Sequence
atgc intronic sequence ATGC exonic sequencegtcaatttctttcattctcttgcctttctttgaatcctgtagaaactggtaatgtttctggaacttagctaggtttcgtgttaatggaattatttgtgtatattgtggctcagAAATGCGTACAACATGGTCCTGCACAAGTTTGGTGAGAAGCTATATACTGGGTTTATTGCTACTATGACTTCTCATCTCAAAGAAAAATCCAAGCTTATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G26830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G26830.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g51180.1 (Oryza sativa), 3'ss of exon 1
gtcaatttctttcattctctt-gcctttctttgaatcctgtagaaactggtaatgtttctggaacttagctaggtttcgtgttaatggaattatttgtgtatattgtggctcagAAATGCGTACAACATGGTCCTGCACAAGTTTGGTGAGAAGCTATATACTGGGTTTATTGCTACTATGACTTCTCATCTCAAAGAAAAATCCAAGCTTATC
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-----tgcttgtcggcctctttggtcgtcacagcaacttggtgata--aataactattctgaacctca-cttgatt----gtaatttgcaatatttcctttcatct--gtgcagGAGTGCCTACAACATGGTGCTCCACAAGTATGGTGAGAAGCTATATGATGGCCTGGAGAGAACTATGACATGGCGCTTGAAGGAAATATCAAAATCAATA
upper sequence: AT1G26830.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G15240.1 (Glycine max), 3'ss of exon 1
gtcaatttctttcattctcttgcctttctttgaatcctgtagaaactggtaatgtttctggaacttagctaggtttcgtgttaatggaattatttgtgtatattgtggctcagAAATGCGTACAACATGGTCCTGCACAAGTTTGGTGAGAAGCTATATACTGGGTTTATTGCTACTATGACTTCTCATCTCAAAGAAAAATCCAAGCTTATC
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-----------ccctacatgtacacattaaaggatcttatgcttaattttctttccacaagggaaaacatatgtttctaatt--ttcctcctttcatttatgtgtgggtttagAAATGCATACAACATGGTGCTTCACAAATTTGGTGAGAAGCTCTACTCAGGGCTGGTTGCAACCATGACTGGACATCTCAAAGATATAGCTCAATCTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaacttagctaggtttcgtgttaatggaattatttgtgtatattgtggctcagAAATGCGTACAACATGGTCCTGCACAAGTTTGGTGAGAAGCTATATACTGGGTTTATTGCTACTATGACTTCTCATCTCAAAGAAAAATCCAAGCTTATC
tgttaat putative branch site (score: 3)
aattatttgtgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaatttctttcattctcttgcctttctttgaatcctgtagaaactggtaatgtttctggaacttagctaggtttcgtgttaatggaattatttgtgtatattgtggctcagAAATGCGTACAACATGGTCCTGCACAAGTTTGGTGAGAAGCTATATACTGGGTTTATTGCTACTATGACTTCTCATCTCAAAGAAAAATCCAAGCTTATC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT