Sequence
atgc intronic sequence ATGC exonic sequenceAAGAGAACTAGGTTTTACATTCTCCTTTCCAGTGAAACAAAAATCATTGGCATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttgttacctcacatatgtaaaccaaatgaaaatcctaaggaaggatatccagcttcattgtgaatttaaaaaaaaaacatgtcgtcctggatggaaattcaccaattgtgaattctcttttagttctgttatatcttatatatccaattagttgtgtataacatacttacttgttgctttgaaggcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g52450.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g52450.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G171373_T01 (Zea mays), 5'ss of exon 3
AAGAGAACTAGGTTTTACATTCTCCTTTCCAGTGAAACAAAAATCATTGGCATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttgttacctcacatatgtaaaccaaatgaaaatcctaaggaaggatatccagcttcattgtgaatttaaaaaaaaaacatgtcgtcctggatggaaattcaccaattgtgaattctcttttagttctgttatatcttatatatccaattagttgtgtataacatacttacttgttgctttgaaggcag
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AAGACAACTTGGTTTTACATTCTCCTTTCCAGTGAAGCAAAATTCAGTTGCATCTGGCACTCTTATCAAATGGACAAAGGGTTTTGCAATTGATGAAATGgtatgatcagttcttgtagcctactttatgtattgaaga-ctaatttaagaatatg-ggcctgtttcaggagtagaacaaatgccatgtttcatcctgtcaa---------------------------------------------------------------------------------------------
upper sequence: LOC_Os01g52450.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G12190.1 (Glycine max), 5'ss of exon 3
AAGAGAACTAGGTTTTACATTCTCCTTTCCAGTGAAACAAAAATCATTGGCATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttgttacctcacatatgtaaaccaaatgaaaatcctaaggaaggatatccagcttcattgtgaatttaaaaaaaaaacatgtcgtcctggatggaaattcaccaattgtgaattctcttttagttctgttatatcttatatatccaattagttgtgtataacatacttacttgttgctttgaaggcag
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AAGGGAACTGGGTTTTACATTCTCATTTCCAGTGAAGCAAACATCCATAGCATCTGGGACTCTAATAAAGTGGACTAAAGGTTTCAATATTGAGGATGCGgtaattcttgttaccttgattatttttttttagt----attctatct---gccttgccttgccattctgtctttttctcatctccttttgatcatg-attgtgatgca---------------------------------------------------------------------------------------
upper sequence: LOC_Os01g52450.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G01070.1 (Glycine max), 5'ss of exon 3
AAGAGAACTAGGTTTTACATTCTCCTTTCCAGTGAAACAAAAATCATTGGCATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttgttacctcacatatgtaaaccaaatgaaaatcc-taaggaaggatatccagcttcattgtgaatttaaaaaaaaaacatgtcgtcctggatggaaattcaccaattgtgaattctcttttagttctgttatatcttatatatccaattagttgtgtataacatacttacttgttgctttgaaggcag
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AAGGGAACTGGGTTTTACCTTCTCCTTTCCAGTGAGGCAAACATCAATTGCATCTGGGAATCTAATAAAGTGGACTAAGAGTTTCAATATTGAGGATATGgtaattcttattaccttgattttg----ctatattcaagtctattttccttgccattctttcttattgtcatctcatttgttttgatcgtgattatgg-tgcata-------------------------------------------------------------------------------------------
upper sequence: LOC_Os01g52450.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G35890.1 (Glycine max), 5'ss of exon 3
AAGAGAACTAGGTTTTACATTCTCCTTTCCAGTGAAACAAAAATCATTGGCATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttgttacctcacatatgtaaaccaaatgaaaatcctaaggaaggatatccagcttcattgtgaatttaaaaaaaaaacatgtcgtcctggatggaaattcaccaattgtgaattctcttttagttctgttatatcttatatatccaattagttgtgtataacatacttacttgttgctttgaaggcag
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AAGAGAACTGGGTTTTACATTCTCATTCCCAGTGAGGCAAACATCGATTGCATCTGGGACTCTAATAAAGTGGACTAAAGGTTTCAATATTGAAGATGTGgtaattcttgtcaacctgattacattat---attcaactttatttgggcaaccattttttcttctagtcatttattttgattgatctatcat-----gtatttgttca---------------------------------------------------------------------------------------
upper sequence: LOC_Os01g52450.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G03730.1 (Glycine max), 5'ss of exon 3
AAGAGAACTAGGTTTTACATTCTCCTTTCCAGTGAAACAAAAATCATTGGCATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttgttacctcacatatgtaaaccaaatgaaaatcc-taaggaaggatatccagcttcattgtgaatttaaaaaaaaaacatgtcgtcctggatggaaattcaccaattgtgaattctcttttagttctgttatatcttatatatccaattagttgtgtataacatacttacttgttgctttgaaggcag
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AAGAGAACTGGGTTTTACATTCTCATTCCCAGTGAGGCAAACATCGATTGCATCTGGGACTCTAATAAAGTGGACTAAAGGTTTCAATATTGAAGATGCGgtaattcttgtta----acctgattagattacattcaattttatttgtgcaaccattttttcttctcgtcattt---atcttgattgctctgtcatgtattg---ttcac--------------------------------------------------------------------------------------Mapped 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|33677814|gb|CF306053.1|CF306053EST: CATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATG GTCGGCAAGGATGTTGTGGCTGAATTAAACATGGCTATCAGAAGTCAAGGA
genomic: CATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttg ... ttgaaggcagGTCGGCAAGGATGTTGTGGCTGAATTAAACATGGCTATCAGAAGTCAAGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGAGAACTAGGTTTTACATTCTCCTTTCCAGTGAAACAAAAATCATTGGCATCTGGCACTCTTATCAAGTGGACGAAGAGTTTTGCAATTGATGAAATGgtcagttttgttacctcacatatgtaaaccaaatgaaaatcctaaggaaggatatccagcttcattgtgaatttaaaaaaaaaacatgtcgtcctggatggaaattcaccaattgtgaattctcttttagttctgttatatcttatatatccaattagttgtgtataacatacttacttgttgctttgaaggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA