Sequence
atgc intronic sequence ATGC exonic sequencegttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactgagctatattttccttgttttctgtttgtctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38280.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
gttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactg-agctatattttccttgttttctgtttgt-ctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG
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----------------------------------tattcaaagtggtatacacctcgttatgttactgatatatttatgatat--ttgatattcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG
upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
gttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactgagctatattttccttgttttctgtttgtctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG
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--------------------------------aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattat--atagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
upper sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 11
gttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactgagctatattttccttgttttctgtttgtctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG
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-------------------------------aagaatttggggagctttttctgctttccatttatggcttaatttg---ctcagccaattgtagtgttagcaattaatggtaattcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTTGACAATATTTTTATTCCACTTTTTGAGGTCACTGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgactgctaactgagctatattttccttgttttctgtttgtctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG
tgctaac putative branch site (score: 1)
ttttccttgttttctg putative PPT
tatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactgagctatattttccttgttttctgtttgtctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC