Sequence
atgc intronic sequence ATGC exonic sequencegtatctcctccatctatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46020.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 3'ss of exon 5
----------------------gtatctcctccatc-tatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttt--tttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
| || | || |||| | ||| || ||| || | | | || | |||| ||| |||| | | | | ||||| || | ||||||||||| || ||||| ||||| || || || || || ||||||||||||||||||||||| || || || |||
gtaggccatttaccttcaacttaattttcttatatgatataatatatatttaaaacatttcaagtctatt-tccaaccaccaaaaaaaatctacaatttgatttgttgcctatcca-cagGTGGGCCTTCAATGGATGCTTTCCTTGTACAATAATAAGTTGAATGGTATTTTGGCTGATGAGATGGGTCTTGGCAAGACCGTACAG
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
gtatctcctccatctatactctatgttgttgcttttttctcactgt---catgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
||| || | || | || | || || ||| ||| |||| | || | | | || || || || | | ||||| || |||| |||||||| || ||||| ||||| || || || || || ||||||||||||||||||||||| || ||||| |||
gtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttacaattcattttgttg-gttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G39380.1 (Glycine max), 3'ss of exon 6
gtatctcctccatctatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
||| | | | | || ||| | || || | || || | | | | || ||||| ||| | | ||||||| || ||||||||||| || |||||||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| |||
gtacgttgctaagtttgatggaat--tgtctgtaattgcttgttttcttgtcttttagagtaaggttttaaggatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 4
-----gtatctcctccatctatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
| | | | | | ||| |||||| || | || | | | ||| |||| || | | | || | | ||||||| || ||||||||||| || |||||||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| |||
gtaggttgctgagtttgatgaaattgtctgtaattgcttcttgttgtcttttggagtaaggttttatggatt-tgacatgttatttttga--------agGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G07550.1 (Glycine max), 3'ss of exon 4
----gtatctcctccatctata-----ctctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttt-tgctctgtgccaatca-gGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
|| || | || | | | | ||| | | || || | | || | || | |||| ||| ||| | | | | | | |||||| || ||||||||||| || |||||||| ||||| ||||| || || ||||| ||||||||||||||||| |||||||| |||
gtaggttgctacattatatgaaacagttttcaagttttcaagtgatt-tctttatgctgtcttcttgagcaagttttcaagactttgatacattatatttttaaagGTTGGTTTGCAATGGATGCTTTCTTTGTATAACAACAAGTTAAATGGAATTTTGGCGGATGAGATGGGTCTTGGTAAAACTGTACAG
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G03950.1 (Glycine max), 3'ss of exon 5
gtatctcctccatctatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttt-tgctctgtgccaatca-gGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
||| | |||| | | | || | | |||| || | |||| ||| ||| | | | | | | |||||| || ||||||||||| || |||||||| ||||| ||||| || || ||||| ||||||||||||||||| |||||||| |||
gtaggttgctacattatatgaaacagtactctttaagtgatttctttatgctgtcttgagcaagttttcaagactttgataccttatatttttgaagGTTGGTTTGCAATGGATGCTTTCTTTGTATAACAACAAGTTAAATGGAATTTTGGCGGATGAGATGGGTCTTGGCAAAACTGTACAG
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 5
--gtatctcctccatctatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttttgctc-------tgtgccaat---cagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
| | | ||||| || | | |||| | ||| | | || ||| | | ||| | || | | ||| | | |||||||| || ||||||||||| || ||||| || |||||| | || || || ||||||||||||||||||||||| |||||||| |||
gtaggttgcaatattagatacttgtcattctgtcattttgccttgtgttccactggttcctgttggagttga--gttctgtgttaacaatggtatgcaatttggcagGTTGGGTTGCAATGGATGCTTTCCTTGTACAACAACAAACTGAATGGAATTTTGGCTGATGAGATGGGTCTTGGGAAAACTGTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactgtcatgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
tttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctcctccatctatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG