Sequence
atgc intronic sequence ATGC exonic sequencegtcagtaccctttacttcttataaatcctcacttcttgattgcttatgttggttctcaattggcactggcttttagttctcttgtttgtgtgttcttggttcgttacttaaatctcttcttactgcattatctaatttgtgcagAATGATGGTAGTGGATGCATGTCAATCTACGGCCACAAGTTTGAGGATGAGAATTTTACTGCTAAACATACTGGACCAGGATTGCTCTCCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G057329_T01 (Zea mays), 3'ss of exon 3
gtcagtaccctttacttcttataaatcctcacttcttgattgcttatgttggttctcaattggcactggcttttagttctcttgtttgtgtgttcttggttcgttacttaaatctcttcttactgcattatctaatttgtgcagAATGATGGTAGTGGATGCATGTCAATCTACGGCCACAAGTTTGAGGATGAGAATTTTACTGCTAAACATACTGGACCAGGATTGCTCTCCATG
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--------------------------------------ttttgtaatctccatgcagaaattggaatgacatcatgacttcatgggttcatattat--attcagtatataaactaaagcctcctgttttgtgt----cctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG
upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 2
gtcagtaccctttacttcttataaatcctcacttcttgattgcttatgttggttctcaattggcactggcttttagttctcttgt-ttgtgtgttcttggttcgttacttaaatctcttcttactgcattatctaatttgtgcagAATGATGGTAGTGGATGCATGTCAATCTACGGCCACAAGTTTGAGGATGAGAATTTTACTGCTAAACATACTGGACCAGGATTGCTCTCCATG
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--------------------------------------------------gttcctccaaactctcttcttctttctcttcataaatcgaccgttttttatt-gttcttttctagttgtctcattttcttctctccctt-tccagGGTGATGGTAGTGGATGCGTTTCCATCTATGGAAGCAAGTTCGAGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttcttggttcgttacttaaatctcttcttactgcattatctaatttgtgcagAATGATGGTAGTGGATGCATGTCAATCTACGGCCACAAGTTTGAGGATGAGAATTTTACTGCTAAACATACTGGACCAGGATTGCTCTCCATG
attatctaatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtaccctttacttcttataaatcctcacttcttgattgcttatgttggttctcaattggcactggcttttagttctcttgtttgtgtgttcttggttcgttacttaaatctcttcttactgcattatctaatttgtgcagAATGATGGTAGTGGATGCATGTCAATCTACGGCCACAAGTTTGAGGATGAGAATTTTACTGCTAAACATACTGGACCAGGATTGCTCTCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG