Sequence
atgc intronic sequence ATGC exonic sequencegtttggcaatataatacttgtcattagcagcccctgttgatccactcctttttttaaaactatttttaatgttggtcttgcagCCACATGTCGATTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTATTCTTTACAGTTTTGTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60350.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G050193_T02 (Zea mays), 3'ss of exon 7
gtttggcaatataatacttgtc---attagc--agcccctgt---tgatccactcctttttttaaaactatttttaat----gttggtcttgcagCCACATGTCGATTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTATTCTTTACAGTTTTGTTCAG
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gtatggttactgattattcgtttgaattattctggtgtctgtgtttgaataatcccgttcaatcatttctttgctaattgtgattggttttgcagCCACATGTTGACTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTGGTCTTTACAGATTTGTTCAG
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G111737_T01 (Zea mays), 3'ss of exon 7
gtttggcaatataatacttgtc---atta----gcagcccctgttgatccactcctttttttaaaactattt-ttaat----gttggtcttgcagCCACATGTCGATTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTATTCTTTACAGTTTTGTTCAG
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gtgtggcaactgattattcgtttgaattactctggtatttgtgtttgaataatcctggtccaccatttgtttgctaattgtgattggttttgcagCCACACGTTGACTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTGGTCTTTACATATTTGTTCAG
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0001g14630.t01 (Vitis vinifera), 3'ss of exon 6
-------gtttggcaatataatacttgtcattagca-gcccctgttgat--------ccactcctttttttaaaactatttttaatgt-tggtcttgcagCCACATGTCGATTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTATTCTTTACAGTTTTGTTCAG
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ttattactgttgttgctgttgttgttgtcattatgatgatgatgatgatgatgatgatgatgattgtgattataattattattattttctaattttgcagCCACATGTTGACTTTGGACTAAAGCTGCTAGGAGCAGACGTAATGGCCATTCCTGGCCTGTATCGGTTGGTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcccctgttgatccactcctttttttaaaactatttttaatgttggtcttgcagCCACATGTCGATTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTATTCTTTACAGTTTTGTTCAG
ttttaat putative branch site (score: 3)
tcctttttttaaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggcaatataatacttgtcattagcagcccctgttgatccactcctttttttaaaactatttttaatgttggtcttgcagCCACATGTCGATTTTGGGCTAAAACTTCTTGGAGCAGATGTAATGGCTATTCCTATTCTTTACAGTTTTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG