Sequence
atgc intronic sequence ATGC exonic sequencegtttggcctgagctagtttctatctttcagtagagtcatctgaaatttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07110.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 4
-gtttggcctgagc-tagt--ttctatctttcagtagagtcatctgaaatttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
| | |||| | || | || ||| | | | | || |||| || || || | | | || | | | ||| | || | |||||||| |||| |||||||||||| |||||||| ||||||||||||||| ||| || || || ||| | | | |||||||| |||
gctataatttgagaatggtggtactgtctatttttgtacttgtcaaaaatatgttgtttccttttctgtcatcttaagttctgacagctgtaact--agcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 7
--------------------------gtttggcctgagctagtttctatctttcagtagagtcatctgaaatttgagaatttttt---atatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
||||| | |||| | ||| | | || || | |||| | | ||| || | || | | ||||| | ||||||||||||||||| ||||| ||||||||||| || ||||| || |||||||| ||||| || || || |||||||||||| | |||||| |||||
gtttgtataaatgatttccatttcttgtttgttgttcaa-agttattgctagtcaactaacttat-tgtgttgtgaggttgtccacaaataattgtttctgttcctttgcctttttattgatagAATTCAATGCCAGCTGCTGCTGGAGCTGTTGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGCAATTATCCTG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 10
gtttggcctgagctagtttctatctttcagtagagtcatctgaaatttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG-----------------
||| |||| || ||||| | ||||||||||||||||| ||||| |||||||| || || ||||| || |||||||| ||||| || || || |||||||||||| | |||||| |||||
-----------------------------------------------------------------gtctgttcctt-tacct-ttttattgatagaattcaatgccagCTGCTGCTGGAGCTGTCGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGCAATTATCCTGGTATTTTTCTGGCATTA
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 6
--------------------------gtttggcctgagctagttt-ctatctttcagtagagtcatctgaaatttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
|||| || | | ||| | | ||| | | || || |||||| || | || || || | | ||||| | ||||||||||||||||| ||||| ||||| || || || ||||| || |||||||| ||||| || || || |||||||||||| | | |||| |||||
gtctgtatacatgatttccatttcttgttta--ttgttcaaatttattgttagtcaactaacttat-tgtgttttgaggtttccacaaataattgtctgttcctttacctttttattgatagAATTCAATGCCAGCTGCTGCTGGAGCCGTCGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGGAATTATCCTG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 5
--------------------------------------------gtttggcctgagctagtttctatc-tttcagtagagtcatctgaaat--ttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
||| ||| || ||| | | ||| ||| || | || | || | ||| | | | ||| | | |||||| | |||||||||| ||||| ||||| ||||||||||| || || ||| | |||||||| ||||| || || ||||| |||||||| | || |||||| ||
gtttgcataaatgatttccatttttttgtttattattaaaatttatttacactggattaatttatgttgcatcaaacttttcaattggggttattaacaaatagttacttctgctccccccccctcctggtttta-tgacagAATTCAATTCCAGCTGCTGCTGGAGCTGTTGCAGCTGCTGCGATTGCTGATCAGATGCTAGGTCCCAAAGAGCATAGACATTTGGCGATTGTCATG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
gtttggcctgagc-------tagtttctatctttcagtagag-tcat-----ctgaa--atttgagaatttttta--tatttttctcacccttgta----ttcgttttaatt-ttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
||||| | || | | ||| ||||| || |||| | || ||||| ||| || | || || | | | ||| || | |||||| ||||||| |||||||||| ||||| ||||||||||| || || || ||||||||||| |||||||| |||||||| ||||||||| | ||||||||||||
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaatttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
ttcgtttt CT-rich tract
tttgagaattttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggcctgagctagtttctatctttcagtagagtcatctgaaatttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG