Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaaaaacctcaagctactgaaatattttggtgctttgttgtgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G26670.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
gtaa--aaaaaaacctcaagctactgaaata--ttttggtgctttgttgtgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgct-tctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
|||| || || || || ||| | || | || ||||| | | ||| | | || | || | | | | ||| | | || | ||| |||||| | |||||||||||||| ||||||| | ||||||||| || || |||||||||||||||||||||||||| || || || || || |||||||
gtaattaagctaattgcaggc-actaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttctctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
upper sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 6
gtaaaaaaaaacctcaagctactgaaatattttggtgctttgtt-gtgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
|| | ||| ||||| || | | | ||| | ||| ||| | | ||| |||||| ||||||||||||||| ||||| ||| ||||||||| || || |||||||||||||| ||||||||||| |||||||| |||||||||||||
--------------------gtatggctaacctaatgcgttgttcatgaggctactctgctgctcttatttgtctaattcaactccatatgc-cctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG
upper sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G477146_T02 (Zea mays), 3'ss of exon 9
gtaaaaaaaaacctcaagctactgaaatatttt----ggtgctttgttg-tgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
| || ||| || | || | | || | || ||| ||| ||| | ||| || | || || ||| ||| ||| |||||| ||||| ||||||| || |||| ||| ||||||||| || || |||||||||||||| ||||||||||| |||||||| || ||||||||||
-------gtatggctaacctaatgtgttgttcctgaggctactccgctgctgctgttttc-ctacgtcgttgtctaattcaa---gttccgtatgc-cttatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG
upper sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G26550.1 (Glycine max), 3'ss of exon 10
-----------------gtaaaaaaaaacc-tcaagct--actgaaatattttggtgctttgttgtgccg-----ttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgtt--gcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
||||| | | ||| | | | | || || |||| || | |||| || | | || | || || | | | | | || ||||||||| || |||||||||||| |||| | | |||||||||||| || ||||| ||||||||||| | |||||||||||||| ||||||||||||| |
gtaaggctttttctttggtaaagattctttgttgggctttatcaatttgtgctgatgttttgatggggtaactttttgaagttaatttatgacaaatgtgaatgctaacccggtcttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAACATGGACTTTCTTCTCAATCTGTACAGGATTTA
upper sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G07510.2 (Glycine max), 3'ss of exon 10
-----------------gtaaaaaaaaacc-tcaagct--actgaaatattttggtgctttgttgtgccg-----ttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgtt--gcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
||||| | | ||| | | | | | || |||| || | |||| || | | || | || || | | | | || ||||||||| || |||||||||||| |||| | | |||||||||||| || ||||| ||||||||||| || |||||||| ||||| || |||||||||| |
gtaaggctttttcttgggtaaagattctttgttgggctttatcaatttgtgctaatgttttgatgaggtaactttttgaagttaatttttgacaaatgtgaatgctaacgaagccttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAGCATGGACTTTGTTCTCAATATGTACAGGATTTA
upper sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 9
-gtaaaaaaaaacctcaagctactgaaatattttggtgctttgttgtgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
| | ||||| ||| || ||| | | |||| | | | || | || | || || | | | | | || || || |||||||| |||| ||||| ||||| ||||| | | |||||||||||| || ||||| |||||||| |||||||||||||||||||| || ||||||||||
agagagaaaaagaaaaaagaaacaaaaaaaaatcaatgctgcaattggttg--gacatgttaaattttgcaaacaactgatatatattat---ctccttctgcagATGGCAAGGTTGAACGAAGGGTTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAAATTGCTTGGACTTTCTTCTCTATTTGTACAGGATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
cttctgtt CT-rich tract
tatatagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaaaaacctcaagctactgaaatattttggtgctttgttgtgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgcttctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG