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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtttttggcaataaagaaagctgccgcactctacatcctactttagagttttgcagggactgacatcgtcaatataaggttgataatttgcttataacttgaccggatctcttgcagAGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGAACCAG

Basic information

species Oryza sativa
transcript LOC_Os01g51380.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 12
gtaaggtttttggcaataaagaaagctgccgcactctacatcctactttagagttttgcagggactgacatcgtcaatataaggttgataatttgcttataacttgaccggatctcttgcagAGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGAACCAG
                |         |   | | |   ||    || ||   || |    | |      ||| |    ||  |||||  | |       |  ||| ||      || ||||||||||||||||  | || |||||||| | |||||||||||| ||||| ||||||
----------------tgtttgctttttaagtatttcccacttaacgtttaggtgtgattgagttatgtatcatttcgatttggttgggactaactgagttccttcac------tcctgcagAGTGCTATTGGACAGGGAATGACTCGAAAGGATCATTCTGAAGTCTCTAACCAG
















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|33811101|gb|CF331441.1|CF331441
EST:     ATCTATCCACCGATTAATGTCCTTCCTTCACTCTCCCGGCTCATGAAG                         AGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGA
genomic: ATCTATCCACCGATTAATGTCCTTCCTTCACTCTCCCGGCTCATGAAGgtaaggtttt ... tctcttgcagAGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGA
EST: gi|58687170|gb|CK075857.1|CK075857
EST:     ATCTATCCACCGATTAATGTCCTTCCTTCACTCTCCCGGCTCATGAAG                         AGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGAAC
genomic: ATCTATCCACCGATTAATGTCCTTCCTTCACTCTCCCGGCTCATGAAGgtaaggtttt ... tctcttgcagAGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGAAC
EST: gi|27576717|gb|CA999411.1|CA999411
EST:     ATCTATCCACCGATTAATGTCCTTCCTTCACTCTCCCGGCTCATGAAG                         AGTGCTATTGGTGAAGGCATGAC
genomic: ATCTATCCACCGATTAATGTCCTTCCTTCACTCTCCCGGCTCATGAAGgtaaggtttt ... tctcttgcagAGTGCTATTGGTGAAGGCATGAC

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: 48 (upstream exon), 54 (downstream exon)
Score: 21

ATCTATCCACCGATTAATGTCCTTCCTTCACTCTCCCGGCTCATGAAGgtaaggtttt ... tctcttgcagAGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcgtcaatataaggttgataatttgcttataacttgaccggatctcttgcagAGTGCTATTGGTGAAGGCATGACTCGCAGGGATCATTCTGATGTCTCGAACCAG
                                             tctcttgc  CT-rich tract
                    ataatttgcttataa  TA-rich tract