Sequence
atgc intronic sequence ATGC exonic sequencegtaattgttttttcctagatatgaatcgtctttagaggattgctataaatattgtctcttatcttaggtcttgtggttggtcttagTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13070.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 2
gtaattgttttttcctagatatgaa-tcgtctttagaggat--------tgctataaatattgtctcttatcttaggtcttgtggttggtcttagTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
|| || |||| | ||| | || || | || | | || | | ||| ||| || ||| || |||| || || || ||||||| ||||||||| || ||||||||||||||||| ||||| ||||| ||||||||||| ||||| || || ||| |||||||
------gtattctccttgcattgatcttatcattgaaaaatatcattttttcagtatagaatgtttctcatgctagtatttt--gttgtatgcagGGTGGTCAATATTGGGGCAACTGCTCTTGTCACTGAAGCAGCAACTGCTATGTTTGGTGAAGCTGGTGTCAGTGCAGCAACAGGAGTGATGACT
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 2
-----gtaattgttttttcctagatatgaatcgtctttagaggattgctataaatattgtctcttatcttag-gtcttgtggttggtcttagTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
| ||| || || ||| | | || || | | | | ||| ||| || ||| || |||| || | || || || ||||||| ||||||||| |||||||||||||||||||| ||||| ||||| ||||||||| | ||||| || || ||| |||||||
gtattctccttgcattgatcttattattgaaaattttccttttttttcggtgtagaatgtttctcatgctagtgttttgttgtatgc---agGGTGGTCAATATTGGGGCAACTGCTCTGGTCACTGAAGCAGCAACTGCTATGTTTGGTGAAGCTGGTATCAGTGCAGCAACAGGAGTGATGACT
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S58_81V6.2 (Physcomitrella patens), 3'ss of exon 5
gtaattgttttttcctagatatgaatcgtctttagaggattg---ctataaatattgtctcttatcttaggtcttgt--ggttggtctt---------agTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
|| || | | | | | | || | || | | | ||| || | | | | ||| | | || |||| || ||||| || ||||| ||||| ||| |||| ||||||||||||||||| ||||||| |||||||| |||| |||||||| || | |||||
tgaaaggtgtgaagttgggtgtagaccggagctcgaaatctagctccgtttgtatgatcaatcgtatcggtacttatttgatttttcttcttttgaacagGGTTGTCAACATTGCAGCAACAGCATTGGTGACTGAAGCAGCAACAGCCTTATTTGGAGAAGCTGGAGTTACAGCTGCCACAGGTGTCATGACG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 3'ss of exon 5
--gtaattgttttttcctagatatgaatcgtctttagagg-attgctataaatattgtctcttatcttaggtcttgtggttg----gtctt-------agTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
|| | | ||| | || | | | |||| ||| || | | | |||| | ||| ||||| || || || || ||||| ||||| ||| |||| ||||||||||||||||| ||||||| |||||||| || | ||||| || || | |||||
tcaaggttcggacctgcagcataaaagctagctctgttcataccatgaattatatcgtcactcacgtgaattctttttgtttttttgtctttataaacagGGTGGTTAACATTGCAGCAACAGCAATGGTTACTGAAGCAGCAACAGCCTTATTTGGAGAAGCTGGCGTCACAGCTGCTACAGGTGTTATGACG
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 3'ss of exon 5
------gtaattgttttttcctagatatgaatcgtctttagaggattg-----ctataaatatt---gtctcttatcttaggtcttgtggttggtct-tagTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
| | ||| ||| || ||| | | || | | | |||||| || | | |||||||| | |||| | ||| | || ||| |||||||| ||||||||| |||| ||||| ||||||||||| ||||||| |||||||| || | |||||||| || | |||||
gttgttgcgaggatttgagttaagacttggatcttaaatctagcactaagcacccataaattttaatggcacttatctt-gttcttttttttgtttaacagGGTTTGTAATATTGCAGCAACTGCATTGGTGACTGATGCAGCAACAGCCTTATTTGGAGAAGCTGGAGTCACAGCTGCCACAGGTGTCATGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagaggattgctataaatattgtctcttatcttaggtcttgtggttggtcttagTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
attgctataaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgttttttcctagatatgaatcgtctttagaggattgctataaatattgtctcttatcttaggtcttgtggttggtcttagTGTTGTGAATATTGCGGCAACTGCACTGGTCACTGAAGCAGCAACAGCTATATTTGGGGAAGCTGGTGTTAGTGCTGCCACTGGATTGATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC