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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACTGGGGCGAGCCGAGGGAGAAGGTGTGCGAGGCTGTGGGGGAGCTCAATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaatgatacgacggtatagcattgacatgtttctagaaactttcggtctggtttctgtttgagcaaccagagattcatcaggggcagcgatacaatatccccttgtagcatcattttcagaaagctgaatttctgatccagtactttgcttgatttttaaattgtttttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g63010.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63010.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G045278_T01 (Zea mays), 5'ss of exon 3
TGTACTGGGGCGAGCCGAGGGAGAAGGTGTGCGAGGCTGTGGGGGAGCTCAATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaatgatacgacggtatagcattgacatgtttctagaaactttcggtctggtttctgtttgagcaaccagagattcatcaggggcagcgatacaatatccccttgtagcatcattttcagaaagctgaatttctgatccagtactttgcttgatttttaaattgtttttgcag
|||||||||| || |||||||||||||||||||| || |||| ||||||| |  |||| |||||||||||||||||||| ||||||||||||||||| ||||  | |      | | | | |      ||||  ||   |    | |||   ||||   ||  ||  | ||||| |                                                                                                       
TGTACTGGGGTGACCCGAGGGAGAAGGTGTGCGACGCGGTGGAGGAGCTCCAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccctgcatg-cagcaattttctgac-cgtgcgtgcgtatttt--atctg--ctccattccatcaacctgcag----------------------------------------------------------------------------------------------------
















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|86846582|gb|CI280881.1|CI280881
EST:     AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAG                         GATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
genomic: AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
EST: gi|33686131|gb|CF314370.1|CF314370
EST:     AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAG                         GACTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
genomic: AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
EST: gi|33686130|gb|CF314369.1|CF314369
EST:     AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAG                         GACTCTGCTGGGNAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCC
genomic: AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGG-AAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCC
EST: gi|86508183|gb|CI150816.1|CI150816
EST:     AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAG                         GATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
genomic: AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
EST: gi|218482834|gb|FG961732.1|FG961732
EST:     AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAG                         GATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
genomic: AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
EST: gi|16573859|gb|BI801155.1|BI801155
EST:     AATCTCGAATCGCTCGTCATGGGCACCCGTGGCCTCGGCCAGATCCAGAG                         GATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGC-TCTTGCCC
genomic: AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
EST: gi|86601571|gb|CI253899.1|CI253899
EST:     AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAG                         GATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC
genomic: AATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCC

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: 8 (upstream exon), 43 (downstream exon)
Score: 1

TGTACTGGGGCGAGCCGAGGGAGAAGGTGTGCGAGGCTGTGGGGGAGCTCAATCTCGAATCGCTCGTCATGGGCAGCCGTGGCCTCGGCCAGATCCAGAGgtgtgtgaat ... gtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCCTGTGACCGTCGTCAAGGCAAAGTAGTCGCTACTCTTACAGCAATGCAAA




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