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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaaagcttagtttgcttgtatttttgttgcttcccagcattgttacacaagtcattaaaattattttgctaatcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA

Basic information

species Oryza sativa
transcript LOC_Os02g58730.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 4
gtattcaaagcttagtttgcttgtatttttgttgcttcccagcattgttacacaagtcattaaaattattttgctaatcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA
               | |||||  | || |   | ||     ||| ||  || |     | |   |  |||  || |||  || ||||||||||||||||||| || |||||||| || || ||||| ||||||||||||||||| ||||| 
-------gtatgctatctgctttgacttgt-cggtttgtgttcatagtggcatataaggtgagcgtcgtttcactgatctgtgcagGGCGAAGAGCTGAGGAAGCTAATTGGTGCTGCCGCCTACATCGAATGCAGTTCAAAAACCCAGCAG
















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|3763167|gb|AU029919.1|AU029919
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACA
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACA
EST: gi|163920266|gb|EG714451.1|EG714451
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|88269641|gb|CI380939.1|CI380939
EST:     TTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: TTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAN                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|163918056|gb|EG713984.1|EG713984
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|88279468|gb|CI400468.1|CI400468
EST:     TACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: TACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|88832933|gb|CI369823.1|CI369823
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|86861523|gb|CI328204.1|CI328204
EST:     GCAATTTTTCGTAGATCACCCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: GCAATTTTTCGTAGATCA-CCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|11233552|gb|AU164964.1|AU164964
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|11233553|gb|AU164965.1|AU164965
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|25807453|gb|CA763414.1|CA763414
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|86869483|gb|CI346343.1|CI346343
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAG
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAG
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     AGCAATTTTTTGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|86415824|gb|CI029835.1|CI029835
EST:     AGCNATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|163929342|gb|EG713767.1|EG713767
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|88834954|gb|CI370257.1|CI370257
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATT-GTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|7134822|gb|AU082691.1|AU082691
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|86599058|gb|CI355675.1|CI355675
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|2431385|gb|C73805.1|C73805
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|88375099|gb|CI523364.1|CI523364
EST:     TTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: TTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|88251317|gb|CI349745.1|CI349745
EST:     AGCAATTTTTCGTAGATCACACTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|218483315|gb|FG958115.1|FG958115
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCAATGCTCAA                         GGCGAATAGCTGAGGAAACTCATTGGTG
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTG
EST: gi|33802329|gb|CF327038.1|CF327038
EST:     GCAATTTTTCGTAGATCACCCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: GCAATTTTTCGTAGATCA-CCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|88260942|gb|CI364518.1|CI364518
EST:     AGCAATTTTTCGTAGATCACCCTGCTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|86598350|gb|CI354967.1|CI354967
EST:     AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATT-GTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     AGCNATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG                         GGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT
genomic: AGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGT

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: 65 (upstream exon), 66 (downstream exon)
Score: 41

ATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAGgtattcaaag ... atcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttcccagcattgttacacaagtcattaaaattattttgctaatcaatgtagGGCGAAGAGCTGAGGAAACTCATTGGTGCAGCGGCATACATTGAATGCAGTTCAAAAACACAGCAA
                                        tgctaat  putative branch site (score: 41)
                           attaaaattattttgc  TA-rich tract