Sequence
atgc intronic sequence ATGC exonic sequencegtaacaaatcttagtttcttataagagagagatttctagtaagtcagatgttttgcggctcaaagttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59140.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g06440.1 (Oryza sativa), 3'ss of exon 9
-gtaacaaatctt-----agtttcttataagagagagat-ttctagtaagtca----gatgttttgcggctcaaagttgtgttatatttttgtt-tatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
|| || || | |||| | | | || |||||| | | | || | | ||| | | | | ||| |||||||||||| ||||| || |||||||||||||| || || ||| | ||||||||||| ||||| |||||||| || || | | ||||| || || || ||
tataccattcttttcgtagatatcttttgccatactcatattctagcatgatataatgaagctacattattcatatgctaactgtgatattgccatatagTTGTGGAAGATGGGTCGAATTGGAGCATGGGTCAAAGGCAGCTCTTCTGTTTAGGACGAGCACTTTTGAGACGATGCCGTATCTTAGTTCTTGATGAGGC
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 8
------------gtaacaaatctt------agtttcttataagagagagat-ttctagtaagtcagatg---ttttgcggctcaaagttgtg-ttatatttttgtt-tatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
| || | |||| | |||| | | || || ||| | | ||| ||| ||| | || | | |||| |||||||||||| ||||| || || ||||||||||| || || ||| ||||||||||||| | ||| |||||||| | | | | ||||| || || || ||
gtaggggtggtatttaccattctttttgtagatatcttttgtcgtactaatgttgtagcataatacatggagccaccttattcatagtactaattgtgatattgtcatatagTTGTGGAAGATGGGTCGAACTGGAGCATGGGTCAAAGGCAGCTGTTCTGTTTAGGACGTGCACTTTTGAGACGGTGTCGCATCTTAGTTCTTGATGAGGC
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: AC234203.1_FGT004 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------------------------------gta-acaaatcttagtttcttataagagagagatttctagtaagtc----agatgttttgcggctcaaa---gttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
| || | | | | ||| || || | | | ||| || | || | | || | | ||||| | |||||||||||||||||| || || ||||||||||| ||||| ||| | |||||||| || | ||| | | |||||| || | || |||||||| ||||| ||
gtaggactccttgctacacctgtactttgttttttcagaacccatagcaaattaaggaattctggaaggattttccattgacagacacacactgaacacaacgttctatggtagcatgacatgtgttttgtcttgtttattctctgtagtctgtactgactgagagttttttttttgtatagTTGTGGAGGATGGCTCGAACTGGAGCATGGGTCAGAGGCAGCTCTTCTGTTTGGGACGTGCACTGCTAAGAAGATGCCGTGTCTTAGTCCTCGACGAGGC
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G28890.1 (Glycine max), 3'ss of exon 17
-----gtaacaaatcttagtttcttataagagagagatttctagtaagtcagatgttttgcggctcaaagttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
| ||| | | | | | ||| | | | | | | || | || | | | | | || | ||| || || ||||| | || |||||||| |||||||||||||| |||||| |||||||||| || | || | ||| | ||||||| | |||| || |||| |||||
gtgcactttcaactttcactatttta-actatatataatgtaagcacttcttcccatgt-tagtaatgattcgtacgaaattgttaccta--gTTGTTGGAGAGGGATCAAACTGGAGCATGGGACAAAGACAGCTGTTCTGTTTGGGGCGTGCCATGTTGCGGAGAAGCAAAATATTGGTGTTGGATGAAGC
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G28910.1 (Glycine max), 3'ss of exon 11
gtaacaaatcttagtttcttataagagagagatttctagtaagtcagatgttttgcggct-caaagttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
||| || | | ||| || | || | |||| | ||| | | || || | | || | | |||||| || ||||||||||| |||||||||||||| || || ||||| ||||| || | || |||| || ||||| || |||| || ||||| |||||
---gtaaactttcatca-tcatatgataactatgt--gacaagt-gcttatttcctagttgtaataactagtaacaaattgatgcacagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTGTTTTGTTTGGGGCGTGCTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC
upper sequence: AT3G59140.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G28900.1 (Glycine max), 3'ss of exon 11
gtaacaaatcttagtttcttataagagagagatttctagtaagtcagatgttttgcggctcaaagttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
| | || | |||| | | | | |||| | | | | ||| | || ||| || || |||||||| || ||||||||||| |||||||||||||| || || || || ||||| || | | |||| || ||||| || |||| || ||||| |||||
---gtacactttcatca-ttatggtaactatgtcacaagtactttttttcctagttgataaaaactagtaatatgttgttac--atagTTGTTGAAGATGGATCAAACTGGAGCATGGGACAAAGGCAATTATTTTGTTTGGGGCGTGTTCTTTTAAGGAGAAGTAGGATATTGGTGCTGGATGAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctagtaagtcagatgttttgcggctcaaagttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
tttttgttt CT-rich tract
ttgtgttatatttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaaatcttagtttcttataagagagagatttctagtaagtcagatgttttgcggctcaaagttgtgttatatttttgtttatagTTGTGGAGGATGGATCAAATTGGAGCATGGGACAGAGACAGTTGTTCTGTTTAGGCAGAGCAGTTTTGAGAAGAAGCAGAGTATTAGTCCTGGACGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC