Sequence
atgc intronic sequence ATGC exonic sequencegtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctgtatgttcctgttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22220.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g33950.1 (Oryza sativa), 3'ss of exon 4
--------------gtgacatatttgaactctagactcccatattgatgtattactttctgt-caaacttagctgtatgttcctgttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
| | | | | | || ||| | | ||| ||| | || ||| | | |||| | ||||| | || | | |||||||| ||||| ||||| | ||||||| |||||||||||| |||| |||||||||||| || | ||||
gtatgggtaaaccccccccctctctctcattttaacagtcatttcttttcgttagttttgctacaggtttatatatggtttccaacaaaaacagGTTCGGAAACGGCGCATATATGACATAACAAATGTACTGGAAGGAACAGGTTTGATAGAAAAGAAGCTTAAGAACAGAATCCGTTGGAG
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g33430.2 (Oryza sativa), 3'ss of exon 3
----------gtgacatatttgaactctagactcccatat-tgatgtattactttctg----tcaaacttagct-gtatgttcctgttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
|| | | | | || ||| | || ||| | | || | | || | | || ||||| || | ||||| ||||| | | ||||||||||| |||||||| | ||||||||||| ||||| || ||||| || |||||||| || | |||||
gtcacagactgttataaactataatactatatcatttcatctgacatctcttttctctcactttatacacaattcacattttcctatt--ttcagGTTCAAAAACGGCGTATATATGATATTACCAATGTACTTGAAGGAATAGGGTTGATTGAAAAGACACTCAAGAACAGAATCCGTTGGAA
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctg--tatgttcctgttgat----gcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
| | | | | | || | | |||| || | ||| || ||| ||| | ||| | |||||| |||||||| ||||||||||||||||| ||||| | ||||| || || | ||||| |||| || |||||| | ||||| |||||
-----gtttatatagtttcatctgctcaaatgattccaagctgtaaagtttgattatttgattattttctttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 4
gtgacatatttgaactctagactcccatattgatgt-attactttctgtcaaacttagctgtatgttcct--gttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
|| | | || || | | | | ||| | | |||| || || | | | | | || |||||| |||||||| ||||||||||||||||| ||||| | ||||| || || | ||||| |||| ||||| || | ||||| |||||
--------gttaa--tataatttcatctgctcaaatgattccatgctgtaaagttttattattttcttttcggtatccgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGCCTTATAGAAAAGAAACTTAAAAATCGAATTCAATGGAA
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S22_60V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------gtgacatatttgaactc---tagactcccatattgatgtattactttctgtcaaacttagctgtatgt--tcctg--ttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
| | ||| | || || || || | | | | | | || | | | | | ||||| ||||| || ||||||||||||||||||||||| || || |||||||| || || ||||| || ||||| ||||||| || ||||| |||| |||||
ttgtttttttgtttttttcttatatcaaatcaaataaaccgctacctgtgtctttagtagtcgttgatatctgacggtatgcaatcctgggttccatcagGTACAAAAGAGAAGGATATACGACATCACCAATGTATTGGAGGGAATTGGGTTGATTGAGAAGAAACTGAAGAATCGGATCAGATGGAA
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S97_96V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctgtatgttcctgttgatg----cagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
| || | ||||| || |||||| | | | | | ||| | | | || || || || || ||||||||||||||||| |||||||| || ||||||||||||||||| || || || || ||||||| ||| || ||| ||||| |||||
aataatgtgtttgtatttctttaaaaatgcattaactc--atctttcatatttacattctgatggcctacaatgctgg--gaattttactatttatttcatcagGTACAAAAGAGAAGAATATATGACATCACCAATGTGTTAGAAGGGATTGGGTTAATTGAGAAGAAGCTGAAAAACCGGATTAGATGGAA
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S38_356V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctgtatgttcctg--ttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
| | ||||| || | | | | | || | | | |||| || | |||| || || || |||||||||||||| |||||||||||||| |||||||| || || ||||| || || || ||||||| ||| ||||| | || |||||
tatgtagcgctgttatcctttcatttatttcaagtaaataactacctctttttaagctgttctctgacatcagacgatgtacaatcttgggtttcaccagGTACAAAAGAGGAGGATATATGATATTACCAATGTATTGGAGGGAATTGGGTTAATTGAGAAGAAGCTAAAGAATCGAATCAGATGGAA
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ05155 (Selaginella moellendorffii), 3'ss of exon 3
gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctgtatgttcctgt-tgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
|| || | || | || | ||| | | | | | || ||| | | | ||||| |||||| ||||||| ||||| || ||||||||||| |||||||| || || ||||| |||| | | || |||||||| |||||
-----gtaagtgcatgctgcattca---gtgtgtgtctctttcgcaacctgcttcagagaggctttcttctgcctttcagGTGCAAAAGCGAAGGATCTATGACATCACCAATGTGTTGGAAGGAATTGGCTTAATAGAAAAGAAGTTGAAAAACAGGATAAGATGGAA
upper sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ05692 (Selaginella moellendorffii), 3'ss of exon 3
gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctgtatgttcctgt-tgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
|| || | || | || | | ||| | | | | | || ||| | | | ||||| |||||| ||||||| ||||| || ||||||||||| |||||||| || || ||||| |||| | | || ||||| || |||||
-----gtaagtgcatgctgcattca-gtgtc--tgtctctttcgcaagctgcttcagagaggctttcttctgcctttcagGTGCAAAAGCGAAGGATCTATGACATCACCAATGTGTTGGAAGGAATTGGCTTAATAGAAAAGAAGTTGAAAAACAGAATAAGATGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatattgatgtattactttctgtcaaacttagctgtatgttcctgttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
ttcctgtt CT-rich tract
tattacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctgtatgttcctgttgatgcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA