Sequence
atgc intronic sequence ATGC exonic sequencegttttaataccatcgttaaccaacgctcttaacgttcttcattccatatagttattattgatttacaaaattttgctaacgattatggctttatctttttagCTACACCACACAGACAAATTCAAAGGTGTACCATATGGGCTGTTTCTTGGACCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 4
-------------gttttaataccatcgttaac--caacgctcttaacgttcttcattccatatagttattattgatttacaa----aattttgctaacgattatggctttatctttt-tagCTACACCACACAGACAAATTCAAAGGTGTACCATATGGGCTGTTTCTTGGACCAAAG
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gtacgagaccaccagctgctcactgacgtttactgcaccactactactagtccacgctgc-tactactactactggctagagagtgtacttttgctgattttctttgtgtggccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGACCCAAG
upper sequence: AT5G52570.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtttta-ataccatcgttaaccaacgct---cttaacgttcttcattccatatagttattattgatttacaa---aattttgctaac-gattatg-gctttatctttttagCTACACCACACAGACAAATTCAAAGGTGTACCATATGGGCTGTTTCTTGGACCAAAG
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gtaagcatgcaccaccacacacacgatccttcatttttctttttcttttccttttcctttttttgtttttttttttaattttcaactgaatccaacggcctgatcttctgatgcatggtctcagCTCCACCACTCAGACAAATTCAATGGGGTCCCATATGGGCTGTTCTTGGGCCCTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagttattattgatttacaaaattttgctaacgattatggctttatctttttagCTACACCACACAGACAAATTCAAAGGTGTACCATATGGGCTGTTTCTTGGACCAAAG
tgctaac putative branch site (score: 1)
ctttatcttttt putative PPT
tattattgatttacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttaataccatcgttaaccaacgctcttaacgttcttcattccatatagttattattgatttacaaaattttgctaacgattatggctttatctttttagCTACACCACACAGACAAATTCAAAGGTGTACCATATGGGCTGTTTCTTGGACCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT