Sequence
atgc intronic sequence ATGC exonic sequence...gcattgtgaaacggaggaagtagcattcaaatttcaatgtttttataaaccaatggcatccacaagaaactaaagagctgttgctgcatttgcattgcagGCCCTTGAACTTGTTCCCAGAAAGATTCATGATAGATCTCCAATATTCCTGGGGAGCTATGATGACGTGGAGGATATCAAAGCATTGTACGCTTCAGAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g36270.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 9
gcattgtgaaacggaggaagtagcattcaaattt-caatgtttttataaaccaatggcatcca---caagaaactaaaga-gctgttgctgcatttgcattgcagGCCCTTGAACTTGTTCCCAGAAAGATTCATGATAGATCTCCAATATTCCTGGGGAGCTATGATGACGTGGAGGATATCAAAGCATTGTACGCTTCAGAGT
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---ttattaa--gaaaagagcactattttaacatgccatgtttttttttaccagtggttggcattgcatataactgaaaatgctcctgctaaatttataatgcagGCGCTTGAACTTGCTCCCGCTAAACTTCACGACAGATCCCCAGTGTTCCTCGGGAGCTACGATGACGTTGAGGAGATCAAAGCACTGTACGCTTCAATGT
upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 12
-------------------------------------------gcattgtgaaacggaggaagtagcattcaaatttcaatgtttttataaac-caatggcatccacaagaaactaaagagctgttgctgcatttgcattgcagGCCCTTGAACTTGTTCCCAGAAAGATTCATGATAGATCTCCAATATTCCTGGGGAGCTATGATGACGTGGAGGATATCAAAGCATTGTACGCTTCAGAGT
|| | ||| | | | ||| | ||| | |||| ||| ||||| || ||| | | || | | || ||||| ||||| | ||||| | ||| | || || ||||||| |||||||| || ||||||||||| || ||||| |||||||| | || ||| | |
gtaatttacatttcttttaactgacactgacaatttttctcttatttttctttccacttgaaattggaatcacccatacatgctggtatagtttcaaaagcatcatttgtgaatcaaattgataaatcttctctgttat--cagGCACTTGATTTAGTTCCAACGAAGTTGCACGAGCGATCTCCCATATTCCTTGGTAGCTATGATGATGTTGAGGAAATCAAAGCTCTTTATGCTGCTGCTG
upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ23220 (Selaginella moellendorffii), 3'ss of exon 10
gcattgtgaaacggaggaagtagcattcaaatttcaatgtttttataaaccaatggcatccacaagaaactaaagagctgttgctgcatttgcattgcagGCCCTTGAACTTGTTCCCAGAAAGATTCATGATAGATCTCCAATATTCCTGGGGAGCTATGATGACGTGGAGGATATCAAAGCATTGTA---CGCTTCAGAGT
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------------------------------------------gtaagaacttatactgttctttc---acacatcttttgttttgtctcttgatttacagGCACTTGACGTTGTTCCAAAAAAGATTCATGAGAGGTCACCAATATTCCTGGGAAGCTTTGAAGACGTTGAAGAGATCAAAAGTCTCTATCACGCATCCG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaccaatggcatccacaagaaactaaagagctgttgctgcatttgcattgcagGCCCTTGAACTTGTTCCCAGAAAGATTCATGATAGATCTCCAATATTCCTGGGGAGCTATGATGACGTGGAGGATATCAAAGCATTGTACGCTTCAGAGT
aactaaa putative branch site (score: 2)
aaactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcattgtgaaacggaggaagtagcattcaaatttcaatgtttttataaaccaatggcatccacaagaaactaaagagctgttgctgcatttgcattgcagGCCCTTGAACTTGTTCCCAGAAAGATTCATGATAGATCTCCAATATTCCTGGGGAGCTATGATGACGTGGAGGATATCAAAGCATTGTACGCTTCAGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT