Sequence
atgc intronic sequence ATGC exonic sequencegtgagctcctaacttactcaatctatgtgtatctgcaagaaagtactttccttgaagctagttttcttatgtgactctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05970.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 4
gtgagctcctaacttactcaatctatgtgtatctgcaagaaagtactttccttgaagctagttttcttatgtgac-tctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
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gtaaggatt--agttcctggatatatgtgttattattggc---ttttgtagctttgttcaaatcttttaaatgatatatgtatggaactttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAACAGGACTGCAATAGGTTCTGGTCTTATTTATCATGGAATACCTGAA
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 4
gtgagctcctaacttactcaatctatgtgtatctgcaagaaa--gtactttccttgaagctagttttcttatgtgactctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
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gtaagaattgg--ttcctggatatatatgtcattattgccttttgtagctttgttaaaa-----tcttttaaatga-tatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 3
gtgagctcctaacttactcaatctatgtgtatctgcaagaaagtactttcctt-gaagct------agttttcttatgtgactctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
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aacagttggggagtaagaattggttcctggatatatatgtcattattgccttttgtagctttgttaaaatcttttaaatga-tatatatgaattgttgcagCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 4
---------------gtgagctcctaac--ttactcaatctatgt-gtatctgcaagaaagtactttccttgaagctagttttcttatgtg-actctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
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gtaagcagctccattgtcaacctatgacactttctgggccttcttcgttttttcattcaaat---ttacttagcatccttctcatcatttccatttttccttcactttttaagGTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAG
upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 4
gtgagctcctaacttactcaatctatgtgtatctgcaagaaagtactttccttgaagctagttttcttatgtgactctgtt--ttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
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--------gtaagttgctca-tctgaataactttgcta-----tttcatcattgaagttcccttattcatttgcattcattgcctacactttcaagGTACAAATGGATGACATATGGAGAAGCAGGTACTGCTCGATCAGCAATTGGTTCTGGTTTAATATACTATGGAATACCGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtactttccttgaagctagttttcttatgtgactctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
ctctgttttgtttttt CT-rich tract
tgttttgttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctcctaacttactcaatctatgtgtatctgcaagaaagtactttccttgaagctagttttcttatgtgactctgttttgtttttttcagCTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC