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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactcttaattattatagaaccgtatgccttctattcatacatattcttgcatttgagtttacttaaattaattttcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGCGTGGTGCTG

Basic information

species Oryza sativa
transcript LOC_Os12g37960.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37960.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AC182617.3_FGT001 (Zea mays), 3'ss of exon 6
----------gttactcttaattattatagaaccgt--atgccttctattcataca----tattcttgcatttg-agtttacttaaattaattttcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGCGTGGTGCTG
            ||  |||    |  |   |||  |  ||   || |  |  || |     || || |  |||| | |||| ||||   | || | || ||||||||| ||| ||||  ||||||||||||||||||||||| | |||||||| ||||||||||
gtaactctttaatatccttgccaaaaaggtaactcttaatttattttgcttctataggtacatcctggtgtttgtattttatttaagcgacttcttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG

upper sequence: LOC_Os12g37960.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G130332_T03 (Zea mays), 3'ss of exon 6
gttactcttaattattatagaaccgtatgccttctattcatacatattcttgcatttgagtttacttaaattaattttcttct-gcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGCGTGGTGCTG
|| ||||||||||            | | |  | | |    | | || |||| |||||  |||  || |||| | |||||| | ||||| |||||| ||||  ||||||||||||||||||||||| |||||||||| ||||||||||
gtaactcttaatt------------tcttctgtttctgtggataaatccttgtatttgtattttatttaattgactttctttttgcagAGTTTGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGAGTCTGGGAACGTGGTGCTG
















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|58603560|gb|CK014088.1|CK014088
EST:     TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAG                         AATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
genomic: TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAGgttactctta ... tcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
EST: gi|29658220|gb|CB654495.1|CB654495
EST:     TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAG                         AATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
genomic: TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAGgttactctta ... tcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
EST: gi|58686153|gb|CK074840.1|CK074840
EST:     TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAG                         AATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
genomic: TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAGgttactctta ... tcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
EST: gi|29644241|gb|CB649248.1|CB649248
EST:     TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAG                         AATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
genomic: TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAGgttactctta ... tcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
EST: gi|41882056|gb|BX927725.1|BX927725
EST:     TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAG                         AAATTTGTAGAAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGA
genomic: TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAGgttactctta ... tcttctgcagAA-TTTGTAGA-GGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGA
EST: gi|29684087|gb|CB680362.1|CB680362
EST:     TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAG                         AATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC
genomic: TGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAGgttactctta ... tcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGC

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: 63

GTTTTGCATGTTGATGATTTAAAGCTTAGTGATATTGGGCCTAAATTCGAGCATCATGAAATGTTTCCTGCCCGCACCAACACAGgttactctta ... tcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGCGTGGTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattcatacatattcttgcatttgagtttacttaaattaattttcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGCGTGGTGCTG
                                    aattaat  putative branch site (score: 63)
                                          ttttcttctgc  CT-rich tract
                     atttgagtttacttaa  TA-rich tract