Sequence
atgc intronic sequence ATGC exonic sequencegtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctttagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22770.3 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggtta-cagtaacatgcattatccatttggtgtgacctttagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
| || | |||||| ||| |||| || | | || || | | | | ||| | || | | |||| || | | |||||||||||||| || ||||| | || ||||| ||||| |||||||| || ||||| ||||||| ||| ||||| || ||||| || || || ||||||
-----------------------------------aacaactgta-gcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatat-------ctgatttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctt-tagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
||| || || |||| |||| || || | | ||||| | || ||| | | | || | || || | ||| | | | | | |||||||||||| ||||| ||||| || || |||||||| || ||||||||||||||||||||||||||||| |||||||||||||| ||||| |||||||||
-------------------------------------gtcacgc---catatttcagtacaaaaa-atacccttgatatttgatcagaacttattgttgatttaatatgtacactgatatcatgccatccct--tttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctttagatccttgcaaatcaactggttaaag-atgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
| | || |||| |||| || | | || ||| | || ||| | || || | | | | |||| | | | | | |||||||||||||||||| ||||| || || |||||||| || |||||||| || ||||||||||||||||| |||||||||||||| ||||| |||||||||
-----------------------------------------tcaccccatatttcagtacaaaaaattcccttgatatcttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatccct--tttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 12
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctttagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
| | ||||| || |||| || | ||| | | | || ||| | || | || | | | | |||| | ||| ||||||||| || |||||||| |||||||| |||||||| || |||||||| || |||||||||||||||||||| || |||||||| ||||| |||||||||
--------------------------------gtgctttcat---tggaaggttggaagcaattgt-tgc-ctgttgaagcaacaagatcttctactgtttatatatgttgtcat-gtattcttcaattgtcatg----cagGTATGTGGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGAC
upper sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctttagatccttgc----aaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
| || || ||| | || |||| ||| | ||| | |||| || || | || || || | ||| ||| || | |||||| |||||||| || | ||| | || || |||||||| ||||||||||| ||||| ||||||| || |||||||| ||||| || || ||||| ||
-----------------------------------------ttgaccttgatatggaatgttcattgtgagttattgattaccta-gacttctagaatactgtgctaaagtgaagtgctttatattgt-gattggga---tcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctttagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
tgttttc CT-rich tract
ttaaagatgttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctttagatccttgcaaatcaactggttaaagatgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA