Sequence
atgc intronic sequence ATGC exonic sequencegtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16830.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatact-gatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
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-------------------------------------------gtaaatgctcaatatcttt----tttggataaatacttcaaaattcaggaaattttaat-tatgcttcc--ttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
gtaagcagcttaatccaactttttctgttctcgggagcatctc-ctaaatactgatac--ctcaggagcta-atgaaactatttgagtaatatgcgaagctaaatgcatttttcc--ctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
|||| || || || || ||| || |||| || | | || | | | | || | | | | | | ||| ||||||| |||||||| ||||||||||| |||||||| ||||| || || |||||||| |||||||| ||||| || || ||||| || ||||| || || | |
----------------------------atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
||| | | || |||||| | | || | | |||| | | ||| ||| ||| ||||||| ||||||| |||||||| || |||||||| ||||| || || |||||||| |||||||||||||| || || ||||| || ||||| || || | |
--------------------------------------------gtaatgtctaactgttttattctgatgaaattttcagatttcaa---gaagatttaatcatgcatcc--ttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 20
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
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-----------------------------------------------------------------gtatgccgatttgttgctttttctccagtgatgaaaccattgtcg------aaacagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGCTA
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 20
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
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-----------------------------------------------------------------gtatgccgatttgttgctctttctccagtgatgaaaccattgtcg------aaacagATTATGACACAATTCATGCCGCCTCCGCCAGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGTTA
upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
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------------------------------------------------------------------gtatgcacatttttccttcttgaccggtgtaaga---acttgccat----gtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
agctaaa putative branch site (score: 3)
tgcatttttccctttc CT-rich tract
tatttgagtaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA