Sequence
atgc intronic sequence ATGC exonic sequence...tatctggtttaattgattaagttcactagaattttgaattttcagcacgttttctaatatttaggccttttgttctaccctttcttattgaacatcccagTTCAGATGCCGCATATGATCTTCACCGGACTTGAAGACTACAAAGCAAGGGGCACTCAAGCAAGCCCTTACTATACGATCACTCATTATACAGAGTTTGC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g20860.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g20860.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G011777_T02 (Zea mays), 3'ss of exon 2
tatctggtttaattgatta--agttcactagaattttgaattttcagcacgttttctaatatttaggccttttgttctaccctttc-ttattgaacatcccagTTCAGATGCCGCATATGATCTTCACCGGACTTGAAGACTACAAAGCAAGGGGCACTCAAGCAAGCCCTTACTATACGATCACTCATTATACAGAGTTTGC
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ggcctaatttatttaaccatgagttcgttagagttc-acactgttggctttggaact--tttttggacttactgtttccttcttttgctatacaatgccccagTCCAGATGCCATACATGGTATTCACAGGACTTGAAGACTATAAAGCACGAGGCACTCAAGCAAGTCCTTACTACACAGTCACTCATTACACAGAGTTTGC
upper sequence: LOC_Os02g20860.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G011777_T03 (Zea mays), 3'ss of exon 3
tatctggtttaattgattaagttcactagaattttgaattttcagcacgttttctaatatttaggccttttgttctaccctttc-ttattgaacatcccagTTCAGATGCCGCATATGATCTTCACCGGACTTGAAGACTACAAAGCAAGGGGCACTCAAGCAAGCCCTTACTATACGATCACTCATTATACAGAGTTTGC-----
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-aatttatttaacca--tgagttcgttagagttc-acactgttggctttggaact--tttttggacttactgtttccttcttttgctatacaatgccccagtccagATGCCATACATGGTATTCACAGGACTTGAAGACTATAAAGCACGAGGCACTCAAGCAAGTCCTTACTACACAGTCACTCATTACACAGAGTTTGCTGAGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|163927364|gb|EG713852.1|EG713852EST: TATACTACCATGTTCATGCAAGGTTATTACTCAGTCTTTTCCATATAGTG TTCAGATGCCGCATATGATCTTCACCGGACTTGAAGACTACAAAGCAAGGG
genomic: TATACTACCATGTTCATGCAAGGTTATTACTCAGTCTTTTCCATATAGTGgtaattatct ... aacatcccagTTCAGATGCCGCATATGATCTTCACCGGACTTGAAGACTACAAAGCAAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacgttttctaatatttaggccttttgttctaccctttcttattgaacatcccagTTCAGATGCCGCATATGATCTTCACCGGACTTGAAGACTACAAAGCAAGGGGCACTCAAGCAAGCCCTTACTATACGATCACTCATTATACAGAGTTTGC
ttctaat putative branch site (score: 2)
tttctaatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatctggtttaattgattaagttcactagaattttgaattttcagcacgttttctaatatttaggccttttgttctaccctttcttattgaacatcccagTTCAGATGCCGCATATGATCTTCACCGGACTTGAAGACTACAAAGCAAGGGGCACTCAAGCAAGCCCTTACTATACGATCACTCATTATACAGAGTTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG