Sequence
atgc intronic sequence ATGC exonic sequencegtaagatctcaccatccatctagcatatcattatatacaaacaattcaaaagatggttcatttagtcacttaccttggatacttccagCAGTACGATGTGGAGTTTGAAAGGATGCCACAAGTTAAACCTACA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g45060.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 3
gtaagatctcaccatcca---tctagcatatcattatatacaaacaattcaaaagatggttcatttagtcacttaccttggatactt-ccagCAGTACGATGTGGAGTTTGAAAGGATGCCACAAGTTAAACCTACA
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gtgagagctggccagcaagtgtataattttttattaagtactcaaaat--aaaagatagtcatgttaagtgcttactttggatgctttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACA
upper sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G179696_T02 (Zea mays), 3'ss of exon 3
gtaagatctcaccatcca---tctagcatatcattatatacaaacaattcaaaagatggttcatttagtcacttaccttggatactt-ccagCAGTACGATGTGGAGTTTGAAAGGATGCCACAAGTTAAACCTACA----------------------------------------------------------
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gtgagagctggccagcaagtgtataattttttattaagtactcaaaat--aaaagatagtcatgttaagtgcttactttggatgctttcctgcagTACGATGTGGAGTTTGAAAGAATGCCACAGATTAAACCTACAGTAAGAATTACTATTTTTATGCACACTATTATCATACCAAACTGAAATGAAGTAATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatacaaacaattcaaaagatggttcatttagtcacttaccttggatacttccagCAGTACGATGTGGAGTTTGAAAGGATGCCACAAGTTAAACCTACA
cacttac putative branch site (score: 2)
tacttcc putative PPT
aattcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatctcaccatccatctagcatatcattatatacaaacaattcaaaagatggttcatttagtcacttaccttggatacttccagCAGTACGATGTGGAGTTTGAAAGGATGCCACAAGTTAAACCTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG