Sequence
atgc intronic sequence ATGC exonic sequence...tcagttaatcaaccccctcacttagatcaactcatgggaacagggacaaatgcctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g13150.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g13150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G379286_T01 (Zea mays), 3'ss of exon 1
tcagttaatcaaccccctcacttagatcaactcatgggaacagggacaaatg--cctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
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-tgtgggggcaatttcttcccttgaactagttcatgagtgcaggaactgttgttcttttggttttcattcaatctcactcccctttg-ttattcctgcgcagATACTTGGTACAGGAATGGACACACAGGACACTTCACCTTCTATTCTACTATTCTTTGACAAACAAAGGTTTATTTTTAATGCGGGCGAG
upper sequence: LOC_Os01g13150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 1
tcagttaatcaaccccctcacttagatcaactcatgggaacagggacaaatgcctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
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----------------gtcatcatcatagacttcttcgtttttttttccaattttggattcttaatctctcacaatactta--aaaatccgatctttcagATACTTGGAACTGGAATGGATACACAGGATACATCATCTTCTGTATTACTCTTCTTTGATAAGCAAAGATTCATCTTTAATGCTGGAGAG
upper sequence: LOC_Os01g13150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G16260.1 (Arabidopsis thaliana), 3'ss of exon 1
tcagttaatcaaccccctcacttagatcaactcatgggaacagggacaaatgcctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
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---gtt--tcaatttcat-atctactccaatctt---aaactgtgaaagatg---atgc--ataattttgaactattcatctg----ttttgtt----agATCCTTGGGACTGGAATGGATACACAGGATACGTCACCTTCTGTATTACTCTTCTTTGACAAACAAAGATTCATCTTTAATGCTGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaatgcctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
atcttac putative branch site (score: 3)
ccccttcgttcttggc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagttaatcaaccccctcacttagatcaactcatgggaacagggacaaatgcctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - aatcaac
- - - - - - - - - - - - - - - - - - - - - -ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - tgccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcttct