Sequence
atgc intronic sequence ATGC exonic sequencegtttgcttccaatctcctcctcctcctcctttttttcatgtcaggcttaccacattcctcttctctattttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g74520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G438673_T02 (Zea mays), 3'ss of exon 2
gtttgcttccaatctcctcctcctcctcctttttttcatgtcaggctt-accacatt-cctctt-ctctattttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
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-gttgctgctgcttaccctttccatttc-ttttatggatatcttcctttatcacttaacctcttattcttttctttcagGCTTATTTCCAAGCTGAACCCCTTTCCGGCAATGAAGCATCTCGATGTGGCTGGTGGAACAG
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G065210_T03 (Zea mays), 3'ss of exon 3
gtttgcttccaatctcctcctcctcctcctttttttcatgtcaggctt-accac--attcctcttctctattttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
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-gttgctgctgcttgcc-ctttctgtttcttttatggatatcttcctttgtcactcaaactccgattcttttctttcagGCTTATTTCCAAGCTGAACCCCTTTTCGGGGATGAAGCATCTCGATGTGGCTGGTGGAACAG
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G044369_T01 (Zea mays), 3'ss of exon 1
gtttgcttccaatctcctcctcctcctcctttttttcatgtcaggctt-accacatt--cctcttctctattttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
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-gttgctgctgcttgccctttccgtttc-ttttatggatatcttcctttgtcactcgaactccgattcttttctttcagGCTTATTTCCAAGCTGAACCCCTTTCCGGGGATGAAGCATCTCGATGTGTCTGGTGGAACAG
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G22890.1 (Glycine max), 3'ss of exon 2
---------------gtttgcttccaatctcctcctcctcctcctttttttcatgtcaggcttaccacattcctcttctctattttt--taagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
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gttacagcattacattctcatttcttcaattgtttcaatcttgttgctattgctgttggactttgcttaaatctgtgattattttctgctcagGTTAGTTTCCAAGCTGAATCCGTTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAG
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G03210.2 (Glycine max), 3'ss of exon 1
---gtttgcttccaatctcctcctcctcctcctttttttcatgtcaggcttacc----acattcctcttctct------atttttta---agGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
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gttacaacattacattctcattttcataatagtttcaatcatattactgttgctttggactttgcttaaatctgtgattattttctgctcagGTTAGTTTCGAAGCTGAATCCATTTCCTGGAATGAAGCATCTTGATGTTGCTGGTGGCACAG
upper sequence: LOC_Os01g74520.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0039g01590.t01 (Vitis vinifera), 3'ss of exon 3
-------gtttgcttccaatctcctcctcctcctcctttttttcatgtcaggcttaccacattcctcttctctattttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
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gtttgaatcttgctgttgtgctcaaatagttatttcaaattatgatgctttgctt-ctatattagtttatttttgcttaacagGTTGGTCTCTAAATTGCATCCATTTCCTGGAATGAAGCATCTTGATGTGGCTGGTGGAACAGMapped 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|55408176|gb|CV720552.1|CV720552EST: CTCATGAACGATCTTATGAGCGTTGGACTACATAGGTTGTGGAAGGACAG GCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGC
genomic: CTCATGAACGATCTTATGAGCGTTGGACTACATAGGTTGTGGAAGGACAGgtttgcttcc ... attttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGC
EST:
gi|88351955|gb|CI625955.1|CI625955EST: CTCATGAACGATCTTATGAGCGTTGGACTACATAGGTTGTGGAAGGACAG GCTCATCTCAAAGATTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGC
genomic: CTCATGAACGATCTTATGAGCGTTGGACTACATAGGTTGTGGAAGGACAGgtttgcttcc ... attttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctcctcctttttttcatgtcaggcttaccacattcctcttctctattttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
ggcttac putative branch site (score: 3)
cttaccacattcctct CT-rich tract
ttctctattttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcttccaatctcctcctcctcctcctttttttcatgtcaggcttaccacattcctcttctctattttttaagGCTCATCTCAAAGCTTAATCCTTTTCCTGGGATGAAGCATCTAGATGTGGCTGGTGGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA