Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagacagcgaactaaaatttgttttcacacacttaccttaagtgcctagttgtgtagcattgtgttagcttgtgggctttctgatcttacttgaatgcagGTACTTCGCAACATGTGCTTGTGTAGATTACTGGGCTATTGTTCTCCCGCTGTTGGACTCACTTAAAGGTTCTCCAATAATTCCTTATCATGGGAAGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G125947_T01 (Zea mays), 3'ss of exon 4
gtaagtagacagcgaactaaaatttgttttcacacacttaccttaagtgcctagttgtgtagcattgtgttagcttgtgggctttctgatcttacttgaatgcagGTACTTCGCAACATGTGCTTGTGTAGATTACTGGGCTATTGTTCTCCCGCTGTTGGACTCACTTAAAGGTTCTCCAATAATTCCTTATCATGGGAAGATG
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gtaagtacatgatgacctgaaatttatgtttggctacttattcttagttg-----tatgtagcattgtgctaacttttgaatcttcctatcgtgattaattgcagATATTTTGCAACATGTGCTTATGTAGATTACTGGGCTGTTGTCCTTCCACTAATTAACCCGCTTAAAGGTTCTCCAATAATTGCTTACCATGGGAAGATG
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G303752_T03 (Zea mays), 3'ss of exon 4
gtaagtagacagcgaactaaaatttgttttcacacacttaccttaagtgcctagttgtgtagcattgtgttagcttgtgggctttctgatcttacttgaatgcagGTACTTCGCAACATGTGCTTGTGTAGATTACTGGGCTATTGTTCTCCCGCTGTTGGACTCACTTAAAGGTTCTCCAATAATTCCTTATCATGGGAAGATG
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gtaagtacatgatgacctgaaatttatgtttggctacttattcttagttg-----tatgtagcattgtgctaacttttgaaccttcctatcgtgattaattgcagATATTTTGCAACATGTGCTTGTGTAGATTATTGGGCTGTTGTTCTTCCACTAATTAAGTCGCTTAAAGGTTCTCCAATAATTGCTTACCATGGGAAGATG
upper sequence: LOC_Os01g07080.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G303752_T02 (Zea mays), 3'ss of exon 4
gtaagtagacagcgaactaaaatttgttttcacacacttaccttaagtgcctagttgtgtagcattgtgttagcttgtgggctttctgatcttacttgaatgcagGTACTTCGCAACATGTGCTTGTGTAGATTACTGGGCTATTGTTCTCCCGCTGTTGGACTCACTTAAAGGTTCTCCAATAATTCCTTATCATGGGAAGATG------
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gtaagtacatgatgacctgaaatttatgtttggctacttattcttagttg-----tatgtagcattgtgctaacttttgaaccttcctatcgtgattaattgcagatattttgcaacatgtgcttgtgtagATTATTGGGCTGTTGTTCTTCCACTAATTAAGTCGCTTAAAGGTTCTCCAATAATTGCTTACCATGGGAAGATGAAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagttgtgtagcattgtgttagcttgtgggctttctgatcttacttgaatgcagGTACTTCGCAACATGTGCTTGTGTAGATTACTGGGCTATTGTTCTCCCGCTGTTGGACTCACTTAAAGGTTCTCCAATAATTCCTTATCATGGGAAGATG
atcttac putative branch site (score: 3)
tcttactt CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagacagcgaactaaaatttgttttcacacacttaccttaagtgcctagttgtgtagcattgtgttagcttgtgggctttctgatcttacttgaatgcagGTACTTCGCAACATGTGCTTGTGTAGATTACTGGGCTATTGTTCTCCCGCTGTTGGACTCACTTAAAGGTTCTCCAATAATTCCTTATCATGGGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG