Sequence
atgc intronic sequence ATGC exonic sequenceCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatttgatatataatcctacaacag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g10784.3 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G168510_T01 (Zea mays), 5'ss of exon 4
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatg-atgatattgtac--tcttgggacttaatttgatatataatcctacaacag
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CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAGgtaaag----agatgcggacatgaacaactcgatggtatattaacataatctgct-gttatgctcaacattaaacggatcttattgcataatcccacag----------------------------
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA09G38010.1 (Glycine max), 5'ss of exon 11
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgt--aaaacctaa---gaggaagctataatgttgccttttgtttcttacattgct-----ttcccagtgacactcca--caaataatgatgata-ttgtactcttgggacttaat-ttgatatataatcctacaacag------------------------------------------
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TTGGATGGAGGAGGTGTGGCAAGTGGAGGTCTTCGAGAACTGATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGgttcggagactaatctatgccagttataat-ttactagtattattataaaaagaaagtagttcagagtaaaatctcagctatatagtcatcatacttgtgattccaagatctgctattcaaagagtatctttatttagtttgtcaatcactgagcttctaaaagccttttgacttttcag
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA18G48370.1 (Glycine max), 5'ss of exon 10
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaaga-----ggaagctataatgttgccttttgtttcttacattgctt---tcccagtgacactcca--caaataatgatgata-ttgtactcttgggacttaat-ttgatatataatcctacaacag-------------------------------------------
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-TGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGGtatggtgaatagcctatgctagttataatttactagaataattataaaagaatgtagttcagagtaaaatctcagctatatagccatcatacttgtgattccaagatctgctattcaaagagtatctttatttagtttgtcaatcactgagcttctaaaagctttttgggttttcagg
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G79500.4 (Arabidopsis thaliana), 5'ss of exon 10
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaa-gctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatt-tgatatataatcctacaacag
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TTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAGgtagtatataccttgtttgataccaaatcgttttagaaattttatcaagctcattggattattggtcaca--taattctggattcgt--tgttccaacttgattatgatcag--------------
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G16340.3 (Arabidopsis thaliana), 5'ss of exon 11
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaa--aacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataat--gatgatattgtactcttgggacttaatttgatatataatcctacaacag
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TTAGATGGTGGGGGTGTTGCTAGTGGTGGCCTTCGCGAATTAATACCATGCATAGCAAGAACCGCCGTAGCTGTTGGTGTCGATGGAATTTTCATGGAGgtatccaactttatcgcaagttttgtcatc-tcgctgaatctttgttccaatttggttatgaaacttggttcattttccggtgaattag---------------------------------------
upper sequence: LOC_Os12g10784.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 5'ss of exon 10
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatttgata-tataatcctacaacag
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CTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAGgtacaaaatcagaatttgtta-agagtggataat--ctttttgccatcttctctcag---------gtttatggtact--tgttgctcgattggg-ttcattttattactaaaat----------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|88252381|gb|CI350809.1|CI350809EST: GCATCCCAA-GACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG GTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGGTA
genomic: GCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaaccta ... cctacaacagGTACATGATGATCCCTTGAACGCACCTTGTGATGGCCCAACTCAATGGGTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAGgtaaaacctaagaggaagctataatgttgccttttgtttcttacattgctttcccagtgacactccacaaataatgatgatattgtactcttgggacttaatttgatatataatcctacaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA