Sequence
atgc intronic sequence ATGC exonic sequencegtatgataaaacattcacacattttcatgttagtgtgtggaatctgattttgttgtacacacgcgtaacttcttgttcaatgttttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g24260.1 (Oryza sativa), 3'ss of exon 4
----gtatgataaaacattcacacattttcatgttagtgtg-tggaatct-------gattttgttgtacacacgcgtaacttcttgttcaatgtt-----------ttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
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gtaaatacaatcagagctttaccttttggctggtgattgcactgcagtcctacacaaggttgtcttgttgttgtgtatctgtatttgtcatatgttgatgtgcaaaattataatttcagTATGTAGCTTACGCTGAAGGATTGATACGCGCTTATAACATCCAGACATATGTTGTTCACTACACCTTGCAAC
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G39110.1 (Glycine max), 3'ss of exon 4
-------------------------------------------gtatgataaaacattcacacatttt-----catgttagtgtgtggaatctgattttgttgtacacacgcgtaa--------cttcttg--ttcaatgttttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
| || | || | |||| || | || | | | | | ||| || || | | | | ||||||| | | || ||| | ||||||| || |||||||| || ||||| ||||| ||||||||||| ||||||||||||||||| ||||| || |
gtattacttcaatatatttctggttacttttgacagggtcttgacttcatgttatatatatgtatttgtgctgcaagaaagacttagtcaccggtctttcttttaatgatacttcagttctgtccttcttgactccgttgcttttctgtcctagTATGTTGCTTATGCAGAAGGTTTGATTCGAGCATATAACATTCACACTTATGCTGTTCATTACACACTTCAAC
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G20310.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------gtatgataaaacattcacacattttcatgttagtgtgtggaatctgat--tttgttgtacacacgcgtaacttcttgttcaatgttttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
| ||| | ||| | | || | | | |||| ||| ||| || | | | | | || || | |||||| | | |||||||| || |||||||| || ||||| ||||| ||||| |||||||| |||||||||||||| |||||||| |
gtaatgttttcagtgtactttttatcatgattacattttccagtaagttcatgggatgtgcatttctgctgtaagagatttcta-gtgttgagtctcttatgtg-aatgagatacttcaatcctttctttcttgaatttgacttaattgtttttccatcccagTATGTTGCTTATGCAGAAGGTTTGATTCGAGCATATAATATTCATACCTATGCTGTTCATTACACACTACAAC
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G10590.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------gtatgataaaacattcacacattttcatgt-tagtgtgtggaatctgattttgttgtacacacgcgtaacttcttgttcaatgttttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
| ||| ||||| | || | | | |||| | | || | || | | | | || || | |||||| | || |||||||| || |||||||| || ||||| ||||| ||||| |||||||| |||||||||||||| || ||||| |
gtaatgttttcagtgtactttttttttatcatgattacattttccagtaagtccacaagatgtgtatttctgctgtaagacatttctagtgttgagtctcttatgtgaatgagatacttcaatcctat-ctttcttgaatttgacttaattgtttttccattccagTATGTTGCTTATGCAGAAGGTTTGATTCGAGCATATAATATTCATACCTATGCTGTTCATTACACGCTACAAC
upper sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s0379g00020.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------gtatgataaaacattcacacattttcatgttagtgtgtggaatctgatttt---gttg-tacacacgcgtaacttcttgttcaatgttttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
| | | || || | || | | ||| | ||||| | | || | | ||| || | ||| || ||| | ||||||||||||||| |||||||| || | ||| |||||||| |||||||| || ||||||||||||||||||||||| |
gtaacatgtttaatttggttgagattgtcctatttagcaccggatatgcatggtatcttatgtgtgcaaaccttttgattcttgcgctgatggatacgtttagcaacttttt--gcctttcat-ttttcagTATGTAGCTTATGCAGATGGTTGGATTCGAGCTTACAACATTCAAACATATGCTGTTCATTATACACTACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgattttgttgtacacacgcgtaacttcttgttcaatgttttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
gcgtaac putative branch site (score: 3)
tgttttgtcttttc putative PPT
attttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgataaaacattcacacattttcatgttagtgtgtggaatctgattttgttgtacacacgcgtaacttcttgttcaatgttttgtcttttcagTATGTAGCATATGCAGAGGGGTTGATACGAGCTTATAACATTCATACTTATGCTGTTCATTATACACTACAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT