Sequence
atgc intronic sequence ATGC exonic sequenceGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcatttagatgtgctcagttttgatgtttctttctgattcttctgttgtctcctaactgtctgtgtacatgattgtttctctgctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55940.2 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G040017_T02 (Zea mays), 5'ss of exon 8
GAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcatttagatgtgctcagttttgatgtttct--ttctgattcttctgttgtctcctaactgtctgtgtacatgattgtttctctgctgcag
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GAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttcacatgagcttgagcttcagtttcatggttctgttacttct--tagttgttcagtattcatgcatgtgattgtctctc--ctgcag
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G143356_T02 (Zea mays), 5'ss of exon 9
GAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcatttagatgtgctcagttttgatgtttctttctgattcttctg-ttgtctcctaactgtctgtgtacatgattgtttctctgctgcag
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GAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGCGCAATAATGTTTGCCATGAAAGATAAGCTTgtaagtgttcaaatgagcttgagctt----ctctttcatggttctgttacttagttgttcagtattcatgcacgtgattatcctcc--ctgcag
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G00380.2 (Glycine max), 5'ss of exon 7
GAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcatttagatgtgctcagttttgatgtttctttctgattcttctgttgtctcctaactgtctgtgtacatgattgtttctctgctgcag
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GAATATGTCAGTGGCTTTTATTTCTGTCATCTTGCTTCCAATTGTAGGCAATGCTGCAGAACATGCCAGTGCTATCATGTTTGCCGTGAAGGACAAGCTTgtaagtggtt-------------ttcaaagcctactctttattctacgaatattgttaatctgctaatgaattcaatctctccttag------
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 7
GAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcatttagatgtgctcagttttgatgtttctttctgattcttctgttgtctcctaactgtctgtgtacatgattgtttctctgctgcag
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GAATATGTCAGTGGCTTTTATTTCTGTCATCTTGCTTCCAATTGTAGGCAATGCTGCAGAACATGCCAGTGCTATCATGTTTGCCGTGAAGGACAAGCTTgtaagtg-------------gctttcaaagcctactctttattctatgaatattgttaatctgctaatggattcaatctctcctcag------
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 5'ss of exon 8
GAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcatttagatgtgctcagttttgatgtttctttctgattcttctgttgtctcctaactgtctgtgtacatgattgtttctctgctgcag
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AAACATGCCAGTGGCTTTTATTAGTGTCATTCTGCTTCCAATTGTAGGAAATGCTGCTGAGCATGCCAGTGCAATTATGTTTGCCATAAAGAACAAGCTTgtgagtgcttagaagaatgcaaatg-gttggttttttttgcttatgttaat-tctgctgattgacc---tacattcttctatag---------
upper sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 5'ss of exon 9
GAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcattta---gatgtgctcagttttga--tgtttctt--------tctgattcttctg-----ttgtctcctaactgtctgtgtacatgatt-gtttctctgctgcag-------------------------------------------------------------------------------
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GAATGTACCCATTGCGTTTATAAGCGTTATCATATTGCCGATTGTTGGAAACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctctcgtgatggtctaagcctagaaatgttactagacaacaacgtgatattcatgagagcttgacatttccaagccctagtcaataattcattccttcgctggtcgtcaatcatcgactttgttgtgtaaactcattggcttcgatttttgtcttcgtcttgttcacatttttctttctggcagMapped 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|286840|gb|D15647.1|D15647EST: ACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTT GACATAACACTGGGTGTTGCAATTGGGTCATCAACGCAGATATCAATGTTT
genomic: ACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcattt ... tctgctgcagGACATAACACTGGGTGTTGCAATTGGGTCATCAACGCAGATATCAATGTTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTGCCATGAAAGATAAACTTgtaagcatttagatgtgctcagttttgatgtttctttctgattcttctgttgtctcctaactgtctgtgtacatgattgtttctctgctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT