Sequence
atgc intronic sequence ATGC exonic sequenceAAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgtttttgcatccttttagtatattgtgtcccttttgtgtgttctttattactatatgtgacagttgctgaaaaaaacatcatttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g52340.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G108115_T01 (Zea mays), 5'ss of exon 3
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgtttttgcatccttttagtatattgtgtcccttttgtgtgttctttattactatatgtgacagttgctgaaaaaa-acatcattt-cag
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AAACCCCAGGCTGCCGTTGATAAAACTCTTGACAGCAAGGTTTTCAAAGGATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaat-ttatctttgccttgatctagtttattgcacattctttgattcttatttatcatcattcatgatgattatcaaattgctgtattgttttcag
upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G521844_T01 (Zea mays), 5'ss of exon 3
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgtttttgcatccttttagtatattgtgtcccttttgtgtgttctttattactatatgtgacagttgctgaaaaaa-acatcattt-cag
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AAACCACAGGCTGCAGTTGATAAAACACTTGACAGCAAGGTTTTCAAAAGATGGGTTGAAACTGACAATCCGTGGACATCTGATGACGAGACTGATAATAgtaat-ttatctttgccttgatctattctattgcacattctttgtttcttgtttattatcattcttgacgattatcaaattgttgtactgttttcag
upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G23150.1 (Glycine max), 5'ss of exon 3
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagt--------tgtttttgcatccttttagtatattgtgtcccttttgtgtgttctttatt--actatatgtgacagttgctgaaaaaaacatcatttcag
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AAACCTCAGGCAGCCGTTGACCGTACTTTAGACAGTAAAGCTTTCAGAGGATGGACAGAAATAGACAATCCATGGACAAATGATGATGAGACTGACAATGgtgcgttactctgtatgctgattcgtatctaaattatttgtggtcatagttgtattttatctaattaattgtgtgaaatattaacggtgaagtatataga-----
upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G10830.2 (Glycine max), 5'ss of exon 3
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgtttttgcatcctt-ttagtatattgtgtcccttttgtgtgttctttattactatatgtgacagttgctgaaaaaaacatcatttcag------
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AAACCTCAGGCAGCTGTTGACCGTACTTTAGACAGTAAAGCTTTCAGAGGATGGACAGAAATAGACAATCCATGGACAAATGACGATGAGACTGACAATGgtgc-gttactct-gtatgctgattcgtatctaaaatttgtggtcatagttgtagtttactaattatgttcttcaaatgagtttatattgatgaataatttt
upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 5'ss of exon 3
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgttt---ttgcatcctttta-gtatattgtgtcccttttgtgtgttctttattacta-tatgtgacagttgctgaaaaaaacatcatttcag
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AAGCCACAGGCGGCTGTTGACCGTACACTAGATACCAAAGCTTTCAAAGGCTGGGTAGAAGTAGACAATCCATGGACAAATGATGATGAGACTGACAATGgtggattcttttaccctgcacattctaacatttttcattttatgtttagttaaacgtttttgttaatttatttcttttcaagccaattgcatctttctga
upper sequence: LOC_Os03g52340.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0027g00090.t01 (Vitis vinifera), 5'ss of exon 3
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgtttttgcatccttttagtatattgtgtcccttttgtgtgttctttatta--ctatatgtgacagttgc---tgaaaaaaacatcatttcag------
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AAGCCACAGGCTACAGTGGATCGGACACTAGATAGTAAAGCTTTCAGAGGTTGGATAGAAACAGATAATCCATGGACAAATGATGATGAGACTGATAATGgtaaac---tctccctagtttgttgatgaa---tgtgcatattttgtgttgtttattaagccatgaaagtcttttccatttgggaggtcaattattttgggatctgMapped 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|29656394|gb|CB652669.1|CB652669EST: ATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATG CTGAGATGACTTATGTGAATCTTCAACTCCACCCTGAACGTTACACTGGCT
genomic: ATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgt ... atcatttcagCTGAGATGACTTATGTGAATCTTCAACTCAACCCTGAACGTTACACTGGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAACCACAGGCTACTGTTGATAGAACCCTTGATGCCAAGGTTTTCAAAGGATGGATTGAAACCGACAATCCATGGACATATGACGATGAGACTGATAATGgtaaagttgtttttgcatccttttagtatattgtgtcccttttgtgtgttctttattactatatgtgacagttgctgaaaaaaacatcatttcag
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