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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtaaatttattgctgattactgacatgtggataagataccaaaatgttctgaattcttttgatggtaacatcttccttcgtagGTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATCGGTGAGTAATTATGCTATACTAGACCTGAGGGTACTCACACTTTAATAG

Basic information

species Oryza sativa
transcript LOC_Os09g06499.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 12
--------gtaagt-gtaaatttattgctgattactgacatgtggataagatacca-aaatgttctgaattcttttgatggtaacatcttccttcgtagGTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATCGGTGAGTAATTATGCTATACTAGACCTGAGGGTACTCACACTTTAATAG
          ||||  |  |||| | | | || |  |   | | | |   ||   | |||  |||     | |||| || |||  || || |||  ||||| | |||||||||||||||||| || ||||||||||||||||| ||||| |                                                
gtaaaatcacaagtcatctatttttagtttatcatagttttatcgttgtcatgaaagaaacattcc----ttttttaattgtattatttttctttttagGTTGCATTCTCATTGGCCTTTGTGATTCATGAGTCAGCAAATCCACATATAG------------------------------------------------
















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|88902671|gb|CI088209.1|CI088209
EST:     CATTCATTACAACATTAATTTTTGGTATTGAGATTGGTGTTCTTGTTGGG                         GTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATC
genomic: CATTCATTACAACATTAATTTTTGGTATTGAGATTGGTGTTCTTGTTGGGgtaagtgtaa ... tccttcgtagGTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATC




















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: 44 (upstream exon), 52 (downstream exon)
Score: 5

TATCTTCTTGTGGAGTATTGATAAGAAGGATTTCTTTCTATGGGCAATCACATTCATTACAACATTAATTTTTGGTATTGAGATTGGTGTTCTTGTTGGGgtaagtgtaa ... tccttcgtagGTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATCGGTGAGTAATTATGCTATACTAGACCTGAGGGTACTCACACTTTAATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataagataccaaaatgttctgaattcttttgatggtaacatcttccttcgtagGTCGGATTCTCATTGGCCTTTGTAATCCATGAGTCAGCAAATCCTCATATCGGTGAGTAATTATGCTATACTAGACCTGAGGGTACTCACACTTTAATAG
                                  tggtaac  putative branch site (score: 5)
                                        catcttccttc  CT-rich tract
                       aattctttt  TA-rich tract