Sequence
atgc intronic sequence ATGC exonic sequence...aaatttcaaggcaaatcaggactagtgtatgtcatttatatattggataatgttttcatctgaatctgctgaactttcttgcatgatattggtcctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46210.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G10030.2 (Glycine max), 3'ss of exon 3
aaatttcaaggcaaatcaggactagtgtatgtcatttatatattggataatgttttcatctgaatc-tgct---gaactttcttgcatgatattggtcctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
| | |||| | | | || | ||| | | | |||||| | ||| || |||| || | | | ||| || ||||| || |||| ||||| |||| |||||||||||||||||||||||| |||||||||||| |||||||||||||| || |||||||||
----ctgattgcaattatagtttctctctcagtataggaaaattagctggcagatccatctgtgttgtgccttagatttttcacttatatgtcttgcttttcagAAAAGGTGAAGCAGTGGATAGAACTCTTCTAAACCATCTTTTGAAGATGTTTACTGCTCTGGGAATTTATGCAGAAAGCTTTGAGAAGCCATTCCTTGAA
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 3
aaatttcaaggcaaatcaggactagtgtat-gtcatttatatattggataatgttttcatctgaatctgc--tgaacttt---cttgcatgatattggtcctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
| | ||| | | | | | || | || | | | |||||| | | | | ||| ||| || | ||| | | ||| || ||||| || |||| ||||| |||| ||| |||||||||||||||||||| |||||||||||| |||||||||||||| || |||||||||
-----cttattccaattattctttctctctcagtataggaaagttagctggcagatccatctgtgttgtccttagatttttcacttttattgttttgctttt-cagAAAAGGTGAAGCAGTGGATAGAACTCTTCTAAACCACCTTTTGAAGATGTTTACTGCTCTGGGAATTTATGCAGAAAGCTTTGAGAAGCCATTCCTTGAA
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 3
aaatttcaaggcaaatcaggactagtgtatgtcatttatatattggataatgttttcatctgaat--ctgctgaactttcttgcatgatattg---gtcctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
| || || || | || | | ||| ||| || || | | | | | || | ||| | | || ||| | | ||| | || ||| | || |||| ||||| |||| ||||||||||||||||||||||| |||||||||||| | |||| ||||||||| || ||||||||
----tacagggaggtggctagctgatccatct-gtatatgaattagaccatttaattcttcaacttactcttagtcttacattttcaattttgtctgattttcagATCAGGCGAATCAGTGGATAGAACTCTTCTAAATCATCTTTTGAAGATGTTTACTGCTCTGGGAATTTATGTAGAAACCTTTGAGAAGCCATTCCTTGAG
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 3
-aaatttcaaggcaaatcaggactagtgtatgtcatttatatattggataatgttttcatctgaatct--gctgaactttcttgcatgatattggtcctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
| | | | | | ||||| | | ||| | ||||| | |||| || | ||| | || || | | || | | ||| | || ||| | || |||| ||||| |||| ||||||||||||||||||||||| |||||||||||| |||| ||||||||| || ||||||||
gcagggagttgactagctattccatctgtatatgaattaggccat--ataat-tcttcaacttactctaagtcttacattttcaattttgtctgatttttcagATCAGGTGAATCAGTGGATAGAACTCTTCTAAATCATCTTTTGAAGATGTTTACTGCTCTGGGAATTTATGCAGAAACCTTTGAGAAGCCATTCCTTGAG
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 3
-aaatttcaaggcaaatcaggactagtgtatgtcatttatatattggataatgttttcatctgaatctgctgaactttcttgcatgatattggt--cctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
|| | | | || | || | || | | || || | | || || | || | || | | | |||| |||| | || ||| |||| ||||| || |||||||||| || | ||||||||||||||||||||||| || ||||||||| ||||||| |||||||| || ||||| ||
aggatgtttggatgatccattgttcttgacta--gcttctttgttaaatgttctatttattt-aacattttgtaatgtagagcattctatttttggtcttcagATTAGGTGAAGCAGTAGATAGGACTCTCCTTAATCATCTTTTGAAGATGTTTACTGCTCTAGGAATTTATTTGGAAAGTTTTGAGAAGCCATTCCTCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataatgttttcatctgaatctgctgaactttcttgcatgatattggtcctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
atgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatttcaaggcaaatcaggactagtgtatgtcatttatatattggataatgttttcatctgaatctgctgaactttcttgcatgatattggtcctgcagGTTAGCAGAAGCTGTTAATAGGACTCTACTAAGCCATCTTTTGAAGATGTTTACTGCACTGGGAATTTATATGGAAAGCTTTGAGAAACCTTTCCTTGAA
- - - - - -caaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctga