-gggtaatttatctttcttgttg-tgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
| | |||| | ||| || |||| | | | | | | ||| | | | | | ||||| || | | | ||| | || | | | ||| || |||| ||||| || || ||||| |||||||| |||||||||||||||||| | || ||| ||||||| || ||||| ||||||||||| || |||||||| |
gtatgcatgaaattttgtcaaagtct-ttgtgaaattccttaagcatcttttatgttttgcacttttcct-tttatttgattgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
upper sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 6
gtta-gcttttctttttatctattacaaaatatgtgtaactttatcttgtgacgaattatagttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
||| ||||| | || | | || | || | || | || || || || | | || | | |||| | | || |||| ||||| |||||||||||||| ||||||||||| || |||||||||||||| ||||||||||| || ||||||||||| || || || ||||||| |
-ttatatttttcctcaaattttctgagaaccaaacatagcctt----tatgttttttttgagggggtt----catggaaagttt------ttgtccttcttcttcttcttgctagGCTTTTGATCAACAACAACAAGATCTTGTTGATGCGGCCTCAAAAGCTCTTTCATACAGACAAGACATTATTGAGGAAAACATTCGTCTCTCATATGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
tgttaac putative branch site (score: 2)
tttatctttcttgtt putative PPT
taatttatctttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcttttctttttatctattacaaaatatgtgtaactttatcttgtgacgaattatagttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA