Sequence
atgc intronic sequence ATGC exonic sequence...ttaattggtattttatgagtggaagacatgaaaatgttatcatttcatttggtgtctgttatatttccagcttgacatactagctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06600.1 |
intron # | 10 |
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 10
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 10
-ttaattggtat-tttatgagtggaagacatgaaaatgttatcatttcatttggtgtctgttatatttccagcttgacatactagctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG
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ttgaaaaaatatattcactagtacatt-tgtttctatgacacgtctcagctaaacgtcaactgtattttcttggtgctaatgttgctgtgcttttgct-cagTGTTCTTGTTCATAGCGGAGGAGTACATGGCGGTCACTACTATGCTTTCATACGGCCTACGCTATCAGACCAGTG
upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 6
ttaattggtattttatgagtggaagacatgaaaatgttatcatttcatttggtgtctgttatatttccagcttgacatacta-gctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG
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-taggtaccattttcagtgtaacagtggtgctccaataggtgccttttttcctcctttccacatctttttctcactatgtttcactgctgcttttattcagTGTTCTTGTTCATAGTGGAGGAGTACATGGCGGTCACTACTATGCCTTCATTCGACCAACGCTATCAGATCAATG
upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 10
ttaattggtattttatgagtggaagacatgaaaatgt-tatcatttcatttggtgtctgttatattt--ccagcttgacat-actagctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG
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----tgactgttttcttcacattattcatgtattcttatggcagtttgcataccacatgatacatttttctatgctgatgttgcctgtttttttttttgttcagTGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTG
upper sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 10
ttaattggtat-tttatgagtggaagacatgaaaatgttatcatttcatttggtgtct-gttatatttccagcttgacata--ctagctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG
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--gatgaccttgtctatga-tgcaatttatgcag-tgttatggtagcatttgcttctgagatatgcatacgtattaacatggctttttcctttcctttttgcagTGTTTTGGTTCATAGCGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACCCTTTCTGATCAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttggtgtctgttatatttccagcttgacatactagctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG
gcttgac putative branch site (score: 4)
tttgtct putative PPT
tgttatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattggtattttatgagtggaagacatgaaaatgttatcatttcatttggtgtctgttatatttccagcttgacatactagctgttatttgtctgcagTGTTTTAGTTCATAGTGGAGGAGTACATGGTGGGCACTATTATGCTTTTATAAGGCCTACGCTCTCAGATCAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA