Sequence
atgc intronic sequence ATGC exonic sequencegtttgacatcttgcttttgaattgcaattggaactgaattggcttttgaagtatcatttgcactgagtattagtgattcctgagcaatgctagatttgagttgttaggttttgatatgctattgttatcttttattttcgattttctggaaatttttaatgacctgactagtgatgcttgctgtttcaatcagGCAAATGATGCACAGCTCAGTACTATGGTTGCTGAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 1
-gtttgacatcttgcttttgaattgcaattggaac----tgaattggcttttgaagtatcatttgca-ctgagtatt--agtgattcctgagcaatgctagatttgagttgttaggttttgatatgctattgttatcttttattttcgattttctggaaatttttaatgacctgactagtgatgcttgct-gtttcaatcagGCAAATGATGCACAGCTCAGTACTATGGTTGCTGAGCAG
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agtgagatattatgagcatgtttaccattttgtaaagcatatattggcatatgca-tattatatacctctggatttctaactgtcttctataaattctcagACAAATGATGCACAGCTCAG-TACAATGGTAGCAGAGCAGGTATTC------CTTGACATCTACTATGAACTGCCAAA-----CTTATTAGTTTTAATGCTATTGTTAATGC----------------------------
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g51430.1 (Oryza sativa), 3'ss of exon 1
gtttgacatcttgcttttgaattgcaattggaactgaattggcttttgaagtatcatttgcactgagtattagtgattcctgagcaatgctagatttgagttgttaggttttgatatgctattgttatcttttattttcgattttctggaaatttttaatgacctgactagtga-tgcttgctgttt-caatcagGCAAATGATGCACAGCTCAGTACTATGGTTGCTGAGCAG
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----------------------------------------------------------------------------------------------agtgagatattatgagcatgtttaccatt-ttgtaaagcatatattggcatatgcatattatatacctctggatttctaactgtcttctataaattctcagACAAATGATGCACAGCTCAGTACAATGGTAGCAGAGCAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 1
gtttgacatcttgcttttgaattgcaattggaactgaattggcttttgaagtatcatttgcactgagtattagtgattcctgagcaatgctagatttgagttgttaggttttgatatgctattgttatcttttattttcgattttctggaaatttttaa-tgacctgactagtgatgct-tgctgtttcaat--cagGCAAATGATGCACAGCTCAGTACTATGGTTGCTGAGCAG
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-----------------------------------------------------------------------------------------------atggatcataaaaat--gctaaattcctaatatttcttatattaaatttatgtaaaaccttcaagttgccttctgaatgttgctatatttttttaatgtcagGCAAATGATGCACAACTTAGTACGATGGTTGCAGAGCAG
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 1
gtttgacatcttgcttttgaattgcaattggaactgaattggcttttgaagtatcatttgcactgagtattagtgattcctgagcaatgctagatttgagttgttaggttttgatatgctattgttatcttttattttcgattttctggaaattttta-atgacctgactagtgatgct-tgctgtttcaat--cagGCAAATGATGCACAGCTCAGTACTATGGTTGCTGAGCAG
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-----------------------------------------------------------------------------------------------atggatcataaaaat--gctaaattcctaacatttcttatattaaatttatgtaaaaccttcatgttgccttctgaatgttgctatatttttttaatgtcagGCAAATGATGCACAACTTAGTACGATGGTTGCAGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgattttctggaaatttttaatgacctgactagtgatgcttgctgtttcaatcagGCAAATGATGCACAGCTCAGTACTATGGTTGCTGAGCAG
acctgac putative branch site (score: 3)
ctgtttc putative PPT
aaatttttaatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgacatcttgcttttgaattgcaattggaactgaattggcttttgaagtatcatttgcactgagtattagtgattcctgagcaatgctagatttgagttgttaggttttgatatgctattgttatcttttattttcgattttctggaaatttttaatgacctgactagtgatgcttgctgtttcaatcagGCAAATGATGCACAGCTCAGTACTATGGTTGCTGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG