Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatactaattactaaaaggagaatattttctagcattgttacagtataaatgattaaactatttgcagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g43750.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 6
gtaaaatactaat--tactaaaaggagaatatttt-ctagcattgttacagtataaatgattaaactatttgcagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCC
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gtaaaaaaatgatgctagtgaaaggaaaccatcttgctagtgttgtctgatttccaacggctgcaatatttgtagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGCGAGGTTTTCCGTGATGCCCAAGAGAAAGCTCTTCC
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 8
gtaaaatactaatt--actaaaaggagaatattttctagcattgttacagtataaatgattaaa--ctatttgcagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCC
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gttagatatgatttgaacttggcattcctgttttactggcagtttttgagattaagtattctatttctgtatgcagATCTTCATGATGAACCTTTCTGCTCCCTTTATATGTGAGTTCTTTAAGGGTGCACTGGACAAAGTTCTGCC
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 8
---------gtaaaatactaattactaaaaggagaatattttctagcattgtta---cagtataaatgat----taaactatttgcagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCC
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gtaattctttttaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattatcttctcattcatgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC
upper sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 8
---------gtaaaatactaattactaaaaggagaatattttctagcattgtta---cagtataaatgattaaactatt----tgcagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCC
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gtaattcttttcaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattattttctcattcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaggagaatattttctagcattgttacagtataaatgattaaactatttgcagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCC
tactaaa putative branch site (score: 1)
agtataaatgattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatactaattactaaaaggagaatattttctagcattgttacagtataaatgattaaactatttgcagGTGTTTATGATGAACCTTTCTGCTCCCTTTATATGTGAATTCTTCCGTGATGCCCAAGAGAAGGCTCTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA