Sequence
atgc intronic sequence ATGC exonic sequencegtaattgacgtgaagttcagcatactttacttatttgtcttgctatataaatataatacatgtctgcttattggttttttttttttttcagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06600.3 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 23
gtaattgacgtgaagttcagcatactttacttat--ttgtcttgctatataaatataatacatgtctgcttattggttttttttttttttcagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG
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--------------gtatattcttctttatttgcgacataagcactacatgaccattgggcttatattttattttcacgcctggcttttgcagACTTCTGACATCTTGTATTACGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACTCTTAAAGTTGCATTCCACCATGCAACTAAAGATG
upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G418232_T01 (Zea mays), 3'ss of exon 2
gtaattgacgtgaagttcagcatactttacttatttgtc-ttgctatataaatataatacatgtctgcttattggttttttttttttttcagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG
|| || | || | | | | | | || || | ||| | | | || | || | | | | |||||||||||||| |||||||||||||| |||| || || || |||||||| || || |||||| | |||||||| || || ||| | |||||||| |
---gttaacctt---ttttgtttggtcaatatgagcatgatttctgtgtaacaaatgtgttggacttcctactaaagcgccatctggtacagACGTCTGACATCTTGTATTATGAAGTGTTGGATATACCACTGCCAGAATTGCAGTTCCTAAAAACCCTGAAAGTTGCATTTCACCATCCTACGAAGGATG
upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 23
gtaattgacgtgaagttcagcatactttacttatt---tgtcttgctatat----aaatataatacatgt-----ctgcttattggtttt-ttttttttttcagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG
|| || ||| | |||| | ||| || || || || ||| || | || | | || ||| | ||| | || ||| ||||| ||||| || ||||||||||| ||||||||||| || || |||||||| || || | ||||| | |||||||| ||||| ||||| || || || |
---------gtcaaattctctttg-tttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG
upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 23
------------------------------------------gtaattgacgtgaagttcagcatactttact---tatttgtcttgctatataaatataatacatgtctgcttattggttttttttt--ttttt----cagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG
| || | || || ||| | ||| | | || ||||||| | | | | ||| || || || ||| ||| |||| ||||| ||||| |||||||||||||| |||||||||||||||||||| |||||||| |||| | ||||||||||| |||||||| || ||||| |
gttgctttcacaaatactgagacaaatttgatgcttgatatgatcgtttgttttttattttttttatttttttatatatatatatttttatataacttttagtaacagaaacttcttccttcttctttggcctttggaacagAGTTCTGATATTTTATATTATGAAGTTCTAGACATCCCTCTTCCAGAATTGCAAGGTCTGAAAAATCTGAAAGTTGCTTTTCATCATGCTACAAAGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttgctatataaatataatacatgtctgcttattggttttttttttttttcagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG
tctgcttattggtttt CT-rich tract
ttattggttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgacgtgaagttcagcatactttacttatttgtcttgctatataaatataatacatgtctgcttattggttttttttttttttcagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA