Sequence
atgc intronic sequence ATGC exonic sequencegtaaggtgtattctcttatcacattgtatcaacccattaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08590.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 7
gtaaggtgta-ttctcttatcacattgtatcaacccattaaaacaattggcttctgagtttggtgccaatggatttt--cagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
|||| | || | | | | | | | ||| ||| | || | || | || | || | ||||| || || ||||| |||||||| ||||||||||| || |||||||| ||||| || || || ||||| || ||||||||||| ||||| | |
gtaaaaaacagcacttgtgtgcgactttgataggtttgttaaattatttacccctaaaattcttaacattctgttcttacagGTCCGCGTTAACCTCCCAAATGGTGATATGGTGGGTCACACTGGTGACATTGAGGCCACAGTGGTTGCTTGCAAAGCTGCTGATGAGGCTGTCAAG
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 7
----gtaag-gtgtattctcttatcacattg-tatcaacccattaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
|||| || | || | ||| || | | || || ||| ||| ||| | ||| | | ||| |||| ||||| |||||||| ||||| || ||||| || || ||||||||||||||||| || || ||||| || | || ||||| || || | |
gtaggtaattgtttcgtcggtgctcagatgactgtttgcctatataaaatgttg-cttaaaatttttat-----tactcttttagGTACGTGTCAACCTGCCGAATGGTGACATGGTTGGTCACACTGGTGATATTGAAGCCACGGTAGTTGCTTGCAAGGCAGCTGACGAAGCCGTTAAG
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 7
gtaaggtgtattctcttatcacattgtatcaacccattaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
|| || | | | | || ||| | || | | || | | | | || | | | | || ||||| ||||| |||||||||||||| || ||||| || || |||||||||||||| || || || ||||| || | || |||||| ||||| | |
-----gtaaataatttga--agtttctattagagcactctttcggtttccctgtt-gcttagc-ctagcgttgttacagGTACGTGTCAACCTGCCAAATGGTGACATGGTTGGTCACACTGGTGATATTGAGGCCACCGTAGTTGCTTGCAAGGCAGCTGATGAAGCTGTTAAG
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 7
gtaaggtgtattctcttatcacattgtatcaacccattaaaacaattggcttctgagtttggtgcca--atggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
|| || | | | | || ||| | | | | |||| ||| | | | || ||| || ||||| ||||| |||||||||||||| || ||||| || || ||||| |||||||| || || |||||||| || | || |||||| ||||| | |
-----gtaaataatttga--aatttctattagaggagt----cttttggtttccatttctcttagcataatgttgttacagGTACGTGTCAACCTGCCAAATGGTGACATGGTTGGTCACACTGGGGATATTGAGGCTACCGTTGTTGCTTGCAAGGCAGCTGATGAAGCTGTTAAG
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 6
---gtaaggtgtattctcttatcacattgtatc--aacccattaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
| || | | | | ||| | | | | |||| || | || | | | | | | |||| || || ||||| |||||||| || |||||||||||||| ||||| ||||||||||| ||||| || || | || |||||| |||||||| |
gtaactaaatggttcaccgtgattttgggaatcgtgatctaattaaacttttatttactc--tcttattttgtctgttgtatagGTACGCGTCAACCTTCCAAATGGTGACATGGTGGGGCATACAGGTGACATTGAAGCAACAGTTGTGGCTTGCAAGGCAGCTGATGCTGCTGTGAAG
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 6
---gtaaggtgtattctcttatcacatt-gtatcaaccca--ttaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
| || | || | || ||| | |||| | || | | | |||| | | || | || |||| ||||| ||||| |||||||| || ||||||||||| |||||||||||||| || || |||| || || | ||||||||| ||||| | |
gtaattagtggacttggcatagggtatttgagacaacatggttcaagctgaacaaatatttgatttgtttcacatctttgtttagGTTCGTGTTAACCTACCAAATGGTGACATGGTGGGGCACACTGGTGATATTGAGGCTACAATTGTAGCTTGCAAGGCTGCTGATGAAGCTGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatcaacccattaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
ttttc CT-rich tract
attaaaacaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggtgtattctcttatcacattgtatcaacccattaaaacaattggcttctgagtttggtgccaatggattttcagGTGCGTGTAAACCTGCCAAATGGAGATATGGTGGGGCATACTGGTGATATTGAAGCAACTGTTGTTGCCTGTGAAGCTGCTGATCGTGCTGTGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT