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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAGATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttactttataccgattctcatatatccttgaacctcctattcagtaacattcaagaagatccaattctctaataagatgaaacaatcaccttactgttttctgcgtctctgcag

Basic information

species Oryza sativa
transcript LOC_Os06g49430.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G135904_T01 (Zea mays), 5'ss of exon 5
TCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAGATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatg----tttactttataccgattctcatatatccttgaacctcctattcagtaacattcaagaagatccaattctctaataagatgaaacaatcaccttactgttttctgcgtctctgcag
||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||| || ||||||||| |||||       | | ||| | | |  | |||    | |   |||||| || |   || |||| ||| || |    || ||||| ||||             |                       
TCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAGATATTATAACAGATCTTCTTGGGACTCCATCATCTGAGACCTTATCCCGGgtactacatctcaattttttctg--tgtcactgttgcccaaacctcgtaat--atatcattaaagtagctaatgttttctaacaagactctgggcctgtttgga--------------------

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G306028_T02 (Zea mays), 5'ss of exon 5
TCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAGATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtat---gtttactttataccgattctcatatatccttgaacctcctattcagtaacattcaagaagat--ccaattctctaataagatgaaacaatcaccttactgttttctgcgtctctgcag
||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| || ||||||||  |||||     | |   ||||  |        | | | | | |||||||||||   || |||| ||| || |      |||||||| ||||  ||         |                       
TCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAGATATTATAACAGATCTTCTTGGAACTCCATCATCTGAGACCTTATCTCGGgtactgcatctcaattatttctgagtcatttttttcctaaacctcctatt--atatcattaaagtagctaatgtgttctctaacaagactaagggtctgttt-----------------------
















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|33795692|gb|CF323716.1|CF323716
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAG
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAG
EST: gi|58652759|gb|CK041439.1|CK041439
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCG
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCG
EST: gi|33381883|gb|CF197226.1|CF197226
EST:     TTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: TTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58663889|gb|CK052575.1|CK052575
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGACGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58693904|gb|CK082591.1|CK082591
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58663177|gb|CK051863.1|CK051863
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58668308|gb|CK056994.1|CK056994
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCA
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCA
EST: gi|58589575|gb|CF987883.1|CF987883
EST:     TATTATAACAGATCTTCTTGGAACTCCATCGATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: TATTATAACAGATCTTCTTGGAACTCCATC-ATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
EST: gi|58661035|gb|CK049715.1|CK049715
EST:     ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGG                         ATTCGAAATGAGAAGGGCAGGAGATACTTGAGCACCATGCGGAAAAAACAT
genomic: ATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACAT

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: 74 (upstream exon), 69 (downstream exon)
Score: 30

TCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAGATATTATAACAGATCTTCTTGGAACTCCATCATCAGAAACCTTATCCAGGgtatgtttac ... gtctctgcagATTCGAAATGAGAAGGCCAGGAGATACTTGAGCACCATGCGGAAAAAACATGCTGTCCCCTTCTCTCAGAAGTTCCGCAATACTGACCCCTTGGCTCTTC




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