Sequence
atgc intronic sequence ATGC exonic sequenceCACTGCGGCGTAAAGGATGAAGCTTGACGTGAATGTGTTGAGATATTTATCCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAACgtcagtgctcctctctaatcgcttttttttttttaaattctggaattgacatttagggttttaaccttttgttttactttttttttctgaaaatcctctgattttttggtttttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51270.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G33320.1 (Glycine max), 5'ss of exon 1
CACTGCGGCGTAAAGGATGAAGCTTGACGTGAATGTGTTGAGATATTTATCCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAACgtcagtgctcctctctaatcgcttttttttttttaaattctggaattgacatttagggttttaaccttttgttttactttttttttctgaaaatcctctgattttttggtttttgcag
|| | | ||| |||||||||||||| |||| ||||||||| | ||||||||||||||| | |||||||||||||| || |||| ||||| || || | | | ||| | | || |||| || | | | | | ||| | | || | || ||| | | || |
GACCTTTTCATTAAGAATGAAGCTTGACGTAGATGTCTTGAGATATCTCTCCAAAGATGATTTTAGGGTTCTCACTGCTGTTGAATTGGGCATGCGGAATgt--gcgtttttctttttcccctccttttaaattccggtttaaatattattttttgagccgaaattaatgaaatt-cttccctctgttgcag--------------------------
upper sequence: AT3G51270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G04910.1 (Glycine max), 5'ss of exon 1
CACTGCGGCGTAAAGGATGAAGCTTGACGTGAATGTGTTGAGATATTTATCCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAACgtcagtgctcctctctaatcgcttttttttttttaaattctggaattgacatttagggttttaaccttttgttttactttttttttctgaaaatcctctgattttttggttt-ttgcag-
|||||||| ||||| |||| ||||||||| | ||||||||||||||| | ||||||||||| || || |||| ||||| || || | | | ||| | | | |||||||||| || ||| ||| || | || | || || |||||| | | |||| | | | ||||||
----------------ATGAAGCTCGACGTAGATGTCTTGAGATATCTCTCCAAAGATGATTTTAGGGTTCTCACTGCCGTTGAATTGGGGATGCGGAATGt--gcgtttttcttt------tcccctccttttaaattccaattttattatta------ttattattattttctgaattcttgagctgaaattaatgagattcctccctctgttgcagc
upper sequence: AT3G51270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0094g01560.t01 (Vitis vinifera), 5'ss of exon 1
CACTGCGGCGTAAAGGATGAAGCTTGACGTGAATGTGTTGAGATATTTATCCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAACgtcagtgctcctctctaatcgcttttttttttttaaattctggaattgacatttagggttttaaccttttgttttactttttttttc----tgaaaatcctctgattttttggtttttgcag------
|||||| | |||||| | || ||| |||| | ||||||||||||||| | |||||||||||||| || ||||||||| | || || |||| | | | || || |||| ||| ||| ||||| ||||| ||| |||| | ||| | | || | ||||| | | | | |
---------------AATGAAGTTGGACGTGGACGTCTTGCGATACCTTTCCAAAGATGATTTTAGGGTTCTCACTGCTGTTGAAATGGGAATGAGGAATgtatgtgcaaatt--tgagcgattctttt-----gaat------attatcattt----ttttatttctttattttgaatatttgataaagataaagagggtctgacatctccatctccacgctttcag
upper sequence: AT3G51270.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ19722 (Selaginella moellendorffii), 5'ss of exon 1
CACTGCGGCGTAAAGGATGAAGCTTGACGTGAATGTGTTGAGATATTTATCCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAACgtcagtgctcctctctaatcgctttttttttt--ttaaattctggaattgacatttagggttttaaccttttgttttactttttttttctgaaaatcctctgattttttggtttttgcag
||||||||||||||||||||| || | ||| | ||||| ||||| ||||| |||||||| ||||| |||||||| ||| || || || || ||| | ||| || | ||| | | |||| | ||||| |
----------------ATGAAGCTTGACGTGAATGTGCTGCGCTATCTCTCCAAGGATGAATTTCGTGTTCTCACGGCTGTGGAGATGGGGATGAAGAATgtaagcgcga-tctgtgatcttcttcctctttgcctgatttcttcga---gcatttcag-------------------------------------------------------------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|86074716|gb|DR370473.1|DR370473EST: CCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAAC CATGAGATTGTTCCTTCTGAGCTTGTGGAGCGCATTGCTTGTCTAAA
genomic: CCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAACgtcagtgctc ... gtttttgcagCATGAGATTGTTCCTTCTGAGCTTGTGGAGCGCATTGCTTGTCTAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACTGCGGCGTAAAGGATGAAGCTTGACGTGAATGTGTTGAGATATTTATCCAAAGATGATTTTCGAGTTCTCACTGCTGTCGAGATGGGAATGCGAAACgtcagtgctcctctctaatcgcttttttttttttaaattctggaattgacatttagggttttaaccttttgttttactttttttttctgaaaatcctctgattttttggtttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG