Sequence
atgc intronic sequence ATGC exonic sequencegtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 2
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
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--ctcttagtatttaa----gactatctgaaaacacttccaaaataaagtatattgtgtacggttgcagca--agtacttgcaatgactagtctttcatattatt-cagGTTGATCCTGATGAGGTCAATGCGTTGGCACAACTAATGACATGGAAGACGGCCGTGGCTAATATTCCATATGGAGGAGCTAAAGGTGGAATAGGATGCA
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG----------------------------------------------------
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---------------------------------------------------gttggtgaaaaatct-ggtcctgatgtttga----aatcctttgacaacc-----caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 3
gtttttgaccttttgact--ttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
| | |||| | | || ||| || | || ||||| || || || | ||| | ||| || | | ||| || | || | ||||||||||| |||||||| || || ||||| || | ||||| |||||||||||||| ||||| || || || |||||||| ||||| || ||||| |||
atccatttccttcaaattaattttcctcttcatttaagactcat-tgaaatccgttggtgaaaaatct-ggtcctgatgtttga----aatcctttgacaacc-----cagGTTGATCCTGATGAAGTTAATGCCTTGGCACAATTGATGACTTGGAAAACAGCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTA
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttctt--gcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
| ||| | | |||| | || |||||| || | | | || || | || || | | ||| | ||| | | || || ||| | ||||||| || ||||||||||| || ||||| || || ||||||||||| |||||||| || || || || || || ||||| ||||||||||| || ||||
------gttatttatattctgacttacaaaa----aactca---gtgatttatctgtttataggtt---ttaagttctatcactcaa-tcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ36429 (Selaginella moellendorffii), 3'ss of exon 2
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
| || |||| | | || || ||||| || | | | | | || || ||| |||||| || |||||||||||| | || ||| | ||||| ||||||||||| || ||||| |||| |||||||| || || |||||||| || |||
------------------------------------------gtaaaagaaacaaaaaagaaaactc--------tatataat-cgcgcttttccttatcctcctgtagGCTGATCCAGACGAAGTGAACGCACTAGCGCAGTTGATGACTTGGAAAACAGCCGTAGCTAATCTTCCATACGGAGGCGCCAAGGGAGGGATAGGCTGTA
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ06180 (Selaginella moellendorffii), 3'ss of exon 2
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
| || |||| | | || || ||| || | | | | | || || ||| |||||| || |||||||||||| | || ||| | ||||| ||||||||||| || ||||| |||| |||||||| || || |||||||| || |||
------------------------------------------gtaaaagaaacaaaaaacaaaactc----------tataat-cgcgcttttccttatcctcctgtagGCTGATCCAGACGAAGTGAACGCACTAGCGCAGTTGATGACTTGGAAAACAGCCGTAGCTAATCTTCCATACGGAGGCGCCAAGGGAGGGATAGGCTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
tcgttttctt CT-rich tract
tatatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG