Sequence
atgc intronic sequence ATGC exonic sequencegtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g48160.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G481261_T01 (Zea mays), 3'ss of exon 5
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
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----------------------------------------------------------gtaggcattggacactggacagc-gcgcaatgttcactcagcact----cagttgctctgtcttaactcgtttgatctcccttgtctctggcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G470653_T01 (Zea mays), 3'ss of exon 4
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgc-tatatgcttttctgattacaccaaaacagc-tgccaattgact--gctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
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----------------------------------------------------------gtaggcattggacactggacagcgcgtacagttcactcagcactcagttgctctgtcttaattcaataagctcgtttgatctcccttgtccccggcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G16070.1 (Glycine max), 3'ss of exon 3
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
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-----------------------------ctgattggaaattttaa--ctggtccttcttactttttgagggtgatatgatggtaagtttt--------------gaaattttctgatcttctaagctttagccatttta-------aacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G30770.1 (Glycine max), 3'ss of exon 4
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
|| | || | | || || | | |||| | || || | || | | | || | | |||||||| || || |||||||| |||||||| ||||||||||||||||||||||| || ||||||
----------------------------------------------------caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagttttgaaattttatgatcttctaagctttcgccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
upper sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgc-cagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
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---------------------------------------gcatgatctctgatcttctc---cctctggacacacaatc---atatgaagtttcgttctc-tcagaat--ttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGMapped 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|88485358|gb|CI422629.1|CI422629EST: AGGAGCTCCTGAATGAAAGAACAAACACTGAGAACCGGTATCTGAAGAAG AAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAA
genomic: AGGAGCTCCTGAATGAAAGAACAAACACTGAGAACCGGTATCTGAAGAAGgtaccaagca ... tatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAA
EST:
gi|86528962|gb|CI169168.1|CI169168EST: AGGAGCTCCTGAATGAAAGAACAAACACTGAGAACCGGTATCTGAAGAAG AAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAA
genomic: AGGAGCTCCTGAATGAAAGAACAAACACTGAGAACCGGTATCTGAAGAAGgtaccaagca ... tatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
aattgac putative branch site (score: 3)
tttcttgtct putative PPT
tatttgtatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA