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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttctcccctttttctttcaggaaatgataatttatgtattctgttttggtgatttgttgttgtttctcctattgaactccttttatttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTGAGGACAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G045241_T07 (Zea mays), 3'ss of exon 9
gtgagtttctcccctttttctttcaggaaatgataatttatgtattctgttttggtgatttgttgttgtttctcctattgaactccttttatttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTGAGGACAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGG
||||||  ||    |||||  |  | |  ||| | ||  |  |||  |   ||   ||    |  |  |||  |  | |    |  | | | |||   || | |  | ||||| |||||||||||||||||||||||  | ||||||||||| ||      ||||||||||||||| ||||| |||||||||||| ||||
gtgagtcacttt--ttttttatcaaagctatggtcatg-acatatcttaactttaagaca-ataataatttaactgaatccttttgtatgactttaacagAAGCTGAACCAAGATTGGAACTGAACCTGTGGGATTTCAGCACAGAACCTGATGATTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGG
















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|29613120|gb|CB618133.1|CB618133
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29644979|gb|CB649986.1|CB649986
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29663527|gb|CB659802.1|CB659802
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29666009|gb|CB662284.1|CB662284
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29666008|gb|CB662283.1|CB662283
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29638287|gb|CB643296.1|CB643296
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29656192|gb|CB652467.1|CB652467
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29613155|gb|CB618168.1|CB618168
EST:     CACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|218497584|gb|FG955131.1|FG955131
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29613395|gb|CB618408.1|CB618408
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
EST: gi|29628841|gb|CB633852.1|CB633852
EST:     CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA                         GACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG
genomic: CTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTG

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: 54 (upstream exon), 67 (downstream exon)
Score: 21

GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTAgtgagtttct ... atttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTGAGGACAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttttggtgatttgttgttgtttctcctattgaactccttttatttttgtagGACCGAATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTGAGGACAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGG
                                     ctccttttatttttgt  CT-rich tract
                                         ttttatttttgta  TA-rich tract