Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatatgctgctacatcttgtgatggacacttatgttactcccaaaacctatgtttttgtagctttatgtgctgccatctgtacagGGAGGGTTGATAATAAGCGATTCTTTGAACCATACTTCGATTGTCAACGGCGCTCGAGGTTCAGGAGCTACTATCCGTGTTTTCCAACACAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 5
-----------------gtaagtatatgctgctaca-----tcttgtgatggacacttatgttactcccaaaacctatgtttttgtagctttatgtgctgccatc-tgtacagGGAGGGTTGATAATAAGCGATTCTTTGAACCATACTTCGATTGTCAACGGCGCTCGAGGTTCAGGAGCTACTATCCGTGTTTTCCAACACAACA
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gtttgtacagttaactaataagagcacttcataacaagggttcacgtggcttagaagctttgtgtcactaatccttgaatgtgaatgttttggcttgttatttctgtttacagGGAGGCTTAATTATTAGTGATTCCTTGAATCATAGCTCCATTGTGAATGGTGCTCGAGGATCTGGAGCTACTATTCGTGTTTTCCAACATAATA
upper sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 5
------------gtaagtatatgctg-ctacatcttgtgatggacactta---tgttactcccaaaacctatgtttt-tgtag----ctttatgtgctgccatc-tgtacagGGAGGGTTGATAATAAGCGATTCTTTGAACCATACTTCGATTGTCAACGGCGCTCGAGGTTCAGGAGCTACTATCCGTGTTTTCCAACACAACA
||| | || || ||| || | | | | || | || || | || ||| ||| | || || | |||||| ||||||||||| || |||||||||||||| | || |||||||| || |||||||| ||||||||||| | || |||||||||||||| |
gtattcagttatttaaattgatattgtctatattgtacaaggcttatgtaatgcatgggcattgaattctttattcaatgtgaaattcttctttcattgtgatgattcacagGGGGGGTTGATAATTAGTGATTCTTTGAACCACAACTCCATTGTCAATGGTGCTCGAGGATCAGGAGCTACCGTTCGAGTTTTCCAACACAATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgttactcccaaaacctatgtttttgtagctttatgtgctgccatctgtacagGGAGGGTTGATAATAAGCGATTCTTTGAACCATACTTCGATTGTCAACGGCGCTCGAGGTTCAGGAGCTACTATCCGTGTTTTCCAACACAACA
tatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatatgctgctacatcttgtgatggacacttatgttactcccaaaacctatgtttttgtagctttatgtgctgccatctgtacagGGAGGGTTGATAATAAGCGATTCTTTGAACCATACTTCGATTGTCAACGGCGCTCGAGGTTCAGGAGCTACTATCCGTGTTTTCCAACACAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT