Sequence
atgc intronic sequence ATGC exonic sequence...tcattttacctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataaatatatgagtcctttttactttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22740.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g42020.1 (Oryza sativa), 3'ss of exon 5
----------------------tcattttac-ctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataa------atatatgagtcctttttactttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
|| || | | | | | | | || || | | || | || | || || | |||| || || ||| | | || |||| | |||||||||||| ||||||||||| || | ||| ||||| | ||| ||||| |||||||| || ||||| ||||| || || ||||||||| | ||||||
gtaaatatgcactagtagcctaacaattcatgcaatatccaatgcatcaat-ttgcgcttctatatattacattgttattaagctatataaggaaggatgtaactaacctggtaatgttgtttgaa--gGTGAAAAGTGAACTTCCAAGTACATTCAAAGCATTCCGGTATCAACAACACAGATGGTCCTGCGGACCGGCAAACCTGTTCAGGAAAATGTTGGTGGAGA
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------------------------------------tcattttacctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataaatatatgagtcctttttactttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
| || | | ||| | | ||| | || | | ||||| || | | | | || | | || | || | || | |||| ||||||||||| ||||||||||| | |||||| || |||||||| || || ||||| ||||| || ||||| || || ||||| ||| | |||||||
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttc-----agGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------------tcattttacctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataaatatatgagtccttttta----ctttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
| |||| || | | || ||| | |||| | ||| | | | || | | || |||| ||| | | || || ||||| |||||||||||||||||||||| ||||||||||||| || ||||| ||| ||||||||||||| ||||| ||||| || | |||||||| |||||||
gtatacattttttttataccaacgcgaccttattaattccaatcaattgtatatactacatgcttataatggatgatatgaagcatggttttgttaattctatcggcaata----tttatctttacattttgtgtattagtaatgttctgtttct-cattagtcatttacaaaaccaaactatgtatagGCGAAAAGTGAGCTTCCAAGTACTCTTAGAGCCTTCCGCTTCCAGCAGCATCGATGGTCTTGTGGTCCTGCTAATCTATTCCGCAAAATGGTGATGGAGA
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G08990.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------tcattttacctttttaaga-agtaaagatattttgttattactt---gttgaaaaattggtatacatcataaatatatgagtcctttttac--tttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
||| | | | | | ||| | || | |||| | || || || || ||||| | | | | | ||| | |||| ||||| |||||||||||||| |||||||| ||||||||| | || ||||| || |||||||||||||| ||||| ||| | || | |||||||| |||||||
gtgaatgaatgttccatctacttacttattagtacttccaaagtcagcaattaatgttctgcatgcaattaatggagaatattaattacatgtgattatgaattatcatttcaattttcttatactaagtcatggtgttttttttttcaatggcaactttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 5
--------------------------------------tcattttacctttttaagaagtaaa-----gatattttgttattacttgttgaaa-aattggtatacatcataaatatatgagtcctttttac----tttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
| ||| | || | | || | | || || | |||| | || | |||| || | | | || | |||||| | |||| ||||| |||||||||||||| |||||||| ||||||||| | || ||||| || |||||||| ||||| ||||| ||| | || | |||||||| |||||||
gttaatcaatgctccatctacttacctattagtacttccaaagttaacaattaacggagaatatgaatgacatatgattatgaattatcatttcaattttcttatactaagtaatggtgccttttttttaaatggtaactttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCATGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
tcattttacctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataaatatatgagtcctttttactttctttgca-tagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
| | |||| | || | ||| | ||| || | || | || || | | | ||| ||| || | || ||||||||||||||||| || |||||||| | |||||||| ||||||||||| || ||||| ||||| || || ||| | || || |||||||| |||||||
--------------gtacatttaaataaatgtcttta--agttggggaccatttcatttaaattgatagcttcttagttgatttaacggcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86052420|gb|DR348177.1|DR348177EST: TCCGAGCAAGTCTTCGCGGCTGGAAATTTCTCTACCTCGGTGACCTTCAG GTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACAT
genomic: TCCGAGCAAGTCTTCGCGGCTGGAAATTTCTCTACCTCGGTGACCTTCAGgtttttattt ... ctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACAT
EST:
gi|86052419|gb|DR348176.1|DR348176EST: TCCGAGCAAGTCTTCGCGGCTGGAAATTTCTCTACCTCGGTGACCTTCAG GTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACAT
genomic: TCCGAGCAAGTCTTCGCGGCTGGAAATTTCTCTACCTCGGTGACCTTCAGgtttttattt ... ctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaaattggtatacatcataaatatatgagtcctttttactttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
tcctttttactttctt CT-rich tract
tatacatcataaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcattttacctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataaatatatgagtcctttttactttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - aagtaaa
- - - - - - - - - - - - - - - - - - - - - - - gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cataaat