Sequence
atgc intronic sequence ATGC exonic sequencegtaagataatacgatcacacttgtgttttgatctctttgaacaacatgaagtgtggttgtatagtttatttcattttgtcacttagctggtacatgcgagacacatataaacgaggactcaaaaactttcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 2
gtaagataatacgatcacacttgtgttttgatctctttgaacaacatgaagtgtggttgtatagtttatttcattttgtcacttagctggtacatgcgagacacatataaacgaggactcaaaaactttcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
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-----------------------------------------------gtaagttcattaaattatcatatccattat-tcactttatttttctgtgaaaagcagatttg---------ttactttgctttttcttccgtc-agGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAG
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 3
gtaagataatacgatcacacttgtgttttgatctctttgaacaacatgaagtgtggttgtatagtttatttcattttgtcacttagctggtacatgcgagacacatataaacgaggactcaaaaactt--tcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
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--------------------------------------------------gtaagttcat-taggttctcatatcccaattattcactcttttttttttctctctctgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g01370.t01 (Vitis vinifera), 3'ss of exon 3
gtaagataatacgatcacacttgtgttttgatctctttgaacaacatgaagtgtggttgtatagtttatttcattttgtcacttagctggtacatgcgagacacatataaacgaggactcaaaaactttcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
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--------------------------------------gatcatagttactgagcatcattcagattgtaatgtgctttgagtttgatcgccgttatgata-gttcttacaccatcattcgga----ttctcttcttggtcagGCATTGGCTATAATGGGTTCCCAAGAGGCTGTTCAGATGACAAGCTCCCTTGGGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtacatgcgagacacatataaacgaggactcaaaaactttcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
ctttcatctttcattt CT-rich tract
acatataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagataatacgatcacacttgtgttttgatctctttgaacaacatgaagtgtggttgtatagtttatttcattttgtcacttagctggtacatgcgagacacatataaacgaggactcaaaaactttcatctttcatttagGGATTGGCTATAATGGTTTTCCAAGAGGCTGCTCTGATGACAAACTTCCTTGGGCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT