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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagcaaaacgatcaacagcacatgtttgcagcaagtcataaattcattttctgattcctattcgacattctggtgcatatcagGTTTCTAAGCACATGAATCATTTGCTGAAAGCACCCTTTTGCATACACCCGAAGACAGGTTAGACCCAAGTATATTTCCTATTTTTTCATCTAATGAATG

Basic information

species Oryza sativa
transcript LOC_Os05g29010.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29010.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G03200.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------gtaaaagcaaaacgatcaacagca-catgtttgcagcaagtcataaattcattttctgattcctattcgacattctggtgcatatcagGTTTCTAAGCACATGAATCATTTGCTGAAAGCACCCTTTTGCATACACCCGAAGACAGGTTAGACCCAAGTATATTTCCTATTTTTTCATCTAATGAATG
                                                              |  |  ||  |   |   || ||   | | |  || |   ||  ||  ||  || ||| |  ||||     |  |  ||  | | |||||||||| ||||||||||||||||| |||||||| || ||  |||| || || ||||                                          
gttcatcttttaactggcctttttctcatatccactgttatctttcatgctattaccatttctgcagtcattatactgcccatcaatgtctctatagaagaccaataa--caccttttgact--tattaagactgttcatg--ttttagGTTTCTAAACACATGAATCATTTGCTTAAAGCACCATTCTGTGTACATCCTAAAACAG------------------------------------------

upper sequence: LOC_Os05g29010.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G45610.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------------------gtaaaagcaaaacgatcaac-agcacatgtttgcagcaagtcataaattcattttctgattcctattcgacatt-ctggtgc-atatcagGTTTCTAAGCACATGAATCATTTGCTGAAAGCACCCTTTTGCATACACCCGAAGACAGGTTAGACCCAAGTATATTTCCTATTTTTTCATCTAATGAATG
                                                                                     || |  |  | ||  |  || |     ||    | | |   || || | | |   ||   | |||   |   ||| | |  | | |||||||||| || |||||||||||||| |||||||| |||||  |||| || || ||||                                          
gtttgtctatcaactggccctctttttcccatatccactgttatatttcatgttattaccatttctgctgtctttacttcccagcaatgtcactctatagatgagtaacaccttttgactaatttgaagtttagtctg-aatgtttgttcattaaaactgttactgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCTAAAACAG------------------------------------------
















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|3759042|gb|C96741.1|C96741
EST:     GTATAGAAGAGATTGTCTTCTCATACACATATCCTAGACTTGATATGGAG                         GTTTCTAAGCACATGAATCATTTGCTGGAAAGCACC
genomic: GTATAGAAGAGATTGTCTTCTCATACACATATCCTAGACTTGATATGGAGgtaaaagcaa ... tgcatatcagGTTTCTAAGCACATGAATCATTTGCTG-AAAGCACC




















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: 54 (upstream exon), 52 (downstream exon)
Score: 8

GGGCTTCGAAGATGTATAGAAGAGATTGTCTTCTCATACACATATCCTAGACTTGATATGGAGgtaaaagcaa ... tgcatatcagGTTTCTAAGCACATGAATCATTTGCTGAAAGCACCCTTTTGCATACACCCGAAGACAGGTTAGACCCAAGTATATTTCCTATTTTTTCATCTAATGAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcaagtcataaattcattttctgattcctattcgacattctggtgcatatcagGTTTCTAAGCACATGAATCATTTGCTGAAAGCACCCTTTTGCATACACCCGAAGACAGGTTAGACCCAAGTATATTTCCTATTTTTTCATCTAATGAATG
                    ttctgat  putative branch site (score: 8)
       tcataaattcatttt  TA-rich tract