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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgaatccatcatttgcagtttgcaaatctcgctatccgtgttgatggtgatcgggtttggatgaactgatcgtgagatgactctctcttcagGATGTGGGGAAATCGATTCTGGAGAGCTACTCGAGGGTTCTGGAGAGCCTGGCGTCGAACATCATCGCGCGGATCGACGACCTGCTGTACGTCGACGAGC

Basic information

species Oryza sativa
transcript LOC_Os05g38000.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G144504_T02 (Zea mays), 3'ss of exon 6
------------------gttggtgaatccatcatttgcagtttgcaaatctcgctatccgtgttgatggtgatcgggtttggatgaactgatcgtgag-atgactc-tctcttcagGATGTGGGGAAATCGATTCTGGAGAGCTACTCGAGGGTTCTGGAGAGCCTGGCGTCGAACATCATCGCGCGGATCGACGACCTGCTGTACGTCGACGAGC
                     |  ||   || | || |    | |    |   ||  | ||| |  |   |       |||   |    |  || ||   |||  |  ||||||||||| ||||| |||||||| || ||||||||||||||||| || ||||||||||| || |||||||||||||||||||||||||||||  ||||||||||||
gttcaattcgcgatacaccgagacgagagcagc-ttcgttcatcgatgtttaggccgtacgtctgaacattttctcttttttttttcctttgtcatgctcatgcgtggtctcttcagGACGTGGGCAAATCGATCCTCGAGAGCTACTCGAGGGTCCTCGAGAGCCTGGCCTCCAACATCATCGCGCGGATCGACGACCTGCTCAACGTCGACGAGC

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0019g02710.t01 (Vitis vinifera), 3'ss of exon 6
gttggtgaatccatcatttgcagtttgcaaatctcgctatccgtgttgatggtgatcgggtt--tggatgaactgatc-gtgagatgactct---ctcttcagGATGTGGGGAAATCGATTCTGGAGAGCTACTCGAGGGTTCTGGAGAGCCTGGCGTCGAACATCATCGCGCGGATCGACGACCTGCTGTACGTCGACGAGC
   | | ||    || |   | | |||    |||   | | | ||  ||||    ||   ||  |  ||       || |  | ||   | |   || ||||||||||||||||||| |||||||| |||||||| || ||| |||| |||||||| |  |||||  | || || || || || ||  | || || || || |
---gttcaaattctcctccacggattgtct-tctgtttgttcttggagatgcatttccttttcctctatttgtcactctgacaaattgtttttgtcttttcagGATGTGGGGAAATCCATTCTGGAAAGCTACTCAAGAGTTTTGGAAAGCCTGGCATTTAACATTGTGGCTCGTATTGATGATCTATTATATGTTGATGACC

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ32418 (Selaginella moellendorffii), 3'ss of exon 5
gttggtgaatccatcatttgcagtttgcaaatctcgctatccgtgttgatggtgatcgggtttggatgaactgatcgtgagatgactctctc--ttcagGATGTGGGGAAATCGATTCTGGAGAGCTACTCGAGGGTTCTGGAGAGCCTGGCGTCGAACATCATCGCGCGGATCGACGACCTGCTGTACGTCGACGAGC
                                          ||   |||  |     | || |   ||  |  ||  ||||    ||| ||  |  |||| || ||  | || |||||||||||||||||| ||||  |||||||| |||| |  |||||| |||| |||||||||||| |  ||| | |||||||  
------------------------------------------gtaaagatctttcaaagcttcgttcgagtttctcacgagagctttctttcgttctagGACGTTGGTCACTCCATTCTGGAGAGCTACTCGCGGGTGTTGGAGAGCTTGGCATTTAACATCCTCGCTCGGATCGACGACGTCTTGTTCATCGACGACG

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ20829 (Selaginella moellendorffii), 3'ss of exon 5
gttggtgaatccatcatttgcagtttgcaaatctcgctatccgtgttgatggtgatcgggtttggatgaactgatcgtgagatgactctctc--ttcagGATGTGGGGAAATCGATTCTGGAGAGCTACTCGAGGGTTCTGGAGAGCCTGGCGTCGAACATCATCGCGCGGATCGACGACCTGCTGTACGTCGACGAGC
                                          ||   |||  |     | || |   ||  |  || |||||    ||| ||  |  |||| || ||  | || |||||||||||||||||| ||||  |||||||| |||| |  |||||| |||| |||||||||||| |  ||| | |||||||  
------------------------------------------gtaaagatctttcaaagcttcgttcgagtttctcatgagagctttctttcgttctagGACGTTGGTCACTCCATTCTGGAGAGCTACTCGCGGGTGTTGGAGAGCTTGGCATTCAACATCCTCGCTCGGATCGACGACGTCTTGTTCATCGACGACG

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: 69 (upstream exon), 52 (downstream exon)
Score: 4

CCTCGCCGACCGCGCCGAGGGCCTCCTCATGTGCCTCAAGCAGAGGTTCCCCGGACTGACGCAGACCAGCCTGGACACGAGCAAGATTCAGTACAACAAGgttggtgaat ... ctctcttcagGATGTGGGGAAATCGATTCTGGAGAGCTACTCGAGGGTTCTGGAGAGCCTGGCGTCGAACATCATCGCGCGGATCGACGACCTGCTGTACGTCGACGAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgatggtgatcgggtttggatgaactgatcgtgagatgactctctcttcagGATGTGGGGAAATCGATTCTGGAGAGCTACTCGAGGGTTCTGGAGAGCCTGGCGTCGAACATCATCGCGCGGATCGACGACCTGCTGTACGTCGACGAGC
                          aactgat  putative branch site (score: 4)
                                           ctctctcttc  putative PPT