Sequence
atgc intronic sequence ATGC exonic sequencegtaagtccaatttctaatacattcccaatccatccaccaccgaaataattcctgcatctctatcaactttctcgtctttcttctaactcttagtccattttttatgacctatcagGTTGCAGACACACAAAAGCATGCAGATATGGCAGCACACCTTGCAGTAGTTGAGTACGATTCAAGGAATATAGGAACACCAGTATTATCTGTGGAGGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------gta-agtccaatttctaatacattcccaatccatccaccaccgaaataattcctgcatctctatcaactttctcgtctttc---ttctaactcttagtccatttttta-tgacctat-----cagGTTGCAGACACACAAAAGCATGCAGATATGGCAGCACACCTTGCAGTAGTTGAGTACGATTCAAGGAATATAGGAACACCAGTATTATCTGTGGAGGATG
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gtaattcgatgattctgtctttctcgtccaccaatatatatatgcatattttgctttctgttgggtttattataaattttctttt--aatgggcgtagcatacaaacacatttgattagtttatgaactgagaagcccagttcagtcactggtcgtatatgtgtatagGTTGCAGACACACAGAAACATGCAAATATGGCTGCAAACCTTGCAGTGATCGATTATGACATGGAAAATCTGGAACCACCCATTTTATCGGTAGAAGAGG
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtccaatttctaatacattcccaatccatccaccaccgaaataattcctgcatctctatcaactttctcgtctttcttctaactcttagtccattttttatgacctatcagGTTGCAGACACACAAAAGCATGCAGATATGGCAGCACACCTTGCAGTAGTTGAGTACGATTCAAGGAATATAGGAACACCAGTATTATCTGTGGAGGATG
| ||| ||| | ||| | || ||| | | || ||| |||| | | ||| || ||| | | |||| ||| |||||||||||||||| || |||||||||||||||||| |||||||||| ||||| || || ||| | | | |||| | |||||||| || || |
----ggttgattataaatttgcttttaataggcatagcatacaaagatatttgattactttatgaactaagat-------tcccaac--ttggtcactgatatatg-tgtat-agGTTGCAGACACACAGAAACATGCAGATATGGCAGCAAACCTTGCAGTGGTTGATTATGACATGGAAAATCTGGAACCACCCATTTTATCTGTTGAAGAGG
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------gta-agtccaatttctaatacattcccaatccatccacc----accgaaata--attcctgcatctctatcaactttctcgtctttcttctaactcttagtccattttt-tatgacctatcagGTTGCAGACACACAAAAGCATGCAGATATGGCAGCACACCTTGCAGTAGTTGAGTACGATTCAAGGAATATAGGAACACCAGTATTATCTGTGGAGGATG
||| | | ||||| | || || || | | | ||| || | || | | | ||| | || | | |||| | | ||| | |||||||||||||||| || |||||| ||||||| ||| |||||||||| ||||| || || ||| | | | |||| | ||||| || || || |
gtaattccatgattctggctttcttgtccaccaatatatatatatatgtatattttgctttctgttgggtttattataaattttcttttaatgggcatagcatacaaacacatttggttagtttatgaactgagatgcccaattcagtcactggtcatatatgtttatagGTTGCAGACACACAGAAACATGCAAATATGGCCGCAAACCTTGCAGTGGTTGATTATGACATGGAAAATCTGGAACCACCCATTTTATCGGTAGAAGAGG
upper sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------gtaagtccaatttctaatacattcccaatccatccaccaccgaaataattcctgcatctctatcaactttctcgtctttcttctaactcttagtccattttttatgacctatcagGTTGCAGACACACAAAAGCATGCAGATATGGCAGCACACCTTGCAGTAGTTGAGTACGATTCAAGGAATATAGGAACACCAGTATTATCTGTGGAGGATG
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gtaattacatgatgtttttgtctttcttgtccactatatatatatatatatcttctttctgtttggttgattataaatgtacttttaatgggcatagcatacaaacacatttgattacttaataaactgagatgtcca--attcagccactgatatatgccgcatatgcgtatagGTTGCAGACACACAGAAACATGCAGATATGGCTGCAAACCTTGCAGTGGTTGATTATGATGTGGGAAATTTGGAACTGCCCATTTTATCTGTAGAAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcaactttctcgtctttcttctaactcttagtccattttttatgacctatcagGTTGCAGACACACAAAAGCATGCAGATATGGCAGCACACCTTGCAGTAGTTGAGTACGATTCAAGGAATATAGGAACACCAGTATTATCTGTGGAGGATG
ttctaac putative branch site (score: 1)
attttttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtccaatttctaatacattcccaatccatccaccaccgaaataattcctgcatctctatcaactttctcgtctttcttctaactcttagtccattttttatgacctatcagGTTGCAGACACACAAAAGCATGCAGATATGGCAGCACACCTTGCAGTAGTTGAGTACGATTCAAGGAATATAGGAACACCAGTATTATCTGTGGAGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG