Sequence
atgc intronic sequence ATGC exonic sequence...actcactgatatgttgcttttcatcctcctttgtctttgtactaaagcggcatatacagcaggctcaatctgtgccttaccccatgatattctcctgcagATTGGTACATTAATATATGCACGAGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g66730.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 4
--actcactgatatgttgcttttcatcctcctttgtctttgtactaaagcggcatatacagcaggctcaatctgtgccttaccccatgatattctcctgcagATTGGTACATTAATATATGCACGAGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATG
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gatctcaactctgagtggtgccataagttgtttccacagtgttttga-gctttatattctatcgattatataatcgtcctatgatggga-gtgttcctgcagATTGGTACATTAATATATGCTCGAGTGGTGAAAGCAAATAGTATCATGAATCCCGGGCTTTCATGCAGAGATG
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 6
-actcactgatatgtt--gcttttcatcctcctttgtctttgtactaaagcggcatatacagcaggctcaatctgtgccttaccccatgatattctcctgcagATTGGTACATTAATATATGCACGAGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATG
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tagtaaatgctatagtaaggaactgaacatgtccaataagttgattccagtgtttcgagctttatattctgttcat--cttaccat-tgggatgttcctgcagATTGGTACATTAATATATGCTCGAGTGGTGAAAGCAAATAGTATCATGAATCCCGAGCTCTCATGCATGGATG
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 6
actcactgatatgttgcttttcatcctcctttgtctttgtactaaagcggcatatacagcaggctca--atctgtgccttaccccat-gatattctcctgcagATTGGTACATTAATATATGCACGAGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATG
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--taaggaactgaacatgtctaataagttgattccagtgt-ttcgagctttatattctgtttattgattatatattcatcttaccattgggatgttcctgcagATTGGTACATTAATATATGCTCGAGTGGTGAAAGCAAATAGTATCATGAATCCCGAGCTCTCATGCATGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcggcatatacagcaggctcaatctgtgccttaccccatgatattctcctgcagATTGGTACATTAATATATGCACGAGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATG
gccttac putative branch site (score: 3)
tattctcct putative PPT
atgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actcactgatatgttgcttttcatcctcctttgtctttgtactaaagcggcatatacagcaggctcaatctgtgccttaccccatgatattctcctgcagATTGGTACATTAATATATGCACGAGTGGTGAAAGCAAATAGCATCATGAACCCAGAGCTCTCGTGCATGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA