Sequence
atgc intronic sequence ATGC exonic sequencegtctttttttgaattgaaaaatcatcctctgtactatcatttgtaattgctcatgttaatttgttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12880.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G05080.1 (Glycine max), 3'ss of exon 2
--gtctttttttgaattgaaaaatcatcctctgtactatcatt--tgtaattgctcatgtt---aatttgttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
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gtatttcatattgtctgcactaataattga-tgaact-tcattaatgaaacactttatattgaaaaggttcactttcttctcttgcaagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGCGAGGCTTTAGAGGAAGCAGGAGTTAAAGGAATACTAAGA
upper sequence: AT1G12880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G26440.1 (Glycine max), 3'ss of exon 1
gtctttttttgaattgaaaaatcatcctctgtactatcatttgtaattgctcatgttaatttgttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
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-gtattgtctgaaccaattcact-tcatcagcatgaaccctttgtattgtat-tgcaaagtatcattttgttctctttccagGGTGGATGGGAGGATGATGAGACTGTTACAGAAGCTGCTTGCCGTGAAGCGCTAGAGGAAGCAGGAGTCAAAGGGATTGTAAGG
upper sequence: AT1G12880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0150g00320.t01 (Vitis vinifera), 3'ss of exon 2
------gtctttttttgaattgaaaaatcatcctctgtact----atcatttgtaattgctcatgttaatttg---ttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
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gtatctgttttcttgctgtctatagtactttactctaatttcggcaagagatgggaattctggacttaactctaatttcctcatttgattgtcagGGTGGATGGGAGAATGATGAGACTGTTGAACAAGCTGCATGTCGTGAAGCATTGGAGGAAGCAGGAGTGAGAGGAATACTTGGT
upper sequence: AT1G12880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0068g00870.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gtctttttttg--aattga---aaaatcatcctctgtactatcatttgtaattgctca-tgttaatttgttgtgtatatta--ttatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
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gtacaattttcctcctctcttcctcccatattggtaattggtatagaaggattgttaccactcttaattaaaattctgaggttttgatttttatcctatgtttgcttgtcagGGTGGATGGGAGGATGATGAGACCGTTGAAGAAGCAGCATGCCGTGAAGCCTTAGAGGAAGCAGGAGTGAAAGGAATTCTTAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtactatcatttgtaattgctcatgttaatttgttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
tgttaat putative branch site (score: 3)
atgttaatttgttgtg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttttttgaattgaaaaatcatcctctgtactatcatttgtaattgctcatgttaatttgttgtgtatattattatcagGGAGGATGGGAAGATGATGAGACTGTTCTTGAAGCTGCTTCTCGTGAAGCCATTGAAGAAGCAGGAGTTAAAGGAATACTTAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA