Sequence
atgc intronic sequence ATGC exonic sequence...cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09840.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
cgtattcagtatagaagaaagcagtaacctttggattgctcag-tctgatttcgaggaaaccttggttttcttattt-catttgctttgata-tgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| || | || || | || | | | | || | | | ||| | || | | ||| | | ||| | | |||||||||| ||||| |||||||||||||| ||||||||||||||||| ||||| || || || || || || || || || |||||||||||||||||
-----------------gtaacatttttctatgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 9
-cgtattcagtatagaagaaa-gcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| || || | | | | | | | || | | ||| ||| ||| || | | | ||| | || || |||||||||| ||||| |||||||||||||| |||||||||||||| ||||||||||| || || ||||| || || || ||| ||||||| |||||||||
gtgattttcttacggtatccatatgaccatatctctactgttttg-ctgccttcttttgcaccatgacatattgagg-catagcatctg---catcttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 8
-----cgtattcagtatagaagaaagcagtaacctttggatt-gctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
|| ||| | | | | | | | || | | | | | | | | | | || ||| || | |||| | | | |||||||| || || ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| |||||||||||||||||||||||||||
ttaggtttaccaagttctgtc-attgttctgatataaagttttgtagactattttcccaatggagtcatgaaca----attacaatc-taatgatttttatttcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCATGGCACAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9
-------cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| || || | | || |||| | | ||| | | | | | | | | || ||| || | |||| | | |||||||| || || ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||
ggttttccaagttttgtcattgttctaatataaagttttgta--gttcactattctcccaatggagtcatgaaca----attacaatc-taatgatttttatctcagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 8
---cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| ||| | || | | | || || || ||| | | ||||| ||| | | ||| ||| || || || || ||||||| || || ||||| || ||||| || || || || |||||||||||||| || |||||||| || || || ||||| ||||||||||||||||||
atgctacttctatttacagaatttttgaaagctc-aaatctgtcatttaaacccaaaggaagcctcagaataag-attccatgtgtttaaat-tgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------cgtattcagtatagaagaaagcagtaacct-ttggattgctcagtctgatt-tcgaggaaaccttggttttct--------tatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| | || | | | || | | | | ||||| | ||| | | | || | || | || ||| | ||| | | | |||||| || || ||||| || | || || ||||||||||||||||| ||||| || || || ||||||||||| || || |||| |||||||||||
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgag----gaaaccttggttttctt--atttcattt--gctttgatatgtcat---------gcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| || | | ||| | | ||| ||| | || || ||| || | | |||| | | || || | | | || |||| | | | ||||||||| || ||||| || | || || ||||||||||||||||| ||||| ||||| || |||||||| || || || | || || ||||||||
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttgg-cggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| | ||| | ||| | | |||| ||| | | || || | | ||||||| ||||||| |||||||| || || | || |||||||| ||||||||||||||||| || || |||||||| || ||||| ||| | ||||| |||||||||
----------------gtacgcatgcattcttgctcttttttttctgttttttttgcgagtcgctcttgctcaa--gacttgcttt---------tgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
| | ||| | ||| | | ||| || |||| |||| || | | ||||||| ||||||| |||||||| || || |||| |||||||| ||||||||||||||||| || || |||||||| || ||||| ||| | ||||| |||||||||
----------------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttg-----ctcaa--gacttgcttt---------tgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
ttttcttatttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtattcagtatagaagaaagcagtaacctttggattgctcagtctgatttcgaggaaaccttggttttcttatttcatttgctttgatatgtcatgcagGTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT