Sequence
atgc intronic sequence ATGC exonic sequencegtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11550.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 7
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataatagatgtatcgatttta-gttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
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-----------------------------------------------------tacttgagcagttctggtgttatgtta-----acttttgataaa-acatgggcttgaagttgtagttttactaatattgcactggcaaatctttttaattttccagCTATGTACCTTGCAAGAGGAAATCATGAAAGCAAGAGCATGAACAAAATATATGGCTTTGAGGGGGAAGTGAGGTCAAAGCTGGGTGAGAAGTTTGTTGA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 8
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA-
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------------------------------------------------------tcttctttcttcactttatctggtt-ctcttgtttgagagaatgctatttgtttttgtc-ttggcacattgtaacttgttttgt---tgccatgtgattttcagcCATATATTTAGCCAGAGGAAATCATGAGAGCAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGAA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataata-gatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatc--cagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
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-------------------------------------------------------------ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgccatatgattttcagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
---------gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattatt--ctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
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gtaagttctctaaaactttgttgtaataattctt-tgatgttcatgttttaattgcttttgcta--tcactggcaag--gattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaa----atcgccatt-tacacacctttg-tactgcagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 2
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattat-tctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
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------------------------------------------------tttgtttcctc-----ttcctttgtttcatgctctctaagtaacaaaatcacaactaattttatt--ctcatgtaaca---tcttgttgactggttcaaaaaatc-ttcagCTATATATCTCTCTAGAGGAAATCACGAGAGCAAGAGCATGAACAAGATATATGGTTTTGAAGGGGAGGTCAGATCCAAGTTGAGTGAAACATTTGTGGA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S80_144V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattcta-acttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
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------------------------------------------------tatatgttctgatgagcttattcagtgtatatcaggagactgatcacactta-actcactctacttcctc-tctaac----ctcgttttatttattgtctgaat-----agGGCTGTACCTTTCTAGAGGTAATCATGAAAGCAAGAGCATGAACAAAATATATGGTTTTGAAGGGGAGGTTAACGCGAAGTTCAATGAGACAATGAATAA
upper sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
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---------------------------------------agtaagt--tgtgatgagtttgttgtttttgtaaatcaggagactgagtcctgtcaatt-------tttttataccctgcctaacatgtttttgtgtgtga-----ttgaat-----agGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAAMapped 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|33684365|gb|CF312604.1|CF312604EST: TGTTGAAGTCATACTCACTCTTTTTGCTTTCAAGTGCCTCTATCCGACAG GTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATAT
genomic: TGTTGAAGTCATACTCACTCTTTTTGCTTTCAAGTGCCTCTATCCGACAGgtaactgcta ... aatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATAT
EST:
gi|109974396|gb|DT806886.1|DT806886EST: TTGAAGTCATACTCACTCTTTTTGCTTTCAAGTGCCTCTATCCGACAG GTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATAT
genomic: TTGAAGTCATACTCACTCTTTTTGCTTTCAAGTGCCTCTATCCGACAGgtaactgcta ... aatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
tttatacata 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC