Sequence
atgc intronic sequence ATGC exonic sequenceAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgttcttaaaattgttaggataaatatattgtttatcctatttatgacattcaaaagttgcttacaaatttctttgatccgacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22780.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 13
AGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgttcttaaaattgttaggataaatata-ttgttt--atcctatttatgacattcaaaagttg-cttacaaatttctttgatccgacag
||||| || || ||| |||| ||||| || || |||||||| || ||||| || |||| ||| ||||| || ||||| || || |||||||| |||||||||||| | | | | | ||| | | | || | ||| | | | || ||| ||| || ||| | |
CGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGATCTGCAGgttcttgcatatttctgattgccgatagctatctcaattttgtttgttgaacttgaagtttgacttgtaattttatcag---------
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
AGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgt---tcttaaaattgttaggataaatatattgtttatcctatt-tatgacattcaaaagttgcttacaaatttctttgatccgacag
|| ||||| ||||| || || |||||||| || |||||||||||||||||||| |||||||| |||||||||||||| ||||| ||||||||| | ||||| | | ||| |||| || | ||| || || | || | |||||| ||| || | || |
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag--------
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 13
AGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgt---tcttaaaattgttaggataaatatattgtttatcctatttatga--cattcaaaagttgcttacaaatttctttgatccgacag
|||||||| ||||| || || |||||||| || |||||||| || |||||||| |||||||| |||||||||||||| ||||| ||||||||| | ||||| | | ||| |||| || | ||| || || | ||||| |||||| ||| || | || |
TGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgtgtgtttgaaacttgtagtgactatgatactgctt-cctaatttacacatcattcacaaggcattttccgtctttgtcag--------
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 13
AGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgttcttaaaattgttaggata-aatatattg------tttatcctatttatga---cattcaaaagttgcttacaaatttctttgatccgacag
|| |||||||| |||||||| |||||||| || |||||||| || |||||||| ||||||||||| || |||||||| ||||| ||||||||||| ||||| | | || || | || |||| | | | |||||| || ||| ||| | || || | | |||| | |||
GGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGACCTACAGgtgatcatcatctttcttgcatgattcattggattggtgtcttctatttcagaagtcatccaataattaatttccttgtactttacatcttcag
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 13
AGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgttcttaaaattgttaggataaatatattgtttatcctatttatgacattcaaaagttgcttacaaatttctttgatccgacag
||||| ||| | ||| | || || |||||||| ||||| ||||||||||||||||||| | || || || ||||| ||||| ||||| || |||||||| || | | | | |||||| || | | ||| |||| |
GGATGTTATCTTACAGCTTATTGAGAAGGCTGGAGATTTCGTTAGCGATGACATTTGGTACAGAGTAGTCCAATTTGTGACAAACAATGATGATCTGCAGgtgggta-------tggcgtttttttattgtc-atttaactcatgtgcttcacag-----------------------------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|301501394|gb|HO206934.1|HO206934EST: ACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAG CCTTATGCGGCATCAAAAGCAAGAGAATATATGGACAAAATTGCAATCCAT
genomic: ACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgttcttaaaa ... gatccgacagCCTTATGCGGCATCAAAAGCAAGAGAATATATGGACAAAATTGCAATCCAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgttcttaaaattgttaggataaatatattgtttatcctatttatgacattcaaaagttgcttacaaatttctttgatccgacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG