Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatattattagtgtactgccatatactttactgagtggaattcatttttattcttggtttgtcggaccagtacatgaccattaagtctctgtacaagaaaactattaggcatcagctagtttaagatattatatgataatgttgtctctgcttaagcaaatgttggtggttgtgatttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34890.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 7
gtaagcatattattagtgtactgccatatactttactgagtggaattcatttttattcttggtttgtcggaccagtacatgaccattaagtctctgtacaagaaaactattaggcatcagctagtttaagat-attatatgataatgttgtctctgcttaagcaaatgttggtggttgtgatttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
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------------------------------------------------------------------------------------tgtgtgtgagtgagtgagtgtagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgca-ttgtgaaaataaca----ttgtg--ttat-tgcagGCTCCTCAGAAGCACCAGAAATATGTTTCCCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAGCGAATTGGTGGTGGATTTGGGGGGA
upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 6
gtaagcatattattagtgtactgccatatactttactgagtggaattcatttttattcttggtttgtcggaccagtacatgaccattaagtctctgtacaagaaaacta---ttaggcatcagctagtttaagat-attatatgataatgttgtctctgcttaagcaaatgttggtggttgtgatttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
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---------------------------------------------------------------------------------------gaacccgtgtgtgtgagtgttagtgtttggcttgtattggcctaaatttatggcttgaaggaaataactgca-ttgtgaaaataaca----ttgtgttgt---tgcagGCTCCTCAGAAGCACCAGAAATATGTTTCTCATGTTCTTGGCCTTCCCATGTCAAAGGTAGTTTGCAAAACAAAACGAGTTGGTGGTGGATTTGGGGGGA
upper sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcatattattagtgtactgccatatactttactgagtggaattcatttttattcttggtttgtcggaccagtacatgaccattaagtctctgtacaagaaaactattaggcatca--gctagtttaagatattatatgataatgttgtctctgcttaagcaaatgttggtggttgtgat--ttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
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------------------------------------------------------------------------------------------tatttgc-ctagaaatttattagcaatggatgccagttcaac-tgctctgtggtggtcacagccttatttag---aattttgacagatttgatctttatgtgcagTGTCCCCAGAAGCATCAGAAATATGTTTCTCATGTTCTTGGTCTTCCAATGTCAAAAGTAGTTTGCAAAACCAAGCGAATCGGTGGTGGATTTGGGGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgataatgttgtctctgcttaagcaaatgttggtggttgtgatttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
tgatttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatattattagtgtactgccatatactttactgagtggaattcatttttattcttggtttgtcggaccagtacatgaccattaagtctctgtacaagaaaactattaggcatcagctagtttaagatattatatgataatgttgtctctgcttaagcaaatgttggtggttgtgatttatatgcagGCTCCTCAAAAGCACCAGAAATATGTGTCGCATGTTCTTGGTCTTCCGATGTCTAAAGTGGTATGCAAAACCAAACGAATTGGTGGTGGCTTTGGTGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG