Sequence
atgc intronic sequence ATGC exonic sequencegtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgatatggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09100.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 9
---------------------------gtatgcatatatcttt-cgtcttagtggttgtaactttaggatgtggatgatatggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT
|||| | || | | | | ||| | | | ||| |||| || | || |||||||| || ||||||||||||||||| || || ||||| |||||||| ||||| | || || ||||| ||||| ||| || || | | |
attgctgctttgactttgtcaatcctgaagcgcatgcaactgtatataggaacaatcataatgtattgctttggctgatcct-------tgtccatcgttcacgcagGTGACACACGAGGATTTCAATGAAGGGATCATACAAGTGCAAGCCAAAAAGAAGTCCAGTTTAAATTATTACGCTTAATTCTTCCGAGAGAGTTATTAGG
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
-------gtatgcatatatctt---tcgtcttagtggttgtaactttaggatgtg-gatgatatggagga--------aatggtaaatgtgtg--tgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTT-TATGTACACTCTT
|||| | || ||| ||| ||||||| | | ||| | | || || | | |||| | ||| ||||||||||||||||||| || |||||||| || || ||||| ||||| ||||||||||||||||||||||| || || || | ||| | | | | |
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG-
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 9
----------------------gtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgat-atggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT-
| | ||| || || || ||| | | || | | | || | ||| | | | | | | | |||||||||||||||| || ||||||||||| |||||||| ||||| ||||||||||||||| | ||||| || || || | |||| | ||| ||
cagtgtcaattgtcaaagctccacaccaacttataatttgtttt-gtgtattttacctgatgttg-gaatgttcgtaaaatctgtttttgttccaaacgtagGTGAACCATGAGGACTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGCCTCAATTATTATGCATAGGCTGGATTTTG-GAACAAGCTAT
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 9
----------------------gtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgat-atggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT-
| | | | || || ||| || || | | | | || | ||| | || | | | | | |||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||||| |||| || || || || | || | | ||| ||
ttcttttcagtaacaaaactccagaccaacttgtaatttgttttatatatttta-cctgatgttg-gaatgttcgtgaaatctgtttttgttccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTG-GAACAAGCTAT
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 6
------gtatgcatatatctt---tcgtcttagtggttgtaactttaggatgtg-gatgatatggagga-----aatggtaaatgtgtgt------gcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT
|||| | || | | |||| |||||| | | ||| | | | || | | || | | | | ||| |||||||||||||||||| || ||||||| || || ||||| ||||| |||||||||||||||||| |||| || || ||
gcaattcaatgccaaagctttggaccatgttagaatttgtaatatgaatgtgtctgcttacgtgaaaaatcattaagtatgattttttgtccaattgcagGTGAACCATGAGGACTTTGATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGGATTATTATGCATAG----------------------
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
-------------gtatgcatatatcttt-cgtcttagtggttgtaa-ctttaggatgtggatga-tatggag-gaaatggtaaatgtgtgtg----cagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAG-TCCTCTTTTATGTACACTCTT
|| | || || | ||| || || | | || || ||| | | || | | | || |||| || || ||||||||||||||||| ||||| |||||||||||||||||||| |||||||||||| ||||||| ||||| || || || | | ||| | | | |
agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT-
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------gtatgcatatatctttcgtcttagtgg----ttgtaactttaggatgtggatgatatggaggaaatggtaaatgt-gtg-tgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT-
| | |||| | | | | || | | | ||| ||| | | | | | || |||| || | ||||| | |||||||||||||| || ||||| | |||||||||||| || |||||||| || | ||||||||||| ||| | | | |
ttatccttttctgtattgtttatatttggtatgccacagaaacacatctttatttttggaggcttctacacactattgacttttatatgttatgctacagGTAACTCATGAGGATTTCAACGAGGGTATCACTCAAGTACAAGCTAAAAAGAAAGCCAGTCTCAATTACTACGCATAAACATTAGTCCTCA-ATGTCTTGA
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 9
gtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgatatggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT
|| | | | | | | | || | | ||||| | || ||||| ||||| || || || || ||||| |||||||||||||| || |||||||| |||||||| | || | |
-----------------------gtaac-gacgcgtgatcgaatacacagctttttcgatctcactcgctctttcacagGTTACGCACGAGGACTTCAACGATGGCATCATCCAAGTGCAAGCCAAGAAGAAGGCCAGCTTGAACTACTACGCATGAGCAAATCATAGAAGGGATAGAA
upper sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 9
gtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgatatggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT
|| | | | | | | | || | | ||||| | || ||||| ||||| || || || || ||||| |||||||||||||| || |||||||| |||||||| | |
-----------------------gtaac-gacgcgtgatcgaatacacagctttttcgatctcactcgctctttcacagGTTACGCACGAGGACTTCAACGATGGCATCATCCAAGTGCAAGCCAAGAAGAAGGCCAGCTTGAACTACTACGCATGA---------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttgtaactttaggatgtggatgatatggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT
ttgtaac putative branch site (score: 2)
taacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgatatggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT