Sequence
atgc intronic sequence ATGC exonic sequenceAGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAACgtaagcttaacattcgttacacttgagtacttgacattccatagacagtaagccggtggtttgcttctggtgctttcaagtttgaacctttgactaacttctcaaaggctttgtgctatacccgcattctag
Basic information
species | Oryza sativa |
transcript | LOC_Os07g22400.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g22400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G130351_T01 (Zea mays), 5'ss of exon 3
AGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAACgtaagcttaacattcgttacacttgagtacttgacattccatagacagtaagccggtggtttgcttctggtgctttcaagtttgaacctttgactaacttctcaaaggctttgtgctatacccgcattctag
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ATGAATTGTGGAAGACACACATGGGGCACCAGGATCCAGCAGAGACTTTGAATAAGGATATAATATCACACTTTGTGCTCCGTCTTGTCTACTGCAGAACgtaagcttaatattcga-acgtttatattgtctacatatattggcta------tggtggttcacttgtggttcttttga--ccaactcaatggaaagctgt------attttatacaacacacag-------
upper sequence: LOC_Os07g22400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G044317_T04 (Zea mays), 5'ss of exon 3
AGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAACgtaagcttaacattcgttacacttgagtacttgacattccatagacagtaagccggtggtttgcttctggtgctttcaagtttgaacctttgactaacttctca-aaggctttgtgctatacccgcattctag
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GTGAATTGTGGAAGACACACATGAGGCACCAGGATCCAGCAGAGAATTTGAACAAGGATATAATATCGCACTTTGTGCTCCGTCTAGTCTACTGCAGAACgtaagattaatattcat-atgtttatattcgctacatatattagcta------cggttgttcacttgtggttct--------------tttgaccaactcaccagaaagctgtatttgatacg-acacacag-
upper sequence: LOC_Os07g22400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G11130.1 (Glycine max), 5'ss of exon 3
AGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAACgtaagcttaacattcgttacacttgagtacttgacattccatagacagtaagccggtggt-ttgcttctggtgctttcaagtttgaacctttgactaacttctcaaaggctttgtgctatacccgcattctag
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AGGACCTGTGGAAAATGAATATGAGACATCAAGACGCATCTCAGGTTCTGAACAAGGATATTATATCACATTTTGTTCTACGTCTGGTGTATTGCAGAACgtaag---agctcttctctctcttttgtgcatt-ctttttctatgttgt---tctgtgccattgaaaagaatcctcggttgtttga--ctaataatggctgatcaaaat------------------------
upper sequence: LOC_Os07g22400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G28150.1 (Glycine max), 5'ss of exon 3
AGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAACgtaagcttaacattcgttacacttgagtacttgacattccatagacagtaagccggtggtttgcttctggtgctttcaagtttgaacc-tttgactaacttctcaaaggctttgtgctatacccgcattctag
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AGGACCTGTGGAAAGTGAATATGAGACATCAAGAGGCAACTCAGGTTCTGAACAAGGATATTATATCTCATTTTGTTCTACGTCTGGTGTATTGCAGAACgtaag---agctcttatcttctctctcttttgtgcattctttttttact------gttgttccatgccattgaaaagaatcctcggttgtttgactaat------aatgcctgat------------------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|58665435|gb|CK054121.1|CK054121EST: AACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAAC GGAGGAGCTGCGGAAGTGGTTTCTCTCCATGGAGACTACGCTTTTTCGCTA
genomic: AACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAACgtaagcttaa ... cgcattctagGGAGGAGCTGCGGAAGTGGTTTCTCTCCATGGAGACTACGCTTTTTCGCTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGGAATTGTGGAAAGCCCATATGAGGCACCAGGATCCTACAGAGACTTTGAACAAGGACATAATATCTCACTTTGTTCTCCGTCTTGTCTACTGCAGAACgtaagcttaacattcgttacacttgagtacttgacattccatagacagtaagccggtggtttgcttctggtgctttcaagtttgaacctttgactaacttctcaaaggctttgtgctatacccgcattctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG