Sequence
atgc intronic sequence ATGC exonic sequencegtattaaaattctctttctctctcttaatctttgatatattaaaaaaaaataaaaaaaaatacattcttacactatgtttgctgttgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04580.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------gtattaaaat-tctctttctctctcttaatctttgata--tattaaaaaaaaataaaaaaaaatacattctta--cactatgtttgctgttgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
| || ||| | | | | || ||| || || || | | | || ||| | |||| ||| | || || |||| | |||||||||| ||||||||| || |||| |||||||||||||||||||| |||||||| | |||||||||||||| || | |||||| |||| |||
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaa--------atgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------gtattaaaat-tctctttctctctcttaatctttgatat--attaaaaaaaaataaaaaaaaatacattcttacactatgtttgctgttgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
| | || | | | | | ||| ||| | || | || | || | | | | || ||| | || |||| | || | | | | |||||||||| ||||||||| || |||| ||||| |||||||||||| | || ||||| | || || |||||||| || | |||||||||| ||||| ||||
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtt-taatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 4
gtattaaaattctctttctctctcttaatctttgatatattaaaaaaaaataaaaaaaaatacattc-ttacactatgtttgctgt-tgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
||| | | | || | | | | | ||| ||| | || | | || || | || |||| | ||| || || ||| | ||||||||||||||||| | |||||||||||||||||||| || ||||| | || |||||||||||||| | |||||||||||||||| |||
gtacttctcatttacttgt-tatacaatttttttctattcctattaatgtttttctttcttgttttggttttatgataaatgctttctgaattgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAGTTCCCGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 4
gtattaaaattctctttctctctct---taatctttgatatattaaaaaaaaataaaaaaaaatacattcttacactatgtt---tgctgt-tgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
| ||||| || || | ||| ||| | |||| | || || | |||| | |||| | ||| || || ||| | ||||||||||||||||| | |||||||||||||||||||| || ||||| | || |||||||||||||| | |||||||||||||||| ||
-----gtacttctcatttacttgttatacaattttttttctattcctattaatgtttttctttcctgttttggttttatgataaatgctttctgaattgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCGGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAGT
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 3'ss of exon 3
gtattaaaattctctttctctctct---taatctttgatatattaaaaaaaaataaaaaaaaatacattcttacactatgtt---tgctgttgattttggt-tatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
| ||||| || || | ||| ||| |||| | | | | | || | |||| | | || | | ||| || ||| | | |||||||||||| || | ||||||||||||||| ||||| || ||||| | ||||||||||| ||||| | |||||||||||| ||| |||
-----gtacttctcatttacttgttatgcaatttttttcctatttatattatttttttcctttctctttttggttttatgataaatactttctaaattgtcacatccagATCAAACTTGGGTCACAATATTACTTCTATATGGAGACCCAAACTGCCCTTGCAGTTCCAGATGAAGATAACTGCATTGTGGTTTACAGTGCAATACAAT
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
gtattaaaattctctttctctctcttaatct-ttgatatattaaaaaaaaataaaaaaaaatacattc-ttacactatgtttg-ctgttgattt-tggttatg--cagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
||||| | | || | | | | | || ||| | | | | || || || ||| | || ||| || | | ||| ||| | | ||||||||||||||||| |||||||||||||||||||| || ||||| | ||||||||||||||||| | |||||||||||||||| |||
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaataaaaaaaaatacattcttacactatgtttgctgttgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
aaaaaaaatacattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaaaattctctttctctctcttaatctttgatatattaaaaaaaaataaaaaaaaatacattcttacactatgtttgctgttgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA