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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcttcagagcacttctttcagttgcttgaattgaaaatttactgattcaccttgcttgaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA

Basic information

species Oryza sativa
transcript LOC_Os11g31640.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G055854_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------------------gtacatcttcagagcacttctttcagttgcttgaattgaaaatttactgattcaccttgcttgaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA
                                                                                           |||   |   | |||||||  |    ||||    |||||| |||| |||||||   |  ||  |||| | ||||||||||||||||||| || | ||| || ||  | ||| | |||||||| |||||||| ||||||| ||| ||||| |||||||| || |||||||| |
gtagatataatgatgggtacttttaccaagtcttttggatcatgtggtggatatattgtcgcgtcaaatgtgcatactactgaaagtgactgtattacactatagcacttggtaagattgc----attgaagatttgctgattcttttcactataacttttagGAGATAATTCAGCACCTTAAACATAGTTGTCCGCCCCATCTGTATGCTACTTCCATGTCGCCACCAGGAGTCCAACATGTTATTTCTGCTATTAAAGTTA

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 8
------------------gtacatcttcagagcacttctttcagtt-gcttgaattgaaaatttactgattcaccttgcttga--actctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA
                  |  ||| ||   |      |  |  ||  |   || | ||| ||| || | |||   || ||  |  ||| ||||||||||||| |||||||||||| ||| |||||||| ||| | || ||||| |||||||||||||||||||| ||||||||||| || || |||||||| |
gtacatactactgaaagcgatcatattacaactgtagcactttgtaagaccgagtagaagattgaccggttccttttactatataactttcagGAGATAATTAAGCACCTGAAGCATAGTTGCCCAGCCCATCTGTACGCTACTTCCATGTCACCACCAGCAGTCCAACAAGTTATCTCTGCTATTAAAGTTA

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G370377_T01 (Zea mays), 3'ss of exon 10
--------------------------------gtacatcttcagagcacttctttcagttgcttgaattgaaaatttactgattcaccttgcttgaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA
                                |||   |   | |||||||  |    ||||    |||||| |||| |||||||   |  ||  |||| ||||||||||||||||||||| || | ||| || ||  | ||| | |||||||| |||||||| ||||||| ||| ||||| |||||||| || |||||||| |
cacatcaaaggtgcatactactgaaagtgactgtattacactatagcacttggtaagattgc----attgaagatttgctgattcttttcactataactttcagGAGATAATTCAGCACCTTAAACATAGTTGTCCGCCCCATCTGTATGCTACTTCCATGTCGCCACCAGGAGTCCAACATGTTATTTCTGCTATTAAAGTTA

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G891276_T01 (Zea mays), 3'ss of exon 5
--------------------------------gtacatcttcagagcacttctttcagttgcttgaattgaaaatttactgattcaccttgcttgaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA
                                |||   |   | |||||||  |    ||||    |||||| ||||  ||||||   |  ||  |||| ||||||||||||||||||||| |||| ||| || || |  ||| | |||||||| |||||||| ||||||||||| |||||||||||||| || |||||||| |
cgcatcaaaggtgcatacttctgaaagtgactgtattacactatagcacttggtaagattgc----attgaagatttgttgattcttttcactataactttcagGAGATAATTCAGCACCTTAAGCATAGTTGTCCGGTCCATCTGTATGCTACTTCCATGTCGCCACCAGCAGTCCAACAAGTTATTTCTGCTATTAAAGTTA

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 1
----------------------gtacatcttcagagcacttctttcagttgcttgaattgaaaatttactgattcaccttgcttgaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA
                      |||   |   | |||||||  |    ||||    |||||| |||| |||||||   |  ||  |||| ||||||||||||||| ||||| |||| ||| || || || ||| | |||||||| |||||||| ||||||||||| |||||||||||||| || |||||||| |
gtgcatactactgaaagtgactgtattacactatagcacttggtaagattgc----attgaagatttgctgattcttttcactataactttcagGAGATAATTCAACACCTTAAGCATAGTTGTCCGGCCCATCTGTATGCTACTTCCATGTCGCCACCAGCAGTCCAACAAGTTATTTCTGCTATTAAAGTTA

upper sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 8
----------------gtacatct-tcagagcacttctttcagttgcttgaattgaaaatttactgattcaccttgcttgaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA
                ||   | | | | |      |  |     | ||| |||||| |||| |||||||   |  ||  || | ||||||||||||||||||||| |||| ||| || || || ||| | |||||||| |||||||| ||||||||||| |||||||||||||| || |||||||| |
gtgcatactactgaaagtgactgtattacactgtagcacttgtaagattgcattgaagatttgctgattcttttcactataaatttcagGAGATAATTCAGCACCTTAAGCATAGTTGTCCGGCCCATCTGTATGCTACTTCCATGTCGCCACCAGCAGTCCAACAAGTTATTTCTGCTATTAAAGTTA

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|58596905|gb|CK007433.1|CK007433
EST:     CTTTCACTAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAG                         GAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATG
genomic: CTTTCACTAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAGgtacatcttc ... gaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATG
EST: gi|29628852|gb|CB633863.1|CB633863
EST:     GTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAG                         GAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCTCATATTTATGCTACC
genomic: GTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAGgtacatcttc ... gaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
EST: gi|29671691|gb|CB667966.1|CB667966
EST:     TATATTGCAGCATCGAAG                         GAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
genomic: TATATTGCAGCATCGAAGgtacatcttc ... gaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
EST: gi|29675002|gb|CB671277.1|CB671277
EST:     TCATTTGGATCATGTGGTGG--ATA-TGNCAGCATCGAAG                         GAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
genomic: TCATTTGGATCATGTGGTGGATATATTG-CAGCATCGAAGgtacatcttc ... gaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
EST: gi|29615692|gb|CB620704.1|CB620704
EST:     CTTTCACTAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAG                         GAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
genomic: CTTTCACTAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAGgtacatcttc ... gaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
EST: gi|29672757|gb|CB669032.1|CB669032
EST:     TAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAG                         GAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC
genomic: TAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAGgtacatcttc ... gaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACC

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: 74 (upstream exon), 69 (downstream exon)
Score: 26

TTGTGAGCTCCTTGGGGTTGATCCAGCTGATGTGGACATAATGATGGGCACTTTCACTAAGTCATTTGGATCATGTGGTGGATATATTGCAGCATCGAAGgtacatcttc ... gaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcagttgcttgaattgaaaatttactgattcaccttgcttgaactctcagGAGATAATTCAGCACCTGAAGCTTAGCTGCCCAGCGCATATTTATGCTACCTCCATGTCACCACCAGCAGTACAACAAGTTATTTCAGCCATTAAAGTGA
                           tactgat  putative branch site (score: 26)
                                                ctctc  putative PPT
             ttgaattgaaaattta  TA-rich tract