Sequence
atgc intronic sequence ATGC exonic sequence...agattacttgataaagcttagaaatttttagattgttatatattggactaaaactgctgtgacttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47290.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 3
agattacttgataaagct-tagaaatttttagattgttatat-attggac-taaaactgctgtgacttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
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----------gtgaggccacgaaaaccctcagattgtgatgtcgttgtgcaccgagccattgttccttg--aacaa-----ttgatgc----ttgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTCATTCTCGGAAAGAAGATGAAG
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 3
agattacttgataaagcttagaaattt---ttagattgttatatattggactaaaactgctgtgac-ttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
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-gtggggctatcaaaacccagatttttcattcagattgtcatgtcgtggtaacggcctaacgggttgttgtgaaccaaaccattgttcc-------tgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTGATTCTCGGTAAGAAGATGAAG
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 2
-----agattacttgataaagcttagaaatttttagatt--gttatatattggactaaaactgctgtg---acttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
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gtaaacaatggtgatgtttctctttaaaactgttggtttaagttggaaactttagtggatttgttgtttgcatgtgtagatgaattggttgttgatgaatttt--ttcagGGACCTTCGAGTAAGAACCCACTTGCTTACAGGTGGTATAACGCTGAAGAAGAGATTCTTGGGAAGAAAATGAAG
upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ07726 (Selaginella moellendorffii), 3'ss of exon 2
agattacttgataaagcttagaaatttttagattgttatatattg-gactaaaactgctgtgacttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
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------------------------------gtctgggatttctcgtgtttctcatctcaatacctttt---ctaa-acgcgctcggatgg--gaatttcagGGACCCTCTAGCAAGAACCCACTTGCTTTCAAGTGGTACAATCCGGAGGAAGAGATCTATGGCAAGAAGATGAAGMapped 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|88309764|gb|CI656505.1|CI656505EST: GGGATTGGGAAGGGGAGTTCTTCCCTGGCATCCCCAAGATCAAGTATGAG GGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAA
genomic: GGGATTGGGAAGGGGAGTTCTTCCCTGGCATCCCCAAGATCAAGTATGAGgtgagggagg ... tgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAA
EST:
gi|29625366|gb|CB630377.1|CB630377EST: GGGATTGGGAAGGGGAGTTCTTCCCTGGCATCCCCAAGATCAAGTATGAG GGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAA
genomic: GGGATTGGGAAGGGGAGTTCTTCCCTGGCATCCCCAAGATCAAGTATGAGgtgagggagg ... tgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactaaaactgctgtgacttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
gactaaa putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agattacttgataaagcttagaaatttttagattgttatatattggactaaaactgctgtgacttgtgagctaagactttgttgcacaattgcactgcagGGTCCAAGCAGCAAGAACCCGCTTGCTTACAAGTGGTACAATGCTGAGGAAGTGATTCTTGGGAAGAAGATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG