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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtctggtttcccaaacaaatgtgtaataatagaattgtgcaggcagcagcatttgattattcctttttgtttctgtctgtagAATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATG

Basic information

species Oryza sativa
transcript LOC_Os02g07490.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 3
gtaagtgtctggtttcccaaacaa--atgtgtaataatagaattgtgcaggcagcagcat-ttgattattcctttttgtttctgtct----gtagAATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATG
||||||  ||| | | || | |||  |    |   |   |||  |||||| | || |    || ||  ||   || |   | ||| |    |||||||||| ||||||||||||||||||| | |||||||| |
gtaagtagctgttgtgcccaccaacgaaacatttcatgtgaaccgtgcagcctgcggtggatttatagttttgttgtccctttgtttctgtgtagAATATTTGAGTGGCGAGAAGACAAAGATCGGCATCAACG

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 3
gtaagtgtctggtttcccaaacaaatgtgtaataatagaattgtgcaggcagcagc--atttga---ttattcctttttgtttctgtctgtagAATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATG
||||||  |||   | || | |||| || | ||    ||  ||||||| | || |   |||||    ||  | |||  | | | | |||||||||||||||||||| |||||||||||| |||||||||| |
gtaagtagctgtcgtgccgaccaaacgtttcatgt--gagctgtgcagcctgcggtggatttgtaattttcttcttcctttgtttctctgtagAATATTCGAGTGGGGAGAAGACAAAGATTGGCATCAACG
















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|58609065|gb|CK037098.1|CK037098
EST:     CATTGAGCTGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCAC                         AATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATGGG
genomic: CATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCACgtaagtgtct ... ctgtctgtagAATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATGGG
EST: gi|8594714|gb|AU093252.1|AU093252
EST:     CATTGAGCCGCTGAGAGCGATAG-TACTCAGGCACCCCCTGCCGTCCCAC                         AATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATG
genomic: CATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCACgtaagtgtct ... ctgtctgtagAATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATG

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: 59 (upstream exon), 39 (downstream exon)
Score: 39

TGCTAGGAACATTGAGCCGCTGAGAGCGATAGCTACTCAGGCACCCCCTGCCGTCCCACgtaagtgtct ... ctgtctgtagAATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagaattgtgcaggcagcagcatttgattattcctttttgtttctgtctgtagAATATTCGAGTGGCGAGAAGACAAAGGTTGGCATCAATG
                       atttgat  putative branch site (score: 39)
                             ttattcctttttgttt  CT-rich tract
                       atttgattatt  TA-rich tract