Sequence
atgc intronic sequence ATGC exonic sequencegtaataactcttttctcctgttttgtcattagatcagtttttttaatggtatccatataacatatctatgttccagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACCGAGACCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g20150.1 (Oryza sativa), 3'ss of exon 5
gtaataactcttttctcctgttttgt-cattagatcagtttttttaatggtatccatataacatatctatgttc-cagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACCGAGACCC
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gtggtgatccctttctgcagttttgaacaatctcttcattggattactttacttagtttgatcttttcatgtcgacagCAAGAAATCAAGCATACTATACAAAACAAACTTCATCGTAATGCTGGACCTGAGGATCTTATTGCTACAGAAGTCATGCTTGCTAGGATTACTAAGACCC
upper sequence: AT5G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G44540.1 (Glycine max), 3'ss of exon 4
---------gtaataactcttttctcctgttttgtcatt--agatcagtttttttaatgg--tatccatataacatatc---tatgttccagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACC-GAGACCC-----------
| | | ||| || | ||||| || ||| | || |||| | | | ||| ||| ||| ||||| | ||| |||||||| |||||||| ||||||||||| |||||||| || |||||| | |||| |||||||| |||||| |||| || || ||||
gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctccagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
upper sequence: AT5G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0062g00890.t01 (Vitis vinifera), 3'ss of exon 4
------------gtaataactctt---ttctcctgttttgtcattagatca-gtttttttaatggtatccatataacatatctatgttccagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACCGAGACCC
|||| | | | || | ||| | | || | ||| ||||| ||| | ||| || ||||||||||||||||| || |||||||| ||||| ||||| |||||||| ||||||||| | |||| ||||| ||||||||| | ||||||| || ||
gttgtattaattataatgagtggtgaattggttcttaatgttttcaaataaagttgcattaat--tatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtcattagatcagtttttttaatggtatccatataacatatctatgttccagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACCGAGACCC
atataac putative branch site (score: 3)
atcagtttttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataactcttttctcctgttttgtcattagatcagtttttttaatggtatccatataacatatctatgttccagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACCGAGACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA