Sequence
atgc intronic sequence ATGC exonic sequencegtaaatacctatcacttgatatttattatatctattaaataaggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21790.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 4
gtaaatacctatcacttgatatttattatatctattaaataaggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
| | || | | || | ||| || | || ||||| | || || | | | | |||||||||| ||||| || || |||||||||||||||| ||||||||||| || ||||| || | || || |||||||| ||||||||||||||||| || |
--------------------gtactgcacatttgaccagaaaaatcctagtcttggactc-tgaaattgcttgcttactctttta--ttctctgcaatgcagTTAAGCAGCTGTTTCCTTATCTGCATGAAAGATGACAGCATTGAGGGAATCTATGATACTTTGAAGGAATGTGCTGTCATAAGCAAATCTGCTGGAGGAA
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 4
gtaaatacctatcacttgatatttattatatctattaaataaggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
| |||| | || | | || | | || | | |||| | || || || | || | ||||||||||||||||||| || |||||||||| ||||||||||||||||| || ||||| || ||| ||| |||||| |||||||||| |||||| || |
---------------gtaatatgcttcctaccattgaagtccaatttggattattaaaaatggtctcttatgctcctctct-------gtttta---tgcagTTAAGTAGCTGCTTCCTCATCTGCATGAACGATGATAGCATTGAGGGAATTTATGATACTCTCTCAGAATGTGCTACCATAAGCAAATGTGCTGGTGGAA
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 4
gtaaatacctatcacttgatatttattatatctattaaataaggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
| | | | | | | | || | | | | | || || ||| | || | || || | | | |||||||||| ||||| ||||| | |||||||||||||| ||||||||||| || |||||||| || |||||||||||||| ||||||||||||||||| || |
---------------gtactgtcttgttt-cccgccagatgatg----tcattgtgggttctgaaattgtttatttactgctgctttttctgtga--tgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAAGAGTGTGCTGTAATAAGCAAATCTGCTGGAGGAA
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 4
gtaaatacctatcacttgatatttattatatctattaaataa-ggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
| | | | | | || | | | | | || | |||| | ||| | | | || || | ||| |||||||||| ||||| ||||| | |||||||||||||| ||||||||||| || |||||||| || || ||||||||||| ||||||||||| ||||| || |
---------------gtactgtct-tgcttcctgccagacgatgtcattgtgggttgaaa-------ttgtttacttactgtttcttttctgtga---tgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAGGAGTGTGCTGTAATAAGCAAATCAGCTGGAGGAA
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 4
gtaaatacctatcacttgatatttattatatctattaaataaggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
| || ||| | | |||| | | | || | | | | | | ||| | ||||||||||| || |||||||||| || ||||||||||| ||||| ||||| || || || |||||||| || || ||||| || || |||||||
-------------------------------------------gttggttgcttcgtgattctccttttgtagtttacttctaactgtgactt---ctacagCTTAGTAGCTGCTTCCTTCTCTGCATGAAGGAGGATAGCATTGAAGGCATTTATGATACCCTGAAGGAGTGTGCAGTAATCAGCAAGTCAGCCGGGGGTA
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ20157 (Selaginella moellendorffii), 3'ss of exon 4
gtaaatacctatcacttgatatttattatatctattaaataaggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
| || ||| | | |||| | | | || | | | | | | ||| | ||||||||||| || |||||||||| || ||||||||||| ||||| ||||| || || || |||||||| || || ||||| || || |||||||
-------------------------------------------gttggttgcttcgtgattctccttttgtagtttacttctcactgtgactt---ctacagCTTAGTAGCTGCTTCCTCCTCTGCATGAAGGAGGATAGCATTGAAGGCATTTATGATACCCTGAAGGAGTGTGCAGTAATCAGCAAGTCAGCCGGGGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
tgctgat putative branch site (score: 3)
tattgaaaataattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatacctatcacttgatatttattatatctattaaataaggcgttttactttgatacgtgtctttgctgatctgctattgaaaataattgaaattgcagTTAAGTAGCTGCTTTCTAGTCTGCATGAAAGATGATAGCATTGAGGGCATATATGAAACACTCAAAGAGTGTGCTGTTATAAGCAAATCTGCTGGGGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA