Sequence
atgc intronic sequence ATGC exonic sequencegtacgtggtcctgaggaacttgttctagatcgtgggagagttctttaagcttctaagttattgttgatttgcctttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G29000.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
-----------------gtacgtggtcctgaggaacttgttctagatcgtgggagagttctttaagcttctaagttattgttgat--ttgcctttgt-agGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
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cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g22670.1 (Oryza sativa), 3'ss of exon 4
------------------gtacgtggtcctgaggaact-tgttctagatcgt----gggagagttctttaagcttctaagttattgttgatttgcctttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
| | || | || | | | | | || | | || | |||| || | | | ||| | || | | | |||| ||| || | | | | | || ||||| ||||| ||||| ||||| || |||||||| || |||||||| || || |||||||||||||
tcttttgaattttcaaactcattttgtttggtagatttatatacaacattctcttcatgtgatatttttatgcatttga-ttaatcttaactgcacacc--agGATGATGCTGGAGCACCAGCCTCACTTCCAAAGCATAATAAAGGTTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAATGCTTTCAAGCAA
upper sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
--------------gtacgtggtcctgaggaacttgttctagatcgtgggagagttctt---taagcttctaagttattgttgatttgcc---tttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
|| | | | || | | || | | | || || | | | ||| | | | || ||||||| |||| | || ||||||| ||||| ||||| ||||| ||||| || ||||||||||| |||||||| || |||||||| ||||| |
ctatcaaatactgaaattatgtcattattgcatttaatttggaccaagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgctagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
---------gtacgtggtcctgaggaacttgttctagatcg-----------tgggagagttctttaagcttctaagttattgttgatttgcctttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
| || || | ||| | || | || | | || | ||| | || | ||| ||| |||||||| || || | ||| || ||||| ||||||||||| || ||||| ||||| || ||||| |||||||||||||| ||||| ||||| |
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
upper sequence: AT4G29000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------gtacgtggtcctgaggaacttgttctagatcgtgggagagttctttaagcttctaagttattgttgatttgcctttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
|| | | || |||| | | |||| |||| || | | || | || | || | ||| |||||||| | || || | || || || || ||||||||||||||||| ||||| || || ||||| |||||||||||||| ||||| ||||| |
cgtattccttctgttgtaccaaattatattccatagtttcattatttttcttaacc-tgggcgagtggttgacga----aactgatggcatcttggttattgcagGAGGATGTTGGAGAGCATCCTCTGGCGGGCAAGCACAACAAAGGATGCCACTGTAAAAAGTCGGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagatcgtgggagagttctttaagcttctaagttattgttgatttgcctttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
tgttgat putative branch site (score: 4)
tttgccttt CT-rich tract
taagttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtggtcctgaggaacttgttctagatcgtgggagagttctttaagcttctaagttattgttgatttgcctttgtagGAGGATATCGGTGAAGTTGTGTTGTTAGGGAAACATAACAAAGGATGCCACTGCAAAAAATCAGGATGCCTTAAGAAGTATTGCGAGTGCTTTCAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA