Sequence
atgc intronic sequence ATGC exonic sequencegtatgccagtaaattctacttctttttgctatgtccagagttcagaaagttatttgcaaatgaaagtaatacatgagcttgctgaacgtactctttgttgtattgattagtccatttatttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21534.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21534.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
-------gtatgccag-taaattcta--cttctttttgctatgtccagagttcagaaagttatttgcaaatgaaagtaatacat-gagcttgctgaacgtactctttgtt------gtatt--gattagtccatttat----ttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
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gtatgccgtgtattagcttgatgctaagcttttttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcc-cactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
upper sequence: AT4G21534.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
gtatgccagtaaattctacttctttttgctatgtccagagttcagaa--agttatttgcaaatgaa-agtaatacatgagcttgctgaacgtactctttgttgtattgattagtccatttatttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
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----------------------------gtatgccacaagcttggaattagttgatcgaatctgaatgatactttcttggct--ctcatctcaccattta--gggataataa--taatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
upper sequence: AT4G21534.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G06300.1 (Glycine max), 3'ss of exon 6
--------gtatgccagtaaattctacttctttttgctatgtccagagttcagaaagttattt--gcaaatgaaagtaatacatgagcttgctgaacgtactctttgttgtat---tgattagtcca--tttatttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
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gtaattataaattactgtcaccatagtcgtgttttggaaacgagtgaatgtgaaaaagcatctaagttacttgtgtcagcatctggttctggccatgatattcgccgtaacatatttgaaaattttaattttatttcagGTCTGGTTGCTGATATTGATATCGAGTCTGAAAAGTATAGGTGGATGGGAAGTGCTCGTATTGATTTTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatgagcttgctgaacgtactctttgttgtattgattagtccatttatttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
tattgat putative branch site (score: 3)
tttatttc putative PPT
atttatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccagtaaattctacttctttttgctatgtccagagttcagaaagttatttgcaaatgaaagtaatacatgagcttgctgaacgtactctttgttgtattgattagtccatttatttcagGTTTAATAGCTGATATAGACATCGAGTCAGAGAAGTTCAGATGGATGGGAAGTGCTCGTATTGACTTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA