Sequence
atgc intronic sequence ATGC exonic sequencegtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17720.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
---------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagct--aaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| ||||||| | ||| || | ||| || | || | || || || || |||||||||| ||| ||||||||||||| ||||| |||||||| |||||||| |||| || || ||||||||| | |||||||| |||||||||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gtgagagcttctt--tctgtggcatcttttatttgttgattctg-----tgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
|||| || ||| | ||| || | ||| || | ||| || |||| ||| | ||| | |||||||| || ||||||||||||||||| || || ||||| |||||||| |||||||||||||| |||||| | | || ||||| || ||||||||
gtga-agtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
gtgagagcttctttctgtggcatcttttatttgttgattctgtg-ttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
|||||| || | || | || || ||| | ||| | | | | | || || ||| |||| ||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||| | || ||||| ||||| || |
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatgactgatacataatctagctgtactctaat---tttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
----------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccgg--ttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| | |||||| || || | | | ||| | || || | | ||| |||| |||| || ||||| |||| ||| |||||||||||||||| || ||||| |||||||||||||||| ||||| |||||||| || |||||||| ||||| |||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacat--atttt-tgctggagccaaactgatccatgtgttacttggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccgg--ttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| | | | || | ||| | || | | || || || | | |||| |||| | ||||| |||| ||| |||||||||||||||| || || || |||||||||||||||| ||||| |||||||| || |||||||| ||||| |||||
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
-------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| || | | || || || || | || | || | | | | | | |||||||| | | | ||||| |||||| |||||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||| | ||||||| |||||||||||
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggttat-attttatgtttgaacatgc--cagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
-----gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| || | | || || ||||| |||| |||| ||| || || | | | | | || || ||||| || ||| ||||||||||||| || ||||| ||||| || || |||||||| ||||| ||||||||| | |||||||| |||||||||||
gtttgataagtgatgaattatg-aatttctttctactgttttgtctgagttataa-ctggttatgctttttgtttgaacgtgccagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
-------gtgagagcttctttctgtggc-atcttttatttgttgattctgtgttgaaagctaaccac--gttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| || | | || | | | | || || | || | | | || || | | |||| || ||||| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | || |||| |||||||||||
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtgagagcttc-tttctgtggcatcttttatttgttgattctgtgttgaaagctaaccac--gttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
|| ||| | | | || | | | | || || | || | | | || || | | | |||| || ||||| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | || |||| || ||||||||
gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctcttttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
--------------gtgagagcttctttctgtggcatcttttatttgttgat-tctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| ||| || | | || | || | |||| | || | ||| | | ||| | | ||| | || ||| ||||||||||||| || ||||||||||||||||| |||||||||||||| |||||| || | ||||| ||||||||||||||
gtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------gtgagagcttctttctgtggc--atcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| |||| | | || || ||| | || | | | | || | | || | |||||||| || ||||| ||||| || ||||||||||| || || ||||| |||||||| ||||| ||||| || | || ||||| ||||| |||||
gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgt-agaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
-----gtgagagct-tctttctgtggcatcttttatttgtt------gattct---gtgttgaaagctaaccacgtta---tgttttac-ccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| | | | | ||| | ||| || || ||| | ||| | ||| || | || | || |||||| || |||||||| | |||| |||| ||||||||||| || || || || |||||||||||||| ||||||||||| || | ||||| || ||||| |||||
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG
upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
----------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
| ||| | | | | || | ||||| | ||| ||||| || || | || |||||||| || ||||| ||||| || || || ||||| ||||| |||||||||||| | ||||||||||| || | |||||||| ||||| |||||
cttcaatcaaaatataactgaaggcagaacaggggaat-tagttggttatgtttgtgtcgtttgtattgaa--ctcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAGMapped 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|116478423|gb|EG521015.1|EG521015EST: ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGG CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT
genomic: ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGGgtgagagctt ... ccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT
EST:
gi|301502468|gb|HO208008.1|HO208008EST: ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGG CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT
genomic: ATTCTGGTCCGGTCGCATCTTACCAGGTTCATGAACATCTGAGACCCAGGgtgagagctt ... ccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
agctaac putative branch site (score: 2)
ttttaccc putative PPT
ttatgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA