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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggattattttcttctattgcatgtttcacacttatatgtcttgttgattcagtgtatttgaacttccaagcaacaattatgctgcatgtgagccaaaactggacagacttttgatcacttaccttttgtttaccattctgcagTCACTGGGTGTTCTTTCTGAAGCACAGTACTTTCAGAATGTCATGCGAACGGGTTTCAGGTTGAGGTCAACATTG

Basic information

species Oryza sativa
transcript LOC_Os04g52900.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 9
gtatggattattttcttctattgcatgtttcacacttatatgtcttgttgattcagtgtatttgaacttccaagcaacaattatgctgcatgtgagccaaaactggacagacttttgatcacttaccttttgtttaccattctgcagTCACTGGGTGTTCTTTCTGAAGCACAGTACTTTCAGAATGTCATGCGAACGGGTTTCAGGTTGAGGTCAACATTG
                                         || | | | |||  || |  |  |   |     | ||| || |      | |  |   |      ||||   ||  |  |||||| | |   ||  |||| | |||||||| || |||||| |||| ||||||||||||||||| ||||||||   |||||||||||||||||| ||||||
-----------------------------------------gtatgggtcattttgtttcctgcatgctgtgcaccacatttgtttcttgtttcggtgcagttgaaacagcaattatagtacttacgtctc--ttctcatttt-cagTCACTTGGGGTTCTTGCTGAGGCACAGTACTTTCAGAACGTCATGCGTGTGGGTTTCAGGTTGAGGTCCACATTG

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 10
gtatggattattttcttctattgcatgtttcacacttatatgtcttgttgattcagtgtatttgaacttccaagcaacaattatgctgcatgtgagccaaaactgga---cagacttttgatcacttacctt---ttg----tttaccattctgcagTCACTGGGTGTTCTTTCTGAAGCACAGTACTTTCAGAATGTCATGCGAACGGGTTTCAGGTTGAGGTCAACATTG
                                                          ||| |||| |   | | || |||||     ||| | |  |||  ||| |        || ||||  |||   ||   |||    |||| | || | |||||| |||| || |||| |||||| ||||||||||||||||| |||||    |||||  || | || |||||  ||
--------------------------------------------------------catatatgaattcaaatgtaaaaattaactgacatctaattcaag-ctgaagttttagtttgtgattccttttattgacttgacaatttaactttgtccagTCATTGGGGGTGCTTTGTGAAGCTCAGTACTTTCAGAATGTTATGCGCGTCGGTTTTCGGCTAAGATCAACTCTG
















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), 61 (downstream exon)
Score: 47

TCTATGCAAAAAGGTGATCCATCTTGGAGCGGTTACATCTATGCTTTCTCAATCTTCGCTGGAGTGgtatggatta ... cattctgcagTCACTGGGTGTTCTTTCTGAAGCACAGTACTTTCAGAATGTCATGCGAACGGGTTTCAGGTTGAGGTCAACATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagccaaaactggacagacttttgatcacttaccttttgtttaccattctgcagTCACTGGGTGTTCTTTCTGAAGCACAGTACTTTCAGAATGTCATGCGAACGGGTTTCAGGTTGAGGTCAACATTG
                           cacttac  putative branch site (score: 47)
                                            ccattct  putative PPT
                                   ttttgttta  TA-rich tract