Sequence
atgc intronic sequence ATGC exonic sequencegtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24764.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 3
gtat-tgttcgataatctttccttggttcgat--gatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
|||| | | ||||| | | || | || | ||| ||| | | | | ||| |||||| ||| |||||||||||||| ||||||| || ||||| || || || || ||||||||||||||||||| || ||||| ||||| | ||||| ||||| || |||||||
gtatgtatcttataatttgtgtttatctgtatccgttgtctctgttttagctgatcttttctttaaca-atgataaaaaca--aatgcagAATCTAGAAGTCAAGAAGATTAATGATGAGAAAAAGGCTGCAATGGCTGCTCAGTTTGCAGCAGAAGCGACTTTGCGGAGAGTACATGCAGCCCAAAAGG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 3
gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
|||||| || | | |||| | | || | || | |||| | | | |||||||||||||| ||||||||| ||||| || || || || | ||||||||||||||||| || ||||| ||| | ||||||| ||||| || ||||| |
-------gtatctatctttatactttttaaagttgtttctgcccccctcttt---ttgattgctccctgatggagaacattttgcagAATCTAGAACTCAAGAAAACAAATGATGAGAAAAAGGCGGCTATGGCTGCTCAGTTTGCAGCAGAAGCAACTCTGCGAAGAGTGCATGCAGCCCAAAAAG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
gtattgttcgataatctttccttggttcgatgatgttcacctttc---gtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
||| || | || | || | | | || | | |||| | || | | | | | | || |||||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||| |||||||||||| | |||| |||||||||||||| ||||
gtaatgcttga-agcctctatcaagcttagcgaggagtaaatttctgaggttacgtggtgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgct-gcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
||| || | || | || | | | ||| | ||| | ||| | | || | | || || ||||||||| ||||| |||||||||||||| ||||| |||||||| ||||| ||||||||||| |||||||||||| | |||| |||||||||||||| ||||
gtaatgcttga-agcctctatcaagcttagtgagaggtaaattttttaggttacgtggtgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 3
gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctg-cagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
|||||| || | | || | || ||| || | | ||| | | ||| || || ||| |||||||| ||||| || |||||||| || |||||||||||||||||||| ||||||||||| |||||||||||| | ||||| ||||||||||| || || |
gtattgcatgaagcctctatcaactttaggaaatagtcattttcccaggttaggtggtat-gttttctgaatcgaatatttctggcagAATCTTGAAATTAAAAAAATCAACGATGAAAAGAAAGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTAGAAGGGTCCATGCTGCCCAGAAAG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 3
gtattgttcgataatctttccttggttcgatga-tgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctg-cagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
||||| | || | || || | | | ||| || | | ||| | | ||| | || || ||| |||||||| ||||| || |||||||| || |||||||| ||||||||||| ||||||||||| |||||||||||| | |||| ||||| ||||| || || |
gtatttcttga-agcctccatcaactttagtaaatagtcattttcccaggttaggtggtat-gttttctgaattaaatatttctggcagAATCTTGAAATAAAAAAAATCAACGATGAAAAGAAGGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCACGCTGCCCAGAAAG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaacc--ttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
|||||| || || | |||| | ||| | | || || | | || || | | || ||| || |||||||||| || ||||||||||||||||| |||||||| || || ||||||||||| ||||| || ||||||||| | ||||| || |||||||| || ||||
gtattgcatga-aacccttccatttttcttt---ataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
ccttgct CT-rich tract
atatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgttcgataatctttccttggttcgatgatgttcacctttcgtttcttaagcttatagacatatgatatcaaccttgctgcagAATCTAGAAATCAAGAAAATCAATGAGGAAAAGAAAGCATCAATGGCTGCTCAGTTTGCTGCTGAAGCCACTTTAAGAAGAGTCCATGCTGCTCAAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT