Sequence
atgc intronic sequence ATGC exonic sequence...tttaagtcaattcactactagttaatcctcaaccatgcattattgcatctgttaaatcatgtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32950.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 8
-tttaagtcaa-ttcactactagttaatcctcaaccatgcattattgcatctgttaaatcatgtctcata-gattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
| | | || |||| | | || | | | ||||| | | || | | | | | | || || |||| | ||||| ||||| ||||| |||||||| | || |||||||||||||| |||||||||||||||||||| || || | || || || |||||||| |||||| ||||
atgaatattaagttcatgaaca--caacaacagatttttggtgtatgcattt-tcaagtaaggacaaaaaagaagaaataattacggctgttgtttatggcagGTGAAAGTGTGGTGCACAAATCAAGAAGCAAGTGTGATCAATATTGATATGAAAGCAAATATTTGCTCGGTTAAATATAATCCTGGATCAAGCTTCTACG
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 11
tttaagtcaatt--cactactagttaatcctcaaccatgca--ttattgcatctgttaaatcatgtctcatagattaaccaattgtgctg-tgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
| |||| || ||| | |||| || ||| ||| ||| | | | | | ||| | ||| || ||||| || ||||| ||||| |||||||| | || |||||||| ||||| |||||||||||||||||||| || |||| || || || |||||||| |||||| |||
--cgatgcaataggtggaacccactaaaacagtggtttgcagcttcttgt-tctattataatgcttgtgcaatactaatggaaggtggtgctgtgtatgg--cagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
tttaagtcaattcactactagttaatcctcaaccatgc-attattgcatctgttaaatcatgtctcatagattaaccaattgtgctgtgtgtttgatc----cagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
||| || || || |||| || | || | | | ||||||| || || | | | | || ||| ||||| ||| | ||||| ||| |||||||||| | |||||||| ||||| | ||||| || |||||||||||||||||||||||||| || |||||||| || |||| || |
tttg---cattttgct--tagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
tttaagtcaattcactactagttaatcctcaaccatgcattattgcatctgttaaatcat-----gtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
| | || || | |||| ||| | | || | ||||||| || || || | | || | ||| ||| ||||| | |||| ||| ||||||| || | |||||||| ||||| | ||||| || ||||||||||||||||| |||||||| || |||||||| || |||| || |
--tttggcattttggt--tagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagc-agGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 9
-tttaagtcaattcactactagttaatcctcaaccatgcattattgcatctgttaaatcatgtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
|| | | | ||| || | ||| | || || || ||| | || | | | ||| ||| | ||||| |||||||||||||| | ||||| || || || |||| ||||| ||||||||||| ||||||||||||||||| |||||||| || |||| || |
agttcattataatcag-ggtactggggactccatattggtttgacatgctaaactaaccatagtttgtatctgttatgaacttaatgtatgtaataaacagGTCAAAGTTTGGTGCACAAACCAGGAGGCTAGCGTTCTTAACATTGACATGAAAGCAAATATATGTTGTGTCAAGTATAATCCTGGATCTAGCATTTATA
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------tttaagtcaattcactactagttaatcctcaaccatgcattattgcatctg---ttaaatc--atgtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
|| | | || | | | | || | |||||| | || | |||| | | ||| | | | ||||| | ||||| || | ||||| |||||||| || |||| ||||| ||||| |||||||||||||| || || ||||| |||||||| || || |||||||||||
gtgatttgttgaaatgttgtgattttatcactcaagtaactgatggaccttcgtttgacaaggccccttaaactggaaggtagtttttgggcttctgcatcaaggatcgaagcgaatgtgtagttgatcctgaagctttttgcattgtttcttgcagGTGAAGATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATG
upper sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------tttaagtcaattc-actactagttaatcctcaaccatgcattatt--gcatctgttaaatcatgtctcata---gattaacc---aattgtgctgtgtgtttgatc-cagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
|| | | ||| | | | |||| | ||||| | | | ||||||| | ||| | || | | ||| | | ||| || | ||||| || | |||||||||||||| || |||| ||||| ||||| || ||||| ||||| || || ||||| ||||| |||||||| ||||||| |||
gtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttatttggagttttccgcatcatgtttaatatgcggttgatccgaaatgtttttatgttactgtttgcagGTGAAGATATGGTGCACGAGGCAAGAGTCAAGCGTGATAAATATAGACATGAAGGCAAATATTTGCTGTGTGAAGTATAATCCTGGATCAAGCAGCTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctgttaaatcatgtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
ttaaatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaagtcaattcactactagttaatcctcaaccatgcattattgcatctgttaaatcatgtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - -caattca
- - - - - - - - - - - - - - tcaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - taaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaat