Sequence
atgc intronic sequence ATGC exonic sequenceTTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaaggaaacaatctacttttgatatttacatctgcaacagttgctaagtgaatatacaaatactttctaaggaattgttcccaattttgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g44330.2 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G151236_T03 (Zea mays), 5'ss of exon 9
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcat-cattttcaaatctcttcttaccttcaaggaaacaatctacttttgatatttacatctgcaacagttgc-taagtgaatatacaaatactttctaaggaattgttcccaattttgcag
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TTATACCGGTAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcttacatgcttgcatgattgttaacat---aacaaatgaataactctttat-tatgtggtagtaggacctgcatgattgcatactcatg-accttttgt----------------------
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G147811_T02 (Zea mays), 5'ss of exon 10
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaag---gaaacaatctacttttgatatttacatctgcaacagttgctaagtgaa--tatacaaatactttctaaggaattgttcccaattttgcag
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TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgt---tagtcatgcttgcatcattgataaccttaacgaatgaatgactctttattttgtggtagcaggaccaatgttttctgagtcgagtcatgcagttaccg---------------------------
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA20G24820.2 (Glycine max), 5'ss of exon 12
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaaggaaacaatcta---cttttgatatttacatctgcaacagttgctaagtgaatatacaaatactttctaaggaattgttcccaattttgcag
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GTATATAGGGAAGGTTCTTTTCCCAGGGTTTACAAACAATGACATGCTACGGCTTCACATGGAACTGAAGGGCCCTTTTCCAAAGAAGATGCTGCGTAAGgtaaacatatattgtttcatttaaattaaacatatattgtttcatttaaattttttatcattagtgtctggcactgtttgagtgttga-gtatgcataatt---------------------------
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA10G42220.1 (Glycine max), 5'ss of exon 15
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaaggaaacaatctacttttgatatttacatctgcaacagttgctaagtgaatatacaaatactttctaaggaattgttcccaattttgcag
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GTATATAGGGAAGGTTCTTTTCCCAGGTCTTACAAACAATGACATGCTACGGCTTCACATGGAACTGAAGGGTCCTTTTCCAAAGAAGATGCTGCGTAAGgtaaacatatattgtttcatttttttttttttt-------atcattagtgtctggccactgtttgagt----gttgagtatgaattattttaatacttgatacaagtttgt--------------
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G25840.1 (Arabidopsis thaliana), 5'ss of exon 10
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgtt---------cttcatcat---tttcaaatctcttcttaccttcaaggaaacaatctacttt-tgata--tttacatctgcaa---cagttgctaagtgaatatacaaatactttctaaggaattgttcccaattttgcag-------------------------------
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TTATAGTGGAAAAGTTCTTTTCCCTGGCGCCACAAACAATGATATGTTACGCCTTCATATGGAACTGAAAGGTCCCTTCCCTAAAAAGATGCTTCGCAAGgttagcattaaactagattgggtgttgtgaatgtcacctgatcactgatcaaaatgtcttccaaatgataactttccttaggcaaatccatatgtatggtggagatatagttgtatgtttaagagaagcagtttttaatgcatgttctaatgtttctgttatttggtttaacag
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 5'ss of exon 10
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaaggaaacaatctacttttgatatttacatctgcaacagttgctaagtgaatatacaaat--actttctaaggaattgttcccaattttgcag
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TTATACGGGAAAAGTTCTTTTTCCGGGTCCTTCAAACAATGACATGCTTCGGCTTCACATGGAGTTGAAGGGTCCTTTTCCAAAAAAGATGCTTCGAAAGgttagagtttaaatt---gtttatttagagatgcaggcaaagattccttttcttct-ttgaagcttgcgctggttttttggtagcggtttaacttgacatgcta-----------------------
upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ31639 (Selaginella moellendorffii), 5'ss of exon 9
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaaggaaacaatctacttttgatatttacatct---gcaacagttgctaagtgaatatacaaa-tactttctaaggaattgttcccaattttgcag
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TTACACTGGCAAGGTTCTTTTCCCAGGCTCCACAAATAATGACATGCTAAGGCTTCATATGGAGCTCAAAGGGCCATTTCCCAAGAAGATGCTGAGGAAGg----tgatcacctt--accctccttctgtgtt-gttctttcatcgttttttaggcattgacacccttggcgtcgggtgacagatggagacttaagctacaacttaa----------------------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|88974595|gb|CI022136.1|CI022136EST: GCTTCATATGGAACTGAAGGGCCCCTTCCCCCAA-AAAATGCTTCGAAAG GGTGCCTTTACGATGCAACATTTTGACCAAGATCTCAACTTTCATGCCACT
genomic: GCTTCATATGGAACTGAAGGGCCCCTT-CCCCAAGAAAATGCTTCGAAAGgttcttcatc ... aattttgcagGGTGCCTTTACGATGCAACATTTTGACCAAGATCTCAACTTTCATGCCACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaaggaaacaatctacttttgatatttacatctgcaacagttgctaagtgaatatacaaatactttctaaggaattgttcccaattttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA