Sequence
atgc intronic sequence ATGC exonic sequence...tgaataattggcactccctaaatcatttgtttgtttgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g05780.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
--tgaataattggcactccctaaatcatttgtttgtt-tgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
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actatttaagtgccactttttcatttggacttcggccctgtcatgtgcccaat---ataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G014610_T01 (Zea mays), 3'ss of exon 3
tgaataattggcactccctaaatcatttgtttgtttgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
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-------------------------gtaagttgttagtcggtctgctagctgcgctc---ttgttctggaactga---tcgttttgtgttgctgctgcagTATGTTCATTTCCTCCAGCGCAAGCACTCTCTCAACTCGTTCAGCCTGCTGGGCCACACGGCGCCGGCGCAGGCAGGGTCGCTGCTGCTGGCAGGGCCGT
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G071378_T02 (Zea mays), 3'ss of exon 4
tgaataattggcactccctaaatcatttgtttgtttgtcacttctttaatta--tagacaaatta-ctcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
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---gctcttgctaccccacgttttcagaaatggaccgttgcccttccatgtagccagtaaaagcagcacagtttactcatttttatttgtgttccttctgcagTATGTCCACTTTCTCCAACGCAAGTACTCTCTGAACTCATTCAACCTGCTGGGCCACACTGCTCCAGCCCAAGCTGGGTCACTCCTGCTAGTGGGACCAT
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
-tgaataattggcactccctaaatcatttgtttgtttgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
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gtaagtgttctgtgctc------ttacggagtaacatatcgtttctttgttta-agataa------tactaatattggtgtggtttttacatga--tgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
tgaataattggcactccctaaatcatttgtttgtttgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
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-----------------gtaagttctttgagctacggtttacacaaagattaagattaagatttacacaaagtttctctcttttg---------ttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCATMapped 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|218493260|gb|FG949071.1|FG949071EST: GTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATAT TATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
genomic: GTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATATgtaagttaaa ... ttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
EST:
gi|325494254|gb|JG458778.1|JG458778EST: GTCTGGCTGCTGCTGTTATAGTTGTTTGGAGCACAGCTTTACAACAATAT TATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
genomic: GTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATATgtaagttaaa ... ttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
EST:
gi|44679067|gb|CR292501.1|CR292501EST: GTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATAT TATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
genomic: GTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATATgtaagttaaa ... ttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
EST:
gi|58595545|gb|CK006073.1|CK006073EST: GTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATAT TATGTTCATTTGCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
genomic: GTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATATgtaagttaaa ... ttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTG
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:
62 (upstream exon),
64 (downstream exon)
Score:
30TATAGGTGTTGCAGTCTGCACAGTTACTGATGTCAGTGTAAATGCAAAAGGTCTGGCTGCTGCTGTTATAGCTGTTTGGAGCACAGCTTTACAACAATATgtaagttaaa ... ttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT
ctttaat putative branch site (score: 30)
ttactcattagtttcc putative PPT
ttttctatttt TA-rich tract