Sequence
atgc intronic sequence ATGC exonic sequence...aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtacttctgacagagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40370.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtacttctga-cagagtgga----tttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA
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----ttctagttttgtttaacacttatgat-gtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG----
upper sequence: LOC_Os01g40370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtact--tctgacaga-gtggatttccattgttttctcc---tttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA
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---actcgctcagcggctcctgtgcctgtttttataagcagccaa---tatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG----
upper sequence: LOC_Os01g40370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
--aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtacttctgacagagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA
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cattgtttagtcgactgct-ctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagat-tcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgttgaagctgtacttctgacagagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA
ttctgac putative branch site (score: 2)
tttccattgttttctc putative PPT
attgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtacttctgacagagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-aaaagaa
- - - - - - - - tgcatgc
- - - - - - - - - - - -ggaaaata
- - - - - - - - - - - - - - - - - - - -aaccata
- - - - - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtac