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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG

Basic information

species Oryza sativa
transcript LOC_Os07g26610.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 11
gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
         ||||| | | ||        ||  |         |  ||||   | ||| |  | |||||||||||||| |||||||||| ||| | |||||| ||||| |||||| ||||||||||||| |||||||| |||||  |||||  ||||||||||||||||||||
--------gtaagattcttttctga---gttgcagttttaatgttctattttgtactattttattgattgccactaactaatccattgcgctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG

upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 10
gcgacagaataagagtg--tcttacagctgattttacccacccaatattattcgatgctactgca-gtgattgccactaacaaatccattgctctgatact----agCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
         | ||  |   | ||  |||| || | |   ||| | | | |    || || ||     |  || |   |||    |    | ||||  |  |    |||| || || || || ||||| ||||| || ||||||||||||||||| || || |||||||| || |||||||
--------gtgaggctcatttttttagct-atctcag--acctagtttaacctcatacttctctgtatacttcctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG

upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 10
-----gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
     ||       |  |  | ||| | | ||  |||| |  |||  ||| |  ||  |     | |  | | | |   |       |  ||| | |     ||||| || || || || ||||| ||||| || ||||||||||||||||| || || |||||||| || |||||||
gtgaggctcattttttgggctatctcagacctagtttt-ctaacctcatacttctctgtatactttctcttaattcttttcct---cctcttgtttt--ccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG

upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 11
------gcgacagaataagagtgtctt-acagctgat-tttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
       |  |   ||     | | || | ||||| | ||||     ||||  ||      ||       |||   |   | |      ||   |  |||     ||||| ||||| || || || || || ||||| || ||||| ||||| ||||||||||| |||||||| |||||||
gtatggtcttccttattcagttatgttcagagctgttgtttataagtccaacttt------tgtctggatagtatatttaatttgttcttcttgttttctttccatagCATCCAGGAACAACCATAGTCACGGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTG

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|29613465|gb|CB618478.1|CB618478
EST:     TAAACCGTAACAGATTGATTGCTTTGATGTCTGCCATAGTTCTTGAAGAG                         CACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACT
genomic: TAAACCGTAACAGATTGATTGCTTTGATGTCTGCCATAGTTCTTGAAGAGgtaagatctc ... ctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACT




















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), 73 (downstream exon)
Score: 39

GTCTGCTGCTGTTGATTCAAGTGGTCGTGAGTTAAACCGTAACAGATTGATTGCTTTGATGTCTGCCATAGTTCTTGAAGAGgtaagatctc ... ctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
                                        ttgctct  CT-rich tract
                             taacaaat  TA-rich tract