Sequence
atgc intronic sequence ATGC exonic sequencegtatgatatatagcatctcattgttccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79990.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
gtatgatatatagcatctcattgttccttcttat-----tctttcgcacatcatttgttgaatct---ctgt-cctggtgttg--tgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
|| | | || || | | | || ||| || | | | |||| || ||| ||| | || | |||| ||||||||||| || ||| ||||||| || |||||||||||||| || || || ||||| ||||||||||||||||||||||| ||||| || | ||
-----gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 4
-------------------------gtatga-tatatagcatctcattgttccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
||||| |||||| ||| | | | || | | | | | | | | | || | || |||| |||| |||||||| ||| || |||| || |||||||||||||| || || |||||||| |||||||||||||||||||| || ||||| || | ||
ggcaccagtaaaagtagaaaacccattatgagtatataacatagaa--gataactcctggcaatcagaatgatgctaatgtatattttaaacttatttt---cagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
----gtatgatatatagcatctcattgttccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgt--gcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
| | ||| || | | | | || | || || ||| | | | | || | |||| |||| |||||||| ||| || |||| || |||||||||||||| || || |||||||| |||||||||||||||||||| || ||||| || | ||
gtgtccaaagcacttagattcacgtggaaagagaac-tcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
gtatgatatatagcatctcattgttccttcttattctttcgcacatcatttgttg--aatctctgtcctggtgttgt--gcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
||| | | | | | ||| || || || ||| | | | || || | |||| |||| ||||| || ||| || |||| || |||||||||||||| || || |||||||| |||||||||||||||||||| || ||||| || ||||
gtacccaaagcacttagttcacgcggagagagaacttttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 6
--------gtatgatatatagcatctcattgttccttcttattcttt---cgcacat---catttgttgaatctctgtcctg-----gtgttg--tgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
| || | | | | |||| | | || | | ||| | ||||| ||| || || |||| ||||||||| || || || || ||||||| |||||| |||||||| ||||| || ||||||||||| || ||||| || ||||| || || ||||||||| ||||
tgagtctaagaagactcaaacaagcccattactgtctacagttttctgtatgcatttgtgtttttgtgcaattatgctcatgtaaccatgttaattgcagTTCGTTCGGCTAAATTTATTGCACAGAAGCAATGGGTTGTTGCTGGTGCCGATGACATGTTCATCCGTGTGTATAACTATAATACCATGGATAAGGTCAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 5
----------------------------------gtatga-tatatagcatctcatt-gttccttcttattctttcgc---acatcatttgttgaatctc---tgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
|||| | | ||||| | | | | ||| | | | | || || | | |||| || || ||||||| ||||||| ||||| |||||||| || ||||||||||| || || || ||||| |||||||||||||| || || |||||||| |||||||| | ||
gtgggtggacgttttttagtctatttcattgatcgtatatctgcctcttgattcatttgcttgatgtcattttctttctttatatatttcatggggtctcatatgcagcatgattttgcagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 5
----------------------------------------------------------gtatgatatatagca--tctcattgt-tccttcttattctttcgcacatcat-ttgttgaatctctgtcctggtgt---tgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
| || | | || | || |||| | ||| | | | | | | | |||| |||| | | ||||||| | || || ||||| |||||||| || ||||||||||| |||||||| ||||| |||||||||||||| || || |||||||| |||||||| ||||
gtacatgaagtcatgaaccttttctggtccatttgtttgtctatatatctcttgatgcatttgcttgaagacacttttctttgtatatttcatgatttcttacttagaagaccactgaagctcttatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTCAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 5
--------------------------------------gtatgatatatag--catctcattgt--tccttcttattcttt-cgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
| || | | ||| | ||| || || || |||||| | |||| || || | | || | ||| ||||| ||||||| ||||| |||||||| || ||||||||||| || || || ||||| |||||||||||||| || || |||||||| |||||||| | ||
gtgggtgaacgttttatagtctatttcattggttgtgtatctgccttttgattcatttgcttgaagtcattttttttctttgtatatttcatgggtctcatatacagcatgattttg--cagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------gtatgatatatagcatctcattgt-tccttctta--ttctttcgcacatcatttgttgaatctctgtcctggtgt----------tgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
| ||| | | || |||| | ||| | ||||| | | | || | || | | | || | | ||||||| | || || ||||| |||||||| || ||||||||||| |||||||| ||||| |||||||| ||||| || || |||||||| |||||||| ||||
gtacttgaagacgtgaaccttttttggtccatttgtttgtatatctacctcttgatgcatttgcttgaagacacacttttctttgtatatttcatgatttcttacttagaagatcactggagctcttatacaagtatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATCCGTGTATATAATTACAACACAATGGATAAAGTCAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------------gtatgatatatagcatctcattgttccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
|||| || |||| | ||| ||||||| | | || | |||| | | | | ||| ||||| ||||||| ||||| || ||||| ||||| |||||||| |||||||||||||| |||||||||||||| ||||| || ||||| ||||||||| | ||
gtatgtacatgtactttatctgtttccatatgctctatttggtgtgattgaattcccttgatccatttttactcaat-ttctctcttattggtaaggttattacatgtttcaattttacattatcattg--cagTTAGGTCAGCGAAGTTTATAGCACGCAAGCAATGGGTTGTTGCTGGAGCTGATGATATGTTTATTCGTGTATACAATTATAACACAATGGATAAGGTTAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 5
gtatgatatata-gcatctcattgttccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
||||| ||| | ||| | || | | |||| | |||| | | ||| |||||| ||||||||||| || || || || ||||||||||| || ||||||||||||||||||||||| ||||| ||||| ||||| |||||||||||| | |
gtatgttattcatacatgacttttaatttctccagtcttggcatggtaatttcatttacatctaaggcatctgcttgcagTCCGGTCAGCAAAATTTATAGCTCGTAAGCAGTGGGTGGTTGCTGGAGCTGATGACATGTTTATCCGTGTATACAATTACAATACTATGGATAAGGTTAC
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------gtatgatatatagcatctcattgttccttctta--ttctttcgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
| | | ||| ||| ||| | | | ||| | | | | | | || || || | ||||||||| |||||||| || ||| | || ||||||||| | ||||| || |||| |||||||| ||||| ||||||||||| ||||| |||||||| | ||
gttgcatttttactttcttccagctttgtttccatttcaaagttattgatgaaattcactgaatgaagttcttctcattcactccttccgtttcttgcagTTCGATCAGCAAAATTTATTCCTCGCAAGCAGTGGATAGTAGCGGGCTCTGACGACATGTTCATTCGAGTCTACAACTATAACACGATGGATAAAGTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
ttattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatatatagcatctcattgttccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgtgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA