Sequence
atgc intronic sequence ATGC exonic sequenceCAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaattttttttcccccccccccccttttaagctctttcctgtcttcccgaggttacagtgttaatcaattgctcttttctttttgtctcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46210.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 5'ss of exon 12
CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaattttttt--tcccccccccccccttttaagctctttcctgtcttcccga-ggttacagtgttaatcaattgctcttttctttttgtctcag
||||| ||| | || ||||||||||| ||||| || |||||||| ||||| ||||| ||| | |||||||||||||| || || || || || |||||||| | | |||| | | | || | |||||| | | ||| | | | | | || ||| || ||
TAGTGGAAGGCGTTTGATGTGGCAAAACTCATTGGGTCACTGTGTATTAAAAGCAGAGTTCCCAAAAGGTAAAAAGGAACTTGCGGTGTCACTATTTCAGgtagggttatttttcccaatttctttggtggtttattgtagctgtaactgtctgatcaataattagaaaatcactgatttattctgtttttcag-------
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA13G29010.1 (Glycine max), 5'ss of exon 13
CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtc-------aaattttt-tttcccccccccccccttttaagctctttcctgtcttcccgaggttacagtgttaatcaattgctcttttct--ttttgtctcag
||||| ||| | | |||||||||||||||||||| |||||||| ||||||||||| || | ||||| ||||| ||| ||||||| ||||| |||||||| | | |||| || | | | | | | ||| | ||| || | | || ||| || |||| | | || || || |||
TAGTGGAAGGCGTCTGATGTGGCAAAATTCATTAGGTCACTGTGTCTTAAAGGCAGAGTTTCCTAAAGGGAAAAAAGAGTTGGCTGTCTCCCTATTTCAGgttggcctgttataaaatcattatctatattttcatttatatcatagtctatattgtgttgcacatatttttctgt-gattaattctgcatgcctggttgtgctccag
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA15G10030.2 (Glycine max), 5'ss of exon 12
CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtc------aaattttttttcccccccccccccttttaagctctttcctgtcttcccgaggttaca---gtgtt-----aatcaattgctcttttct--ttttgtctcag
||||| ||| | | |||||||||||||||||||| |||||||| |||||||||| || | ||||| ||||||||| ||||||| ||||| |||||||| | | ||| || || | ||| | | || |||| | ||| || |||| || |||| | | || || || |||
TAGTGGGAGGCGTCTGATGTGGCAAAATTCATTAGGTCACTGTGTCCTAAAGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAGgttggcctgttataaaccattgtttttcttttaaaattttcatttttattgtagtctatcttgtgttgcacacatgtttctgtgattaattctgcatgcctgattgtgctccag
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA08G10180.1 (Glycine max), 5'ss of exon 12
CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaattttttttcccccccccccccttttaagct--ctttcctgtcttcccgaggttacagtgttaatcaattgctcttttcttt---ttgtctcag--------------------
|||||| || | ||||||||||||||| |||| |||||||| || |||||||| || ||||||| | ||||||| ||||||| ||||| |||||||| ||| || || | | | | ||| | |||| | || | | || ||| | | ||| ||| || || |
CAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgtttcaaaaaccattatttaaaatgttaaaatctccatttgtttttgcagtctatcttagcatcttttattgcacaaatttccatttttttaaattaattctgcatgcctggctgtcctctag
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA05G27240.1 (Glycine max), 5'ss of exon 12
CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaattttttttcccccccccccccttttaagct--ctttcctgtcttcccgaggttacagtgttaatcaattgctcttttctttttgtctcag-------------------------
|||||| || | | ||||||||||||||| |||| || ||||| || |||||||| || ||||||| | ||||||| ||||||| ||||| |||||||| ||| || || | | | | ||| | || | | || | | || ||| | | ||| ||||| | | |
CAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAGgtttcaaaaaccattatttaaaatgttaaaatctccatttatttttgcagtttatcttagcatcttttattgcacaaatttccatttttttttatattaattctgcacgcctggctgtcctccag
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 5'ss of exon 12
CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaatttt----ttttcccccccccccccttttaagctctttcctgtcttcccgaggttacagtgt----taatcaattgctcttttctttttgtctcag--------------
|||||| ||| | |||||||||||||| |||||||| ||||||||||| || ||||| || | |||||||||||||||||||| ||||| || |||||||| ||| | | || | |||| | | ||||||| || | | ||| | | | ||||| | || | | |
CAGTGGGAGGCGATTAATGTGGCAAAACTCATTAGGACACTGTGTTTTGAAAGCAGAGTTTCCAAAAGGTAAAAAGGAGCTGGCAGTTTCTCTATTTCAGgttggtcttttctagacacttgtttattctttttctttccatgtttttcctgagttttattaatccctgtgcacaatgctttagtgctcaagttttagcattttgggggtgtgtctgcagMapped 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|125045817|gb|EL118086.1|EL118086EST: AGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAG GCTGTTGTGTTAA
genomic: AGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaa ... tttgtctcagGCTGTTGTGTTAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaattttttttcccccccccccccttttaagctctttcctgtcttcccgaggttacagtgttaatcaattgctcttttctttttgtctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT