Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G09810.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
-------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaa--gtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
|| |||| | | | | |||| | | | |||| | | ||| ||| | || ||||||| || ||| | || || |||||||||||| |||||||||||||| ||||||||||||||||||||||||| ||| | | || ||| | || || |
aacagaaattttgtccctcgctgctgttttcacttttaatggtgaggttttggataattagcactt-gttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 4
------------------gtaagttctttgagctacg-gtttacacaaagattaagattaagatttacacaaagtttctctcttt-------tgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
|| || | ||||| || || | | |||| | | || ||| | ||||| || |||||||||| ||| | || || | |||||||||||| ||||||||||||| ||||||||||||||||||||||||| ||| | ||| | || | || || |
gtttgtctgctaatagaagtcttgtcccttttctacgcactttcatggcaaattttcttaacactattacttgttttgtttctttgcttctgtgctgcagTATGTTCATCACCTTCAAAGGAAGTACTCGCTTGGCTCATTCAACCTCTTGGGTCATACTGCTCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 3'ss of exon 4
-------------------------gtaagttctttgagctacggtttacacaaagat-taagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
|| | || | | | || || | || | || |||| | || ||||||||||| |||| ||| || ||||||||||| || | |||||||||||| |||||||| ||||||||||| || || | | | | || |||| || || |
tttgtcatttcttaagttatagccaaatagcaccttaatttcttttccttacctggacgcatagacaatacaattttaactcttctattttcctttgcagTATGTTCATTTTCTCCAACGAAAGTACTCTCTGAACTCATTCAACCTCCTGGGTCACACTGCTCCAGCCCAAGCAGGATCCCTTCTGCTAGTGGGGCCCT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
-----------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttg---------ttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
||| | |||| || | |||| || | || | || || || ||| ||||||||||| |||| ||| || | |||||||| || | |||||||||||| ||||| || ||||||||||| || || | | | | || |||| || || |
tgaataattggcactccctaaatcatttgtttgtttgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 3
--------------------gtaagttctttga-gctacggtttacacaaagattaagattaagatt----tacacaaagttt-ctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
|| || || | | | | | | | |||| | | | | |||| ||| |||| |||||||||| || | || || | |||||||||||| ||||||||||||| | || |||||||||||||| ||||| ||| |||| || || | ||||| |
tagtgttgggcctgttggccgtgccctcccccctgccatgatatccttattagggcatattatcactgtgttctatttggtttactcctctttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G071378_T02 (Zea mays), 3'ss of exon 4
-------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgtt--gcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
| | ||| || | | || || | | | | ||||| || || | || || ||||||||| || | ||| || || |||||||| || | |||||||||||| ||||| || ||||||||||| || |||| | | || |||| || ||||
gctcttgctaccccacgttttcagaaatggaccgttgcccttccatgtagccagtaaa-agcagcacagtttactcatttttatttgtgttccttctgcagTATGTCCACTTTCTCCAACGCAAGTACTCTCTGAACTCATTCAACCTGCTGGGCCACACTGCTCCAGCCCAAGCTGGGTCACTCCTGCTAGTGGGACCAT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G823629_T02 (Zea mays), 3'ss of exon 4
---------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
|| || | || | | |||| | || | |||| | || |||| ||| | |||||||| || |||| || | |||||||||||| |||||||||| || | || |||||||||||||| ||||| ||| | || || ||||| || || |
atgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgat-ttcctcttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
------------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
| | || | | | | | | || | | ||| ||| | || | || ||| || |||||||||| |||| ||| || || |||||||| || | |||||||||||| ||||| || || |||||||| || |||| | | || |||| || ||||
actatttaagtgccactttttcatttggacttcggccctgtca--tgtgcccaatataatgggcacaatttagactcacttttatttctgctccttc--tgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
upper sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------------------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
|| || | || | | |||| | || | |||| | || |||| ||| | |||||||| || |||| || | |||||||||||| |||||||||| || | || |||||||||||||| ||||| ||| | || || ||||| || || |
gtaagcaaaagaatccagcactctgttgctgctttgatcaccgcagttcaaagccttctggatcttgttaatctttatttaactagtgttgtccatgtgacctcccacagtcccacccctcctacacctttcacgatagcctaatgggtcatattatcactatgttttatttgat-ttcctcttcttttctacagTATGTTCACCATCTTCAATGGAAGTACTCGCTTGGCTCATTCAATCTCTTAGGCCATACTGCTCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
tttctctcttttgttg CT-rich tract
aaagattaagattaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA