Sequence
atgc intronic sequence ATGC exonic sequencegtaagcctttcatcatttgttgggttgaatcttttgtccagatgggtggaaaatcatctgaatttcctttttttttcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g63060.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G004949_T01 (Zea mays), 3'ss of exon 5
gtaagcctttcatcatttgttgggttgaatcttttgtccagatgggtggaaaatcatctgaatttcctttttttttcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
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gtaagttttctgt----tgttgg------cctactgtt---gtgggtggaaagttctgttgattcaaatcgt-----ccttgcagTTCCTCGCGGAGTGCTTTTTGGTTGTGGCGATCTGATATTTTCATCTCACATGATCTTCACCCTAGTTTTCGTGCGCACGTACCATAAATATGGCTCAAA
upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G169293_T01 (Zea mays), 3'ss of exon 7
gtaagcctttcatcatttgttgggttgaatcttttgtccagatgggtggaaaatcatctgaatttcctttttttttcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
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gtaagttctctgt----tgctgg------cctactgtt---gtgggtggaaagttctgttgattcaaattgat----ccttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGTGATCTGATATTTTCATCTCACATGATCTTCACTCTGGTTTTTGTGCGCACATACCATAAATATGGCTCAAA
upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G15850.1 (Glycine max), 3'ss of exon 7
----gtaagcctttcatcatttgttgggttgaatcttttgtccagatgggtggaaaatcatctgaatttcctttttttttcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
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gtgagtatacattatagtattgaaggtgttca-tatttgatgcctttgtgtt-----tgttttggcactcatttcaattatatgtacagTTCCGCGTGGCGTGGTCTATGGATGTGGTGATTTGATATTCTCATCACACATGATCTTTACTCTTGTCTTTGTGCTCACGTATCAGAAATATGGCACTCG
upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G26700.1 (Glycine max), 3'ss of exon 7
gtaagcctttcatcatt-tgttgggttgaatcttttgtccagatgggtggaaaatcatctgaatttcctttt----tttttcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
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gtgagtata-cattatcgtattggagttgttcatattt---gatgcctatgtatttgttttgttgctcatttcaattatattatgtacagTTCCACGTGGTGTGGTCTATGGATGTGGTGATTTGATATTCTCATCACACATGATCTTTACACTTGTTTTTGTGCTCACGTATCAGAAATATGGCACTCG
upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G41820.1 (Glycine max), 3'ss of exon 7
gtaagcctttcatcatttgttgggttgaatcttttgtccagatgggtggaaaatcatc-tgaatttcctttttttttcctt-tgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
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gttagtatactattgttc-ttgagtt----ctttagctttgactcctttttggttgttatggtgctcatttggttttcatcatgcagTTCCACGTGGCGTGATATATGGATGTGGTGATTTGATATTTTCATCACACATGATCTTTACTCTAGTCTTTGTTAATACATATCATAGATACGGCACAAG
upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0007g01510.t01 (Vitis vinifera), 3'ss of exon 7
gtaagcctttcatcatttgttgggttgaatcttttgtccag-atgggtggaaaat---catctgaatttccttt---ttttttcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
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gtgagcatcccgtgtgttaatcttttg--tctttagctcattactagtaggcaataaatatttatgtgctcattaagttgttgaatgtgcagTTCCTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGMapped 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|33675715|gb|CF303954.1|CF303954EST: GGCCACTCTTCCACCGCCCCATAATGTACTTGAAGTGCTCCTGATCAACT TTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACA
genomic: GGCCACTCTTCCACCGCCCCATAATGTACTTGAAGTGCTCCTGATCAACTgtaagccttt ... tcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACA
EST:
gi|2312423|gb|C28578.1|C28578EST: GGCCACTCTTCCACCGGCCCATAATGTACTTGAAGTGCTCCTGATCAACT TTCCTCGTGGAGTGCTTTTTTGGTTGTGGCGNTCTGATTTTGTNATCTCAC
genomic: GGCCACTCTTCCACCGCCCCATAATGTACTTGAAGTGCTCCTGATCAACTgtaagccttt ... tcctttgcagTTCCTCGTGGAGTGCTTTTT-GGTTGTGGCGATCTGATTTTTTCATCTCAC
EST:
gi|300215948|gb|HO088574.1|HO088574EST: GGCCACTCTTCCACCGCCCCATAATGTACTTGAAGTGCTCCTGATCAACT TTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACA
genomic: GGCCACTCTTCCACCGCCCCATAATGTACTTGAAGTGCTCCTGATCAACTgtaagccttt ... tcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
57 (upstream exon),
73 (downstream exon)
Score:
29GGCTCAAAAATGGCCACTCTTCCACCGCCCCATAATGTACTTGAAGTGCTCCTGATCAACTgtaagccttt ... tcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgtccagatgggtggaaaatcatctgaatttcctttttttttcctttgcagTTCCTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAA
tcatctgaatttcctt CT-rich tract
aatttccttttttttt TA-rich tract