Sequence
atgc intronic sequence ATGC exonic sequenceTGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGAgtacgtatcctaacatatttaactgatccatttgcgtttcattctacttctgatttaacttattactcatttttttattgtttttacag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g18360.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g18360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G074742_T01 (Zea mays), 5'ss of exon 3
TGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGAgtacgtatcctaacatatttaactgatccatt--tgcgtttcattctacttctgatttaacttatta-ctcatttttttatt-gtttttacag----
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TGGAGTACCATCAGCGGGTTCCTCACGAGAAGGCCGCGCATGTTCTCACCTATGAAGACCATGATGGAGACTGGATGATGGTTGGGGATGTACCGTGGGAgtaatgtttcttctccgctcaaatgattcactcttgcatttcatt-tactgttagtt-aattaatagtcttgtctccccgtccattttttccggcag
upper sequence: LOC_Os01g18360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G853479_T01 (Zea mays), 5'ss of exon 2
TGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGAgtacgtatcctaacatatttaactgatccatttgcgtttcattctacttctgatttaacttattactcatttttttattgtttttacag
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TGGAGTACCATCAACGAGTTCCTCACGAGAAGCCTGCACATGTTCTCACCTATGAAGACCGGGATGGAGACTGGATGATGGTTGGGGATGTACCGTGGGAgtatgtttctcctcctcctccgcttcatcaatca----ttattcacctgtgcatttcatttacaagaaactaggat-ttgttctggcag
upper sequence: LOC_Os01g18360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0005g02550.t01 (Vitis vinifera), 5'ss of exon 4
TGGAGTGCCATCAACAAGTTCCTGG--CCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGAgtacgtatcctaacatatttaactgatccatttgcgtttcattctacttc-tgatttaacttattactcatttttttattgtttttacag
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-GGGCTGAGGTGGATGGAGTTCTGCATTCTGAGAAATGCC-ATGTGCTAACATATGAAGACAAGGAAGGAGACTGGATGATGGTTGGGGATGTTCCTTGGGAgtgagtttc--actttaacc--cccatccacttcttgtctactctttttaatggattaaa--gttgcccaacttct-gttttttgtgcag
upper sequence: LOC_Os01g18360.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv05s0020g01070.t01 (Vitis vinifera), 5'ss of exon 3
--TGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGAgtacgtat--cctaacatatttaactg--atccatttgcgtttcattctacttctgatttaacttattactcatttttttattgtttttacag------------------
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ATCCTCATGTTGGTGGCGCTGATCATTCCGGAAAATA--TCATATCTTGACTTATGAAGACAAGGAAGGGGACTGGATGATGGTCGGAGATGTTCCTTGGGAgtatgcataacctaattaacatactcacaatcactccattcttcatatttttcatatttttccttgtcagttatttatttatt-tatttatttccatttgaatatctatagMapped 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|89185778|gb|CI047647.1|CI047647EST: TATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGA ACTCTTCCTGAGCAGCGTAAAGAAGCTCAGGATTGCAAGGATGGATAAATG
genomic: TATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGAgtacgtatcc ... gtttttacagACTCTTCCTGAGCAGCGTAAAGAAGCTCAGGATTGCAAGGATGGATAAATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGAGTGCCATCAACAAGTTCCTGGCCAGAAGGCTGCCCATGTCCTCACCTATGAAGACCAGGACGGGGACTGGATGATGGTTGGGGACGTCCCATGGGAgtacgtatcctaacatatttaactgatccatttgcgtttcattctacttctgatttaacttattactcatttttttattgtttttacag
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