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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGAAGTTAGCAAGCAGTGCTCTGCTCTTCCTAGGGGAGAATTTGCTTCGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttcattcctgcccactctcgaattatttataatttgtaaggcacgtactatacatcactggagtttgaggtcgtagaattttgcagcatgcatgaaggtaaatgaaaattatctgatctattgccgttcccagggattgttgacaagccccctctttcttccttatgtag

Basic information

species Oryza sativa
transcript LOC_Os01g13190.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G058584_T01 (Zea mays), 5'ss of exon 13
GGCAGAAGTTAGCAAGCAGTGCTCTGCTCTTCCTAGGGGAGAATTTGCTTCGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttcattcctgcccactctcgaattatttataatttgtaaggcacgtactatacatcactggagtttgaggtcgtagaattttgcagcatgcatgaaggtaaatgaaaattatctgatctattgccgttcccagggattgttgacaagccccctctttcttccttatgtag
||||||||||||||||||||||   || ||||| || || ||||| ||||| ||||| ||| ||||||| |||||||| || |||||||| |||||||||||| || |||| |||||   | ||  | |                | |||  ||   | |  || | | |||| | || | |  |   | |  |    |     ||   |   ||||||        | | | || ||  |||   | ||||      || ||||| | || || ||
GGCAGAAGTTAGCAAGCAGTGCAACGCGCTTCCAAGAGGTGAATTCGCTTCAAAAGCACTTAGCCACAGCTTCACTGTGTTCGCGAAAGATATGGTTGAGgtagtttttcactcctg---attcctgcaacg------------gatgcatctatgctgc-ccatttgtgttttaagt-gcaccaccattctactgtgacctcagtgccttccaattatgc------tggacatttccgaggaacttcgaca-----tctgtttctactttttgcag
















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|88907696|gb|CI091094.1|CI091094
EST:     CCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|29685418|gb|CB681693.1|CB681693
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|86493486|gb|CI136119.1|CI136119
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|58607312|gb|CK035345.1|CK035345
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|29680233|gb|CB676508.1|CB676508
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|88222978|gb|CI222827.1|CI222827
EST:     TTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: TTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|29662202|gb|CB658477.1|CB658477
EST:     GGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|86481451|gb|CI124084.1|CI124084
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|86500662|gb|CI143295.1|CI143295
EST:     CGAAAGCTCTTGCCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         CCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|29685419|gb|CB681694.1|CB681694
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|86831296|gb|CI297565.1|CI297565
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
EST: gi|29663864|gb|CB660139.1|CB660139
EST:     CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAG                         GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA
genomic: CGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTA

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: 75 (upstream exon), 60 (downstream exon)
Score: 19

GGCAGAAGTTAGCAAGCAGTGCTCTGCTCTTCCTAGGGGAGAATTTGCTTCGAAAGCTCTTGGCCACAGTTTCACTGTTTTTGCGAAAGACATGGTTGAGgtaattcttc ... ccttatgtagGCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAG




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