Sequence
atgc intronic sequence ATGC exonic sequencegtgttcgacgaaattcctctgtgaagactttttgtttttatgtttttttggttatgtgttctgatgattttgatttttagGAGTTTTGGGTAGGCAATGAAGAGCTTGTTAATTTGTACGAGAAGAGACTTGGAGACGCTGGTTATCTAAGTTACAAGCTTGGTCGTACTAATAATCGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54130.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G40460.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------gtgttcgacgaaattcctctgtgaagactttttgtttttatgtttttttggttatgtgttctgatgatt-------ttgatttt---tagGAGTTTTGGGTAGGCAATGAAGAGCTTGTTAATTTGTACGAGAAGAGACTTGGAGACGCTGGTTATCTAAGTTACAAGCTTGGTCGTACTAATAATCGTG
| | || | | || | ||||| | | | | | || |||||| | | |||| |||| |||||||| || |||||||||||||||||||||||||| ||||| |||||||||||||||||| | |||| ||||||||| | || || || ||||
gtttgtgttgtgaaagtgaaattgattgcagtgagattttatctatctatctatctatattataatgggtcatatgtttgcatgtgaggggctaaacaccagagaaatttttaccaatgggccatgagtgcaccataggctaatgattaattacgtgggttttgtgcagGAATTTTGGGTTGGAAATGAAGAGCTTGTTAATTTGTACGAAAAGAGCCTTGGAGACGCTGGTTATGTCAGTTTCAAGCTTGGAAGGACGAACAACCGTG
upper sequence: AT5G54130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G14300.1 (Glycine max), 3'ss of exon 2
--gtgttcgacgaaattcctctgtgaagactttttgtttttatgtttttttggttatgtgttctgatgattttgatttt---tagGAGTTTTGGGTAGGCAATGAAGAGCTTGTTAATTTGTACGAGAAGAGACTTGGAGACGCTGGTTATCTAAGTTACAAGCTTGGTCGTACTAATAATCGTG
||| | || | | |||| |||| || | ||| | || ||| | || | | | |||| |||| |||||||| || ||||||||||||||||||||||| ||||||||||| || |||||||||||| | |||| ||||||||| | || || || ||||
gtttgtgttgtggaagtgaaattgaaagagattttattataatgggccatagg--atgatgattaattaagtgggttttgcgcagGAATTTTGGGTTGGAAATGAAGAGCTTGTTAATTTGTATGAGAAGAGACTAGGTGACGCTGGTTATGTCAGTTTCAAGCTTGGAAGGACGAACAACCGTG
upper sequence: AT5G54130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G38700.1 (Glycine max), 3'ss of exon 2
-----------gtg-ttcgacgaaattcctctgtgaagactttttgt---ttttatgtttttttggttatgtgttctgatgat---tttgattttt--agGAGTTTTGGGTAGGCAATGAAGAGCTTGTTAATTTGTACGAGAAGAGACTTGGAGACGCTGGTTATCTAAGTTACAAGCTTGGTCGTACTAATAATCGTG
|| ||| | || | | | | |||| | | | | ||| | || | || || || || || ||||| |||| |||||| | || || || ||| ||||||||||||| || ||||||||||| || ||||||||| | | || |||||||| || || || |||||||
ttcaaactttgttgcttccatgagaactgtttatttcttctttgcatgaaatctgtttttgtgagggtggtggtgctaataatatgttggatttgcgcagGAATTTTGGATTGGAAACGACGAGTTTGTTAATTTGTATGACAAGAGACTTGGTGATGCTGGTTATATTAATTTGAAGCTTGGACGAACCAACAATCGTG
upper sequence: AT5G54130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0098g00750.t01 (Vitis vinifera), 3'ss of exon 2
-----------------gtgttcgacgaaattcctctgtgaagactttt----tgtttttatgttt--ttttggttatgtgttctgatgattttgatttttagGAGTTTTGGGTAGGCAATGAAGAGCTTGTTAATTTGTACGAGAAGAGACTTGGAGACGCTGGTTATCTAAGTTACAAGCTTGGTCGTACTAATAATCGTG
|| | ||| || | | ||| || ||| |||| ||| || | |||| | ||| ||||| || ||||| || |||||||||||||| |||||||| ||||||||||| || || || || ||| | | || ||| |||| || || || || | |
gttggcattgctttcacccctttaagccaatcaatccagattgtcctttatgttgcgtttgtgttgaatttctcttctatgtttggcatgctttttggcatagGAATTCTGGGTTGGGAATGAAGAGCTTGTAAATTTGTATGAGAAGAGACTAGGCGATGCCGGCTATATCAATTTCAAACTTGCCCGGACGAACAACAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactttttgtttttatgtttttttggttatgtgttctgatgattttgatttttagGAGTTTTGGGTAGGCAATGAAGAGCTTGTTAATTTGTACGAGAAGAGACTTGGAGACGCTGGTTATCTAAGTTACAAGCTTGGTCGTACTAATAATCGTG
ttttt CT-rich tract
tttttatgtttttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttcgacgaaattcctctgtgaagactttttgtttttatgtttttttggttatgtgttctgatgattttgatttttagGAGTTTTGGGTAGGCAATGAAGAGCTTGTTAATTTGTACGAGAAGAGACTTGGAGACGCTGGTTATCTAAGTTACAAGCTTGGTCGTACTAATAATCGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT