Sequence
atgc intronic sequence ATGC exonic sequencegtttgagcttactccgtgatcaatgaacaatgatgcaatgtttctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19940.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------gtttgagcttactccgtgatcaatgaacaatgatgcaatgtttctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
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gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgatt--actagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG
upper sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 9
----------------------------------------------------------gtttgagcttactccgtgatcaatgaacaatgatgcaatgttt-----ctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
| | || || || | | |||| || || || | | || | | | ||| | ||||||||| |||||||| || ||||| ||| | |||||||||||||||||| | ||||||| | | | || || ||||
gtatgcattttgcatgagatactctgactattaagtaattatatatatatatatatatatatatatatatatatatatatatatatatatatgccatcattattagctgatatgctgtgtaacacatgtattttgt-agGACGTGGAGCTAAGGAAGCCAATCTCTACACCGAGATAGCTGAAGGCATTCATGCTTATGGAATAAAAGGCCACCGGCATG
upper sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
----------gtttgagcttactccgtgatcaatgaacaa-tgatgcaatgtttc-tagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
|||||| ||| || | | | | || | ||| | | ||| | || | | | ||||||||| |||||||| |||||||||||| |||| || ||||| || || | ||||||| | || | ||||| ||||
gttcgtatttatttgagattaatcgattcattttatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
upper sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
---------------------gtttgagcttactccgtgatcaatgaacaat---gatgcaatgt--------ttctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
||| | | | | || | | | | ||| | | | || || ||| || || || |||| |||||||| |||||||||||||| ||| |||| ||||||||||||||| |||||||||| | || | ||||||||||
gttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgaacaatgatgcaatgtttctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
gactgat putative branch site (score: 3)
ttttcatc putative PPT
atatgaaattttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgagcttactccgtgatcaatgaacaatgatgcaatgtttctagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG