Sequence
atgc intronic sequence ATGC exonic sequenceTGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09090.2 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 5'ss of exon 11
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgc----aagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
|||||||||||| ||||||||||| |||||||||||||| | || |||||||| || ||||| |||||||| || || ||||| |||||||| ||||||| | || | || || || | | | ||| | | ||||| | || | ||| || | | ||
TGATAATGTTGATGGTGGAGATGACCTCGATCTTATTGTTACTACCATGAATGGCAATGTCTTCTGCTTCTCCACTCCCTCTCCGCACCATCCACTTAAGgtacatagcatgtttttttatgtcaataatttagagtaaattacacaaaaccataggtattgtgtcc-aagttacacaaaaccacaggagttttggcacgt---------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G479744_T01 (Zea mays), 5'ss of exon 7
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
|||||| || || ||||||||||| || ||||||||||| | ||||||||||| |||||||| |||||||| || | || || |||||||| ||||||| | | ||| | | | ||| | || | || ||| | | | | | | | | ||| || || || ||| | || | | |
TGATAACGTGGATGGTGGAGATGACCTTGATCTTATTGTTACCACTATGAATGGCAACGTCTTCTGCTTCTCCACTCAATCACCACACCATCCGCTTAAGgtagg--caatctg----tttctttaggtattcattttactttacag---tataacacatctcggataaagcattaatctctcggttaaccctttgcaacctatatgct---
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA01G27250.2 (Glycine max), 5'ss of exon 11
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
|| || ||||| ||||| |||||||| ||||| |||||| ||||||||||||| || ||||| ||||||||||| || |||||||| |||||||| |||||| ||| || | || || | || | | | || | ||| || || |
AGACAACGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACTATGAATGGCAATGTCTTCTGCTTCTCAACCCCGTCTCCTCATCATCCCCTAAAGgcaggatatgtttgtaatttgatcattgaaacaactttggttgttac----tgaatggctttatacgttgtttcag------------------------------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA03G14690.1 (Glycine max), 5'ss of exon 13
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
|| |||||||| ||||| |||||||| ||||| |||||| |||| |||||||| || ||||| ||||||||||| || |||||||| |||||||| |||||| ||| || | || || | | | | || | ||| || | || |
AGACAATGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACAATGAATGGCAATGTCTTCTGCTTCTCAACCCCATCTCCTCATCATCCCCTAAAGgcaggatatgtttgaaatttgatcattgaaacaacctcggtt--ttgttactgaatggctttatacattgtttcag------------------------------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 5'ss of exon 11
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
|| |||||||| |||||||||||||| ||||||||||| |||| |||||||| || || |||||||| ||||| ||| |||| || |||||||| |||||| ||| |||| |||| |||| | || || || | | ||| || | ||| | | | | || || || ||| | || | || |||
GGACAATGTTGATGGTGGAGATGATCTTGATCTTATTGTTACAACCATGAATGGCAATGTATTTTGCTTTTCAACTCCTGCTCCACATCATCCCCTCAAGgcaggatagacccaaaactgaatttt--atttttttgtgtataaattttatttcataggtttgtgat-tcataaaggtttctaatatcatattttacac-----ttttccag
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ23254 (Selaginella moellendorffii), 5'ss of exon 11
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
|| ||||||||||| || || ||||||||||| || || |||| |||||||||||||||| || ||| ||| || ||||| ||| | |||| | || | ||| | | | | ||| || ||| |
GGAGAATGTTGACGGAGGCGACGATCTCGATCTGATAGTTACAACCATGAATGGAAACGTCTACTGTTTCCAAACCCCAGTGAAACACCACCCCTTGAAGgtatgaatgtgcattgcctcgtgtattcaaagtgatcttatctccatttgcag-----------------------------------------------------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ25263 (Selaginella moellendorffii), 5'ss of exon 11
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
|| ||||||||||| || || ||||||||||| || || |||| |||||||||||||||| || ||| ||| || ||||| ||| | |||| | || | ||| | | | | ||| || ||| |
GGAGAATGTTGACGGAGGCGACGATCTCGATCTGATAGTTACAACCATGAATGGAAACGTCTACTGTTTCCAAACCCCAGTGAAACACCACCCCTTGAAGgtatgaatgtgcatagcctcgtgtattcaaagtgatcttatctccatttgcag-----------------------------------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125002199|gb|EL074468.1|EL074468EST: ATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAG GCTTGGAGATCTAGTGAT
genomic: ATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaa ... aattcatcagGCTTGGAGATCTAGTGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATAATGTTGACGGTGGAGATGATCTCGATCTTATTGTCTCAACTATGAATGGAAACGTCTTTTGCTTCTCAACGCCTTCTCCTCACCATCCCCTTAAGgcaagatcaaccccgaactctatttgcgagcgggttctgctcaacatctctttgattgttttttaaaatgggggaaattactgatttcacacttggttcccgaattcatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC