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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaaacgcaaccacctcaaaatgatcgttcatcacacagcccttcagcagcatgacatctgacggcacaaagcgagatctgaatcaagcaaacgcatgctgttgctttaaccactgttttccatttctgacgaacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAGGAACCTACAACGGCGGCCTCCTGTCGACAGAGGCCGGGACGCTGGCCCG

Basic information

species Oryza sativa
transcript LOC_Os04g48390.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48390.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G018018_T02 (Zea mays), 3'ss of exon 9
gtatgtaaacgcaaccacctcaaaatgatcgttcatcacacagcccttcagcagcatgacatctgacggcacaaagcgagatctgaatcaagcaaacgcatgctgttgctttaaccactgttttccatttc-tgacgaacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAGGAACCTACAACGGCGGCCTCCTGTCGACAGAGGCCGGGACGCTGGCCCG
|||||||     |      | || |||  || | |     |  || ||    ||||| || |            ||| | | || ||| |||||    || |||  || ||| | ||  ||    ||  |  |  | |||  | |||||||||| ||||| |||||||||||||| |||||||| |||||  | ||||| |||||||| || || |||||                           
gtatgtatgtttata---attaatatg--cgatga--gtgcgaccatttcaaagcattacgtgc----------agcaaaacctaaattaagca----cacgctactgattttatca--gTCACGCACCTAATACCAAACCATACAGGAGTGAATCTGTCCTTGCTTTCACGAGTGATGTCGTCAAGGCTTTCCCGAGGGACCTACAATGGTGGACTCCT---------------------------

upper sequence: LOC_Os04g48390.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G086430_T01 (Zea mays), 3'ss of exon 10
gtatgtaaacgcaaccacctcaaaatgatcgttcatcacacagcccttcagcagcatgacatctgacggcacaaagcgagatctgaatcaagcaaacgcatgctgttgctttaaccactgttttccatttctgacgaacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAGGAACCTACAACGGCGGCCTCCTGTCGACAGAGGCCGGGACGCTGGCCCG
                                       |      || |    ||| |    ||     | | ||||| | || |||||| || |||| ||||| |   | | |||||    | |    ||  ||| |  |||||||||||| ||||| ||||| |||||||||||||| ||||||||  | ||||| |||||||| || || ||||| |||||||||||||||||| |||||||
-------------------------------------gtatgtatgtttatatacattaa---tggtttgagacagcgaaacctaaatcaatcatacgc-tgctgatttatcagccactcaacttctaacct--cgagctatgcagGAGTGAATCTGTCCTTGCTCTCACGAGTAATGTCATCGAGGCTTTCCCGAGGGACCTACAATGGTGGACTCCTTTCGACAGAGGCCGGGACGTTGGCCCG

upper sequence: LOC_Os04g48390.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G018018_T01 (Zea mays), 3'ss of exon 9
gtatgtaaacgcaaccacctcaaaatgatcgttcatcacacagcccttcagcagcatgacatctgacggcacaaagcgagatctgaatcaagcaaacgcatgctgttgctttaaccactgttttccatttc-tgacgaacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAGGAACCTACAACGGCGGCCTCCTGTCGACAGAGGCCGGGACGCTGGCCCG
|||||||     |      | || |||  || | |     |  || ||    ||||| || |            ||| | | || ||| |||||    || |||  || ||| | ||  ||    ||  |  |  | |||  | |||||||||| ||||| |||||||||||||| |||||||| |||||  | ||||| |||||||| || || ||||| || ||||||||||||||| |||||||
gtatgtatgtttata---attaatatg--cgatga--gtgcgaccatttcaaagcattacgtgc----------agcaaaacctaaattaagca----cacgctactgattttatca--gtcacgcacctaataccaaaccatacagGAGTGAATCTGTCCTTGCTTTCACGAGTGATGTCGTCAAGGCTTTCCCGAGGGACCTACAATGGTGGACTCCTTTCAACAGAGGCCGGGACGTTGGCCCG

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|112786055|gb|EE591965.1|EE591965
EST:     GTACGTCTTGTCCGCTCTCATCACATTTGTGTTTGCTGAGGTCCTCGAAG                         GAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAG
genomic: GTACGTCTTGTCCGCTCTCATCACATTTGTGTTTGCTGAGGTCCTCGAAGgtatgtaaac ... aacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAG
EST: gi|86870525|gb|CI320621.1|CI320621
EST:     TACGTCTTGTCCGCTCTCATCACATTTGTGTTTGGCTGAGGTCCTCGAAG                         GAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCATCGAGGCTCGCGCGAG
genomic: TACGTCTTGTCCGCTCTCATCACATTTGTGTTT-GCTGAGGTCCTCGAAGgtatgtaaac ... aacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAG
EST: gi|88203552|gb|CI203401.1|CI203401
EST:     GTACGTCTTGTCCGCTCTCATCACATTTGTGTTTGCTGAGGTCCTCGAAG                         GAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAG
genomic: GTACGTCTTGTCCGCTCTCATCACATTTGTGTTTGCTGAGGTCCTCGAAGgtatgtaaac ... aacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAG
EST: gi|86510237|gb|CI152870.1|CI152870
EST:     GTACGTCTTGTCCGCTCTCATCACATTTGTGTTTGCTGAGGTCCTCGAAG                         GAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAG
genomic: GTACGTCTTGTCCGCTCTCATCACATTTGTGTTTGCTGAGGTCCTCGAAGgtatgtaaac ... aacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAG

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: 68 (upstream exon), 40 (downstream exon)
Score: 28

ATTGGTATAATCATGAGCTTCCGTTACACCCCTCACTACTCCGTTCCGCAGTACGTCTTGTCCGCTCTCATCACATTTGTGTTTGCTGAGGTCCTCGAAGgtatgtaaac ... aacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAGGAACCTACAACGGCGGCCTCCTGTCGACAGAGGCCGGGACGCTGGCCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaacgcatgctgttgctttaaccactgttttccatttctgacgaacattgcagGAGTGAACCTGTCGTTGCTTTCACGAGTAATGTCGTCGAGGCTCGCGCGAGGAACCTACAACGGCGGCCTCCTGTCGACAGAGGCCGGGACGCTGGCCCG
                                     ttctgac  putative branch site (score: 28)
                  tttaa  TA-rich tract