Sequence
atgc intronic sequence ATGC exonic sequence...tgaagtgaagtatataccattttctcatctctgctcgctgtatattttttgtcactgtgttggttggtagtcctcattctctcttctcttattgtctcagACAGACCAGAAGCTGCGTCTATGTGACATATGCGGAGCATTTTTGAGCGTCTATGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G17440.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------tgaagtgaagtatataccattttctcatctctgctcgctgtatattttttgtcactgtgttggttggtagtcctcattctctcttctct-tattgtctcagACAGACCAGAAGCTGCGTCTATGTGACATATGCGGAGCATTTTTGAGCGTCTATGACAG
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gtaagtgtggtgaatcgctcattgcagtgcacataaaaaattgatatatttagttgttttgttttcactccaagaaattatcactgtgttgaactgtggatgcattttgttgtgatgct--tttatattgatgatttttatttttcaatctctgtttagACTGATCAAAAGTTGCGCCTGTGTGACATATGTGGAGCATTCTTGAGCGTATATGACAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G028096_T02 (Zea mays), 3'ss of exon 8
-----tgaagtgaagtatataccattttctcatctctgctcgctgtatattttttgtcactgtgttggttggtagtcctcattctctcttctcttattgtctcagACAGACCAGAAGCTGCGTCTATGTGACATATGCGGAGCATTTTTGAGCGTCTATGACAG
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catattcttgttgggaatct-tagtacagatagagttgtagagttagtattttgcggtattatttcaatgtaatgtcctctttttttctatttttgtt----tagACTGACCAAAAGCTGCGCCTGTGTGACATATGTGGAGCATTCTTGAGCGTATATGACAG
upper sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 8
tgaagtgaagtatataccattttctcatctctgctcgctgtatattttttgtca--ctgtgttggttggtagtcctcattctctct---tctcttattgtctcagACAGACCAGAAGCTGCGTCTATGTGACATATGCGGAGCATTTTTGAGCGTCTATGACAG
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--aattgaaa---acacgagttgatgataatggatgcatatgtttttatatttatcctgtatttcttactcttttaatttctttttaattctgatgttacctcagACTGATCAGAAGCTACGCGTATGTGACATTTGTGGAGCATTTTTGAGCGTTTATGATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgtcactgtgttggttggtagtcctcattctctcttctcttattgtctcagACAGACCAGAAGCTGCGTCTATGTGACATATGCGGAGCATTTTTGAGCGTCTATGACAG
tcctcattctctcttc CT-rich tract
tcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaagtgaagtatataccattttctcatctctgctcgctgtatattttttgtcactgtgttggttggtagtcctcattctctcttctcttattgtctcagACAGACCAGAAGCTGCGTCTATGTGACATATGCGGAGCATTTTTGAGCGTCTATGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - -catctct