Sequence
atgc intronic sequence ATGC exonic sequencegtagttgaactctgtttattatattttttaacatcattttttttttcagatcaatggctctgattcccaccatttattctccttgtgcagGGACACTTGTATATCATTGATGTTTCGCAGTCCGTTGACCTTGATCATCCTTCAGCGTTGGAATTCTTGAAGGAAGATTGCTTGCATGTTACT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g06820.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G120329_T02 (Zea mays), 3'ss of exon 8
gtagttgaactc-tgtttattatatttttt---aacatcattttttttttcagatcaatggctctgattcccaccatt-tattctccttgtgcagGGACACTTGTATATCATTGATGTTTCGCAGTCCGTTGACCTTGATCATCCTTCAGCGTTGGAATTCTTGAAGGAAGATTGCTTGCATGTTACT
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gtagtgaacctcatattaaatataccatttccaaacatattgtacttttcaagtttactgttccttatctctatcctgatgtacctattgcctagGGTCACTTGTATATTATTGATGTTTCACAATCCGTCGATCTTGATCACCCTTCAGCTTTGGATTTTCTGAAGGAAGATTGCTTGCATGTTTCT
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 9
-----gtagttgaactc-tgtttattatatttttt---aacatcattttttttttcagatcaatggctctgattcccaccatt-tattctccttgtgcagGGACACTTGTATATCATTGATGTTTCGCAGTCCGTTGACCTTGATCATCCTTCAGCGTTGGAATTCTTGAAGGAAGATTGCTTGCATGTTACT
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ttgaggtagtgaacctcctattaaatataccttttccaaacatattgtagttttcaagtttactgttccttatctctatcctgatgtacctattgcctagGGTCACTTGTATATTATTGATGTTTCACAATCCGTCGATCTTGATCACCCTTCAGCTTTGGACTTTCTGAAGGAAGATTGCTTGCATGTTTCT
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 8
gtagttgaactctgt-ttattatattttttaac-atcattttttttttcagatcaatggctctgattcccaccatttattctccttgtg-cagGGACACTTGTATATCATTGATGTTTCGCAGTCCGTTGACCTTGATCATCCTTCAGCGTTGGAATTCTTGAAGGAAGATTGCTTGCATGTTACT
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gtgaacaccccctttgccagtttatatttcattgattgaatgtgtctttctgtcaatagttaattcatatggtctttatttgtcacttgtcagGGTCACTTGTATATCATTGATGTTTCTCAAGCTGTTGATCCTGAACATCCTCATGCCCTTGATTTTCTGCGTGAAGATTGTGTTCATGTATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttttttttcagatcaatggctctgattcccaccatttattctccttgtgcagGGACACTTGTATATCATTGATGTTTCGCAGTCCGTTGACCTTGATCATCCTTCAGCGTTGGAATTCTTGAAGGAAGATTGCTTGCATGTTACT
ctctgat putative branch site (score: 4)
ttcccaccatttattc CT-rich tract
atttattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttgaactctgtttattatattttttaacatcattttttttttcagatcaatggctctgattcccaccatttattctccttgtgcagGGACACTTGTATATCATTGATGTTTCGCAGTCCGTTGACCTTGATCATCCTTCAGCGTTGGAATTCTTGAAGGAAGATTGCTTGCATGTTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA