Sequence
atgc intronic sequence ATGC exonic sequencegtattttttttgatgctcaggaagttaaaaactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
gtattttttttgatgct----caggaagttaaa------aactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
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gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttg---tcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 6
gtattttttttgatgctcaggaagttaaaaactct--ttgtgtatcacaaaaatattttcttaccctaagtttgaat---ctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
|||| | || | || || || |||| | || ||| ||| | | || | | ||| | | | | | || ||| ||||| |||||| |||||||||||||||| ||||||||| |||||||||| ||||| |||||||| ||
gtatgtgttgttggcctattgactacaagaacttgaatcttgaatcttgaaacttgtcaattgtcatttatttaactgcacactaaattttacttt--cagGTCATGATGAGATTGTTTAGTCCACGAAAAACAACATTGCTGTTTGTCATACGTGATAAAACAAGG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 6
gtattttttttgatgctcaggaagttaaaaactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
|||| || | || || || | || ||| |||| | || ||| | | ||| || ||| | ||| || ||||| |||||| |||||||||||||||| |||||||||||| ||||||| ||||| ||||| || |
gtatcattcaataacctattgactacaagcaacagtttccaatctaaaaagttgttatttatctaa---ttgcatgcttgtatttgcttt---cagGTCATGATGAGATTGTTTAGTCCACGCAAAACAACAATGTTGTTTGTCATACGTGATAAGACAAAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 7
gtattttttttgatgctcaggaagttaaaaactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
|||| || || || || | | || ||| |||| | | ||| | | ||| || ||| | ||| || ||||| |||||| |||||||||||||||| |||||||||||| ||||||| ||||| ||||| || |
gtatcattcaactacctattgattacaagcaatagtttccaatctaaaaagttggtatttatctaa---ttgcatgcttgtatttgcttt---cagGTCATGATGAGATTGTTTAGTCCACGCAAAACAACAATGTTGTTTGTCATACGTGATAAGACAAAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 6
gtattttttttgatgctcaggaagttaaaaactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
|||| | || | | || || || | | | || ||| ||| | | || | | ||| ||| | | ||||| |||||| |||||||||||||||| ||||||||| || ||||||| ||||| |||||||| ||
gtatgtgttgtcagcctattgactacaagcaattatcttgaatcttgaaacttgtcgattgacatttatttaaatgcacattcattttactttcagGTCATGATGAGATTGTTTAGTCCACGAAAAACAACATTGTTGTTTGTCATACGCGATAAAACAAGG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 6
gtattttttttgatgctcaggaagttaaaaactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtt-tggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
| ||| | | | | || | || || ||| ||| | | | || | | | | || ||| | | ||||| ||||||||||||||||||||||| |||||||| || ||||||| || || |||||||| ||
-----------gtatctctttatgctgacaattattc-tgaatctcaagagcttcagtt--------gtctaactttatgatgttatatccttacagGTTATGATGCGATTGTTTAGTCCACGAAAAACAACTTTGATGTTTGTTATTCGTGATAAAACAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
ttcttac putative branch site (score: 2)
aaaaatattttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttttttgatgctcaggaagttaaaaactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT