Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtattcctgccggtaggctgtaggagtttgtcacaatcacgtggttaatgcaaggcactagtgttgattctgcatttctgctgaattatgtacagGTACTTGGCTCCAGAGTATGCATCCACAGGAAAGCTGACCGAGAAATCGGACGTGTTCTCCTTCGGCGTCGTCCTTCTGGAGCTCATCACAGGCCGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g29340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g29340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G028731_T01 (Zea mays), 3'ss of exon 5
gtaatgtattcctgccggtaggctgtaggagtttgtcacaatcacgtggttaatgcaaggcactagtgttgattctgcatttctgctgaattatgtacagGTACTTGGCTCCAGAGTATGCATCCACAGGAAAGCTGACCGAGAAATCGGACGTGTTCTCCTTCGGCGTCGTCCTTCTGGAGCTCATCACAGGCCGGAAG
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gtaat-cactcgcgc-gatatatattaacggacgctagcaaagagaagaataaaacaaaagg--------gattgtacgt------------acacacagGTACCTGGCTCCAGAGTATGCGTCCACGGGGAAGCTGACCGAGAAATCAGACGTCTTCTCCTTCGGCGTCGTGCTCCTGGAGCTCATCACCGGGCGGAAG
upper sequence: LOC_Os06g29340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ20011 (Selaginella moellendorffii), 3'ss of exon 4
gtaatgtattcctgccggtaggctgtaggagtttgtcacaatcacgtggttaatgcaaggcactagtgttgattctgcatttctgctgaattatgtacagGTACTTGGCTCCAGAGTATGCATCCACAGGAAAGCTGACCGAGAAATCGGACGTGTTCTCCTTCGGCGTCGTCCTTCTGGAGCTCATCACAGGCCGGAAG
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-------------------------------------gtaaggacattaccaaccaaatatatcagtttcccatatgaattttt--caaact---tccagGTACCTTGCGCCTGAGTACGCCTCCACAGGAAAACTGACGGAGAAGTCAGACGTGTACTCCTTCGGAGTCGTCCTATTGGAACTTCTAACGGGAAGGAGG
upper sequence: LOC_Os06g29340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07415 (Selaginella moellendorffii), 3'ss of exon 4
gtaatgtattcctgccggtaggctgtaggagtttgtcacaatcacgtggttaatgcaaggcactagtgttgattctgcatttctgctgaattatgtacagGTACTTGGCTCCAGAGTATGCATCCACAGGAAAGCTGACCGAGAAATCGGACGTGTTCTCCTTCGGCGTCGTCCTTCTGGAGCTCATCACAGGCCGGAAG
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-------------------------------------gtaaggacataaccaaccaaatatatcagtttcccatatgaattttt--caaact---tccagGTACCTTGCGCCTGAGTACGCCTCCACAGGAAAACTGACGGAGAAGTCAGACGTGTACTCCTTTGGAGTCGTCCTACTGGAACTTATAACGGGAAGGAGG
upper sequence: LOC_Os06g29340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07414 (Selaginella moellendorffii), 3'ss of exon 4
gtaatgtattcctgccggtaggctgtaggagtttgtcacaatcacgtggttaatgcaaggcactagtgttgattctgcatttctgctgaattatgtacagGTACTTGGCTCCAGAGTATGCATCCACAGGAAAGCTGACCGAGAAATCGGACGTGTTCTCCTTCGGCGTCGTCCTTCTGGAGCTCATCACAGGCCGGAAG
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------------------------gtaaggacatg----agtca--tgaccaac-caatatatcatttttccatctgaattttt--caaact---tccagGTACCTTGCACCTGAGTACGCCTCCACAGGAAAACTGACGGAGAAGTCAGACGTGTACTCCTTCGGAGTCGTCCTATTGGAACTTATAACAGGAAAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggttaatgcaaggcactagtgttgattctgcatttctgctgaattatgtacagGTACTTGGCTCCAGAGTATGCATCCACAGGAAAGCTGACCGAGAAATCGGACGTGTTCTCCTTCGGCGTCGTCCTTCTGGAGCTCATCACAGGCCGGAAG
tgttgat putative branch site (score: 4)
aattatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtattcctgccggtaggctgtaggagtttgtcacaatcacgtggttaatgcaaggcactagtgttgattctgcatttctgctgaattatgtacagGTACTTGGCTCCAGAGTATGCATCCACAGGAAAGCTGACCGAGAAATCGGACGTGTTCTCCTTCGGCGTCGTCCTTCTGGAGCTCATCACAGGCCGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA