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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgcgtttttcctgtttgtccttctatatccttcacagatgtatgaatatcatttatcgatctttttgaattttgagtgtttgaaaatcgaatggttttctgtag

Basic information

species Oryza sativa
transcript LOC_Os09g24910.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24910.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G127717_T01 (Zea mays), 5'ss of exon 13
TCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgcgtttttcctgtttgtccttctatatccttcacagatgtatgaatatcatttatcgatctttttgaattttgagtgtttgaaaatcgaatggttttctgtag
||| |||||| |||||||||||||||| ||||||||||| |||||||| || || |||||||||||||||||  | ||||| |||||||| ||||||||||| ||||    | ||| |  |||||  |  |||    ||||   ||| | || ||         ||| |||    |     | ||| || |  ||   | |          
TCCCGCTGATCTAAAATACATTGATCCAACATATATGGTTCGGGCCTGCCGGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgatttcttttcattttgtgttagtattcatttca---atgcaagagtag--------gatttttacagaacaaaattgtatggatgtcctttag----------

upper sequence: LOC_Os09g24910.2 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv14s0108g00540.t01 (Vitis vinifera), 5'ss of exon 13
TCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgcgtttttcctgtttgtccttctatatccttcacagatgtatgaatatcatttatcgatctttttgaattttgagtgtttgaaaatcgaatggttttctgtag
|||||||||||| |||||||||||||| || |||||| | || || ||||| || ||||||||||||||| |  | |||||||| ||||| || |||||||| |||    |  | || |  |  |  |  |       || ||| | ||  |   |  | ||| |||| ||                                        
TCCAGCTGATGTTAAATACATTGATCCCACTTATATGATTCGAGCGTGTCGAGCAAATGCATCTGATGCTGTTCTTTGCACTGTTCTTGGCCAGAATGCTgtaagtgtatgaatatcttcatgataatcttgagatgatc-caggtctacaatggtggtatat-gatccttgcag------------------------------------
















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|13165026|gb|AU173823.1|AU173823
EST:     GTGCGAATGCATNTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|88520444|gb|CI448098.1|CI448098
EST:     AATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: AATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|88545285|gb|CI474835.1|CI474835
EST:     GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|86838031|gb|CI343299.1|CI343299
EST:     GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|88507304|gb|CI434810.1|CI434810
EST:     GTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|86493701|gb|CI136334.1|CI136334
EST:     GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|88521524|gb|CI449220.1|CI449220
EST:     GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|86884674|gb|CI313053.1|CI313053
EST:     GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|88486126|gb|CI423397.1|CI423397
EST:     CATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: CATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|86600964|gb|CI356721.1|CI356721
EST:     TGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: TGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|88491972|gb|CI429244.1|CI429244
EST:     GTGCGAATGCATCTGATGCTATCTTTTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|86504245|gb|CI146878.1|CI146878
EST:     GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|87018028|gb|CI275842.1|CI275842
EST:     GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
EST: gi|15008778|gb|AU223166.1|AU223166
EST:     GAATGCATNTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCT                         GTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC
genomic: GAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAAC

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: 68 (upstream exon), 8 (downstream exon)
Score: 1

TCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgc ... ttttctgtagGTTCATGGAGCCTTTGCCGGGTTCAGTGGTATCACATCTGGTATTTGCAACACGCACTACGCTTTCCTCCCGATCACAGAAGTCATCACAAAACCAAAGC




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