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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataaccaggctctaagtttctcaatagcacgctgttttcatgcccaaaagattgttctgaactcaatgccatacgtaaaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT

Basic information

species Oryza sativa
transcript LOC_Os05g33810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g33810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G109354_T01 (Zea mays), 3'ss of exon 4
gtatataaccaggctctaagtttctcaatagcacgctgttttcatgcccaaaagattgttctgaactcaatgccatacgtaaaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT
   ||||  |  ||||||||||  |   || ||        |            ||| || | ||    |||| ||| || || | ||||||| || || ||| |   |||||||||||||||| |||||||||| |||||||| |||||||  ||||||||||||||| ||||||||||||| |||||||
--gtatagtcttgctctaagttcatt--taacatagaaccat------------attattttaaagg-gatgctatatgtgaa-tgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT

upper sequence: LOC_Os05g33810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G18830.3 (Arabidopsis thaliana), 3'ss of exon 4
-----gtatataaccaggctcta-agtttctcaatagcacgctgttttcatgcccaaaagattgttctgaactcaatgccatacg------taaaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT
      |  | ||  |     || |||||     |   |  || | || |    |  |  ||      ||||| |||  | | ||      |  ||| ||||||||||| | ||| |  | | |||||||||||| |||||||||||||| || || || ||||||||||| ||||| ||| | ||||||||| |   |||||
gtattctcaagaattatatattacagtttagtgttcaaagactatgtttaccttctcagaatctcaaagaact-aatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT

upper sequence: LOC_Os05g33810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0020g02160.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtatataaccaggctctaagtttctcaatagcacgc-tgttttcatgcccaaaagattgttctgaactcaatgccatac-gtaaaatatg----cagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT
           |  ||| |  |   | ||   ||   |  || |    |||||| ||     | ||||      |||   | |  || || |   ||| ||    ||||| ||  ||||| |  ||||||||||| ||||  ||||||||||||| |||||||| ||||  || |||||  | ||| ||||||||||| |   |||||
gtattttaaaggattattattacagtttagtatttatatgagaataaatgtttttataagtcagagat-accaggaatatattaacacactgctcaatgtgtttacagATTTTCCAGTGGTTGGCTAGCATGCCTATTGAGTTGGAGGGCTATATCCGTCCTGGGTGTATCATCTTAACAATTTTTATTGCAATGCCAAAGTTTATGT

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|33381888|gb|CF197231.1|CF197231
EST:     AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAA                         ATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
genomic: AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
EST: gi|29682373|gb|CB678648.1|CB678648
EST:     CTGAATTTCCTCGACCCTTACGCCACCAA                         ATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
genomic: CTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
EST: gi|58656998|gb|CK045678.1|CK045678
EST:     AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAA                         ATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
genomic: AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
EST: gi|29679742|gb|CB676017.1|CB676017
EST:     AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAA                         ATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
genomic: AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
EST: gi|29643203|gb|CB648210.1|CB648210
EST:     AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAA                         ATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
genomic: AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
EST: gi|58662678|gb|CK051364.1|CK051364
EST:     AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAA                         ATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
genomic: AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
EST: gi|58670185|gb|CK058871.1|CK058871
EST:     AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAA                         ATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT
genomic: AGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGT

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: 57 (upstream exon), 66 (downstream exon)
Score: 20

TGTCCCACAGGACGTGTATCATTCAAGTTGTACGATTGGAATCCTGCTGAATTTCCTCGACGCTTACGCCACCAAgtatataacc ... aaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcatgcccaaaagattgttctgaactcaatgccatacgtaaaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT
                                           taaaatat  TA-rich tract