Sequence
atgc intronic sequence ATGC exonic sequencegtttattaagtttctttaacaacccatattagattgtgttccctgatttttgcttaatagtctcaatcatgttataagcatgacatcttcatctccatgttatttatgtaaccatacttttacgaactgcagATTTGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16650.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 6
gtttattaagtttctttaacaacccatattagattgtgttccctgatttttgc-ttaatagtctcaatcatgttataagca-tgacatcttcatctccatgttatttatgtaaccatacttttacgaactgcagATTTGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTG
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-------gtatgcttttacttgtttcttttgatttagtttctttgaaaatggtactactgagtttttttcccctgaaagtactcatatggagtgttttgaataacctctttacttttgcttgact---cctcagGTTTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTA
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G03640.1 (Glycine max), 3'ss of exon 7
gtttattaagtttctttaacaacccatattagattgtgttccctgattt-ttgcttaatagtctcaatcatgttataagcatgacatcttcatctccatgttatttatgtaaccatacttttacgaactgcagATTTGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTG
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----------------------------caaaagtatgaaatagaataaattacataagagtttggg--aggcgaggaggatc-catgttaattgacac-taaccacagaaatcatgattg-gtttatgacagGTTTGAACCAGATATGCTAGCATTTTCAGGTTGTTATTTTGGTGGGGGAGAAAAAGAGAGACGTGAGCTTGGTGAAATCAGAAAAAGGTGGACAACATTA
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0229g00100.t01 (Vitis vinifera), 3'ss of exon 6
gtttattaagtttctttaacaacccatattagattgtgttccctgatttttgcttaatagtctcaatcatgttataagcatgacatcttcatctcc-atgttatttatgtaaccatacttttacgaactgcagATTTGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTG
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gtttgt-accttccaccaaaaa-----aggggagaatggaactgagaacttatttaaaattcacaa--aaaaaattgaaataatgctttcattttttgggttcatgatatgaaaccattttcatga----cagGTTTGAAGCTGATATGCTAGCATTTTCTGGATGCTACTATGGTGGGGGTGAAAAGGAGAGATATGAGCTTGGTGAAATAAGGAAACGCTGGGCAACATTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatgacatcttcatctccatgttatttatgtaaccatacttttacgaactgcagATTTGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTG
atgtaac putative branch site (score: 3)
cttttac putative PPT
atgttatttatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttattaagtttctttaacaacccatattagattgtgttccctgatttttgcttaatagtctcaatcatgttataagcatgacatcttcatctccatgttatttatgtaaccatacttttacgaactgcagATTTGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA