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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCGCACTACCTCACCCCCAAGGCCCTCAACCACCGCTTCTCCTCCGGCGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcctgaattctctccttttttttctccccttgattcgttcgtacgataaatctttgggcttacggatgagtttgcgtggtttgatttttggcag

Basic information

species Oryza sativa
transcript LOC_Os03g21030.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21030.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G031001_T01 (Zea mays), 5'ss of exon 1
GTCTCGCACTACCTCACCCCCAAGGCCCTCAACCACCGCTTCTCCTCCGGCGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcctgaattctctcctt--ttttttctccccttga---------ttcgttcgtacga--taaatctttgggcttacggatgagtttgc-gtggtttgatttttggcag--------------------------------------------------------
 |||||||||||||||||| |||||||||| |||||||||||  |||||||||||||||||| ||||||||||||| |  |||||||||| |||| ||||||| |  |         || |||  |   | ||| |||  |         |      | ||    |   | ||||   ||  |  ||   | |  ||  ||   ||| |  | |                                                        
ATCTCGCACTACCTCACCCACAAGGCCCTCGACCACCGCTTCGTCTCCGGCGTCATCGGCGAGGTCGACCTCAACAGGATCGAGCCATGGGACCTGCCAGgttagcactgcgcgctactgcttgatacgtcctcacctcaaagagccaaatagacctgcacctcttttttttttgactttgtgcttgtactagtagtacttctctttctctcggctgggaatcatggcggcctaaatttaactgggaagcttgcgttttgatttctccag

upper sequence: LOC_Os03g21030.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G159500_T01 (Zea mays), 5'ss of exon 1
GTCTCGCACTACCTCACCCCCAAGGCCCTCAACCACCGCTTCTCCTCCGGCGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcctgaattctctccttttttttctc----cccttgattcgttcgtacgataaatctttgggcttacggatgagtttgcgtggtttgatttttggcag-----------------------------------------
 |||||||||||||| |||  |||||||||||||||||||||  |||||| ||||||||||| ||||||||||||||||||||||||||| |||| ||||||| || | ||      || | |      |||    | ||  |   |  | |    |     | ||    |||   |     | |  || | ||      ||                                           
ATCTCGCACTACCTCGCCCATAAGGCCCTCAACCACCGCTTCGTCTCCGGTGTCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGACCTGCCAGgttagtacttgctgctactgcatcgacgcctcatagctctaaacctgcaccttttttccccttgtgcttctactagtagtacttctcggctggaaaccatgccctaaccaaaaaaaggacggaactttgcgttggatttctccag
















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|88333698|gb|CI643730.1|CI643730
EST:     CGTCATCGGCGAAGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAG                         CCATGGCGAAGATGGGGGAGAAGGAGTGGTACT
genomic: CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcct ... tttttggcagCCATGGCGAAGATGGGGGAGAAGGAGTGGTACT
EST: gi|38470276|gb|CF954407.1|CF954407
EST:     CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAG                         CCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAA
genomic: CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcct ... tttttggcagCCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAA
EST: gi|58593199|gb|CF991507.1|CF991507
EST:     CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAG                         CCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGACC
genomic: CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcct ... tttttggcagCCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGACC
EST: gi|5005498|gb|AU070263.1|AU070263
EST:     GTCATCGGCGACGTCGACCTCAACAAGTGGCGAGCCATGGCACCTCCCAG                         CCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGGAC
genomic: GTCATCGGCGACGTCGACCTCAACAAGTG-CGAGCCATGGCACCTCCCAGgtttgttcct ... tttttggcagCCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGG-AC
EST: gi|117227342|gb|CT848708.1|CT848708
EST:     CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAG                         CCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGACC
genomic: CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcct ... tttttggcagCCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGACC
EST: gi|88298912|gb|CI567915.1|CI567915
EST:     CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAG                         CCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGACC
genomic: CGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcct ... tttttggcagCCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGACC

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: 70 (upstream exon), 33 (downstream exon)
Score: 2

GTCTCGCACTACCTCACCCCCAAGGCCCTCAACCACCGCTTCTCCTCCGGCGTCATCGGCGACGTCGACCTCAACAAGTGCGAGCCATGGCACCTCCCAGgtttgttcct ... tttttggcagCCATGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTTCTGCCACAAGGACCGCAAGTACCCGACCGGGACGAGGACGAACCGGGCGACGGAGAGCGGCTA




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