Sequence
atgc intronic sequence ATGC exonic sequencegtaactaatataccagttctgttcttgtctatgtttttgactctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50620.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 2
gtaactaatataccagttctgttcttgtctatgtttttgactctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT
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gtaatgaggataaacttgcgagttggaattctatgtttatgttttccatgtcagcaagtaactgggtatttcctttcttaaatttcttcg-ctagGAAAGAATGTGCATGCACACCAGTTAGATTCTTCGCTATCTTGTCGATGCAGAGGTCAGGAAGTGGGTGGATTGAAACATTATTGAATAGCCATGAGAAC
upper sequence: AT3G50620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G877077_T01 (Zea mays), 3'ss of exon 2
gtaactaatataccagttctgttcttgtctatgtttttgactctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT-----
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gtaacgaagatat--actgtgtcctc-----tgattttgcctttttcaggttagt------gactgacttgtgggtgttctttgtct---gttaggaaagAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAATATTAG
upper sequence: AT3G50620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G877077_T02 (Zea mays), 3'ss of exon 2
gtaactaatataccagttctgttcttgtctatgtttttgactctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT
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gtaacgaagatat--actgtgtcctc-----tgattttgcctttttcaggttagt------gactgacttgtgggtgttctttgtct---gttagGAAAGAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAAT
upper sequence: AT3G50620.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0031g00880.t01 (Vitis vinifera), 3'ss of exon 3
gtaactaatataccagttctgttcttgtctatgtttttga-ctctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT
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----gtaacttacaattgatgcattaggttttgaatttgggctcccttgtgaaaatgaatttgccca--tttttcatttggggtgtgcttg--cagGGCTGAATGTGCAAATAATCCTGTGAGATTCTTTGCCATAGTGTCGATACAGAGATCAGGAAGTGGATGGTTTGAGACACTATTAAATAGTCATATTAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT
ttgtctt CT-rich tract
tttaaatctttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactaatataccagttctgttcttgtctatgtttttgactctctttggtttgttcctttgtttaaatctttgttttgggttgtcttaaactagAGCTGAATGTGGACATAATCCGGTGAGGTACTTTGCGATATTGTCGATGCAGAGATCAGGAAGCGGTTGGTTCGAAACATTGTTGAATAGTCATAACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA