Sequence
atgc intronic sequence ATGC exonic sequence...tttcaggcaagtgtcttcagacttgtagcgatggttttcatctcatatattatgttgatgaaacactgaaaacttcttctattcactcgaatgaaagcagGGACATCATCTGGATTTACGGCTTATTAGAAACCAATGGATACTGTGTGATCCTGGAGCTGAGTGCCTACTGTCTCAGACAAATGAAGACAGAACATGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g06690.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g06690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G05480.1 (Glycine max), 3'ss of exon 14
--tttcag--gcaagtgtcttcagacttgtagcgatggttttcatctcatatattatgttgatgaaacactgaaaacttcttctattcactcgaatgaaagcagGGACATCATCTGGATTTACGGCTTATTAGAAACCAATGGATACTGTGTGATCCTGGAGCTGAGTGCCTACTGTCTCAGACAAATGAAGACAGAACATGTG
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tttactagttacagaagtttatgaaattccttgtttaatgtttgtg-cttgttttgactggatcctttgactaagacaccctttgct-actcaaacaaa--cagGGACATCATTTAGATTTACGGCTTATTAGGAACCAGTGGCTTTTAATAGACCCCAAAATACAGGTTCTTATGTCAGAGACAAACGAAGATAAAACATCTG
upper sequence: LOC_Os11g06690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G19570.1 (Glycine max), 3'ss of exon 13
tttcaggcaagtgtcttcagacttgtagcgatggttttcatctcatatattatgttgatgaaacactgaaaacttcttctattcactcgaatgaaagcagGGACATCATCTGGATTTACGGCTTATTAGAAACCAATGGATACTGTGTGATCCTGGAGCTGAGTGCCTACTGTCTCAGACAAATGAAGACAGAACATGTG
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------------gtttgtgaaattccttgtttaatgtttgtg-cttgttttgactggatcgtctgactaagacaccctttgct-actcaaacaaa--cagGGACATCATTTAGATTTACGGCTTATTAGGAACCAGTGGCTTTTAATAGACCCCAAAATACAGGTTCTTATGTCAGAGACAAATGAAGACAAAACATCTG
upper sequence: LOC_Os11g06690.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G26570.1 (Glycine max), 3'ss of exon 12
----tttcaggca-agtgtcttcagacttgtagcgatggttttcatctcatatattatgttgatgaaacactgaaaacttcttctat-tcactcgaatgaaagcagGGACATCATCTGGATTTACGGCTTATTAGAAACCAATGGATACTGTGTGATCCTGGAGCTGAGTGCCTACTGTCTCAGACAAATGAAGACAGAACATGTG
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ttacatcaaagcacagcattgacagatttactctatttgtatctttttcat------tgttgaaagatggttgaatgcttattcttcatcacttaaaatgttgtagGGGCATCATCTGGATCTACGGCTTATTCGAAATCAATGGCTTTTGATAGATCCCAAGGTAGAATTTCTAATGTCGGAGACTAATGAAGATAAAACTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattatgttgatgaaacactgaaaacttcttctattcactcgaatgaaagcagGGACATCATCTGGATTTACGGCTTATTAGAAACCAATGGATACTGTGTGATCCTGGAGCTGAGTGCCTACTGTCTCAGACAAATGAAGACAGAACATGTG
tgttgat putative branch site (score: 4)
aaaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcaggcaagtgtcttcagacttgtagcgatggttttcatctcatatattatgttgatgaaacactgaaaacttcttctattcactcgaatgaaagcagGGACATCATCTGGATTTACGGCTTATTAGAAACCAATGGATACTGTGTGATCCTGGAGCTGAGTGCCTACTGTCTCAGACAAATGAAGACAGAACATGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- -caggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg