Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttttatcaatctctgattttccaaagattaagattagtttgattaaaatttcttcatcctctttgttttcagGCCAGAGTCATTGGGTATTGTTGTTGGTATTGTCTTTTTGATCGTGGCGATAATATTTCAGTATTTTAACTTCACTGAAGATTCTAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41490.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G34640.1 (Glycine max), 3'ss of exon 1
--------------------------gtgagtttttatcaatctctgattttccaaagattaagattagtttgattaaaatttcttcatcctctttgttttcagGCCAGAGTCATTGGGTATTGTTGTTGGTATTGTCTTTTTGATCGTGGCGATAATATTTCAGTATTTTAACTTCACTGAAGATTCTAAT
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agtatttatatgtcttgtatgcataggagggaaagtattgtaatctgctatcataaatttttgg--tactaagttttga--ttgtgctacctttttcttcgcagGCCTGAGTCATTAGGTATAGTTGTTGGTATTGTCTTCTTGGTTGTGGCAATCTTGTTTCAGTATTTTAACTTCACAGCAGATTCGAAT
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 1
------------------gtgagtttttatcaatctctgattttccaaagattaagattagtttgattaaaatttcttcat----cctctttgttttcagGCCAGAGTCATTGGGTATTGTTGTTGGTATTGTCTTTTTGATCGTGGCGATAATATTTCAGTATTTTAACTTCACTGAAGATTCTAAT
|| | || | | | || | ||| | | ||| ||| | || ||| || ||| |||||| || ||||| ||||| |||||||||||||| || ||| | ||||| || | |||||||||||||||||||| |||||| |||
gatgtatttatgtcatgtatgcataggagggaaagtattgtaatctgccatcataaatttttggtactaagttttgattatgctaccttattctttgcagGCCTGAATCATTAGGTATAGTTGTTGGTATTGTGTTCTTGGTTGTGGCAATCTTGTTTCAGTATTTTAACTTCACATCAGATTCAAAT
upper sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 1
--------------------gtgagtttttatcaatctctgattttccaaagattaagattagtttgattaaaatttctt-catcctctttgtttt-cagGCCAGAGTCATTGGGTATTGTTGTTGGTATTGTCTTTTTGATCGTGGCGATAATATTTCAGTATTTTAACTTCACTGAAGATTCTAAT
| || | || | | | |||| || | | ||| | |||| || || | | ||| || |||||| || ||| |||||||||||||||| |||||||| ||| || |||| || |||||||||||||||| ||||| |||||| |||
aaatagaagctaagagcttgatatgtatctaatatttgcctcctttcttttttatatcaatgctttatcttgaattactggtattatttctgtcttgcagGCCTGAATCACTGGGTATTGTTGTTGGGATTGTCTTCTTGGTCTTGGCAATCTTATTTCAGTATTTTAATTTCACATCAGATTCAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccaaagattaagattagtttgattaaaatttcttcatcctctttgttttcagGCCAGAGTCATTGGGTATTGTTGTTGGTATTGTCTTTTTGATCGTGGCGATAATATTTCAGTATTTTAACTTCACTGAAGATTCTAAT
gtttgat putative branch site (score: 5)
tttcttcatcctcttt putative PPT
aaagattaagattagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttttatcaatctctgattttccaaagattaagattagtttgattaaaatttcttcatcctctttgttttcagGCCAGAGTCATTGGGTATTGTTGTTGGTATTGTCTTTTTGATCGTGGCGATAATATTTCAGTATTTTAACTTCACTGAAGATTCTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA