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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatttccattcattcttcatccatgtggtttacattattttgaaaggtccccaccacatatttacatgggtaaagaaactttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG

Basic information

species Oryza sativa
transcript LOC_Os12g40550.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G130034_T01 (Zea mays), 3'ss of exon 7
gttagcatttccattcattcttcatccatgtggtttacattattttgaaaggtccccaccacatatttacatgggtaaagaaactttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG
|||||||| | | |||||| || ||   || | ||||||||  | |||| | || |||| | |||||||  | |   ||| |   || ||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| ||  |||||||||||||||||||||| ||||| || ||||
gttagcatattctttcatt-tttat---tgcgatttacatttgtgtgaaggatctccac-aaatatttatgtag---aaggagtgttctacagAAATGATGCTGGACTGGCAGCAGCTGAATTAGCATTAGCAGTCGAGAAACATGTCCTGGAATCAGGATCAATTGATACGGTTGGCACCGTTG

upper sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 7
-----gttagcatttccattcattcttcatccatgtggt--ttacattattttgaaaggtccccaccacatatttacatgg-gtaaagaaactttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG
     || |  ||||  |  | |     | | || |  |  ||   ||||||| |  |  |   || | || |||   ||   ||   |   ||    |||||||||||| ||| |||| || || ||||| ||| |||| ||||||||||| || || ||||| ||||| |||||||||||||| || || |
tagctgtcaaaatttgaagccttgtggaagcaattttataatttagttatttt-attgtgctgaacaagatcttttactgttatatgtatgattggagcagAAATGATGCAGGATTGGCAGCTGCAGAGTTAGCACTAGCTGTTGAGAAACATGTGTTAGAATCTGGATCTATTGATACTGTTGGTACTGTGG
















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|58601255|gb|CK011783.1|CK011783
EST:     GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAG                         AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCA
genomic: GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAGgttagcattt ... ctttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCA
EST: gi|29665068|gb|CB661343.1|CB661343
EST:     GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAG                         AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA
genomic: GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAGgttagcattt ... ctttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA
EST: gi|25801425|gb|CA757386.1|CA757386
EST:     GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAG                         AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA
genomic: GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAGgttagcattt ... ctttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA
EST: gi|38471018|gb|CF955149.1|CF955149
EST:     GAAGGGAATGGGGGCCATG-TAGGAGCAGTGCTCATGCCTGCAAG                         AAATGATGCTAGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAAC
genomic: GAAGGGAATGGGGGCCATGCT-GGAGCAGTGCTCATGCCTGCAAGgttagcattt ... ctttttacagAAATGATGCT-GGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAAC
EST: gi|27578088|gb|CB000783.1|CB000783
EST:     GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAG                         AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA
genomic: GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAGgttagcattt ... ctttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA
EST: gi|58682834|gb|CK071521.1|CK071521
EST:     GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAG                         AAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA
genomic: GAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAGgttagcattt ... ctttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACA

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), 71 (downstream exon)
Score: 10

TCAAAATTGGCGTTGTCACTGCTATTGCTGCTCCTGCAAGTATTAAGGTGGAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGCAAGgttagcattt ... ctttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattttgaaaggtccccaccacatatttacatgggtaaagaaactttttacagAAATGATGCTGGACTGGCGGCAGCTGAGTTGGCATTAGCAGTTGAGAAACACGTTTTGGAATCAGGATCAATTGATACTGTTGGGACAGTTG
                                             ctttttac  CT-rich tract
                                     taaagaaacttttta  TA-rich tract