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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatttcaacttgattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGT

Basic information

species Oryza sativa
transcript LOC_Os06g06030.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 3
-------gttagatttcaact--tgattgta-cttgcatttcatcattgcagag--aactaaaagtaggttatgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGT
       ||  | || |      | ||| |  |||   || |  | |||||| |       ||  ||||||   |||||||||| || |||||||||||  | |||||||| ||||||||||||||||||||||| || || ||||| |||||||| || || || ||||||||||||||||
gtcagaagtcggcttcctttcaataattatctcttatgttgcccctttgcagggtggggctaacataggtt---cttttcagTGTCGTCTCCATGAGCTTTCAAACAAGCGAAGGATCTCTATTGCTGGTGCTTCCAAACTGTTGGCTAACATCCTTTATTCATATCGTGGGATGGGACTGT

upper sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ25863 (Selaginella moellendorffii), 3'ss of exon 3
gttagatttcaacttgattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGT
  ||  |||    | | |  | ||| |  | ||  |||        ||    ||  ||| ||  |  |||||||| || || ||||| ||||||||| ||||||| ||| |||| |||||||| ||||| ||||| |||| ||| |||||||||||||| ||||| ||||
-gtaagtttgtcttcgctccttcttcc--tccacgattttgacactct----gttcgtt-tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGT

upper sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ04804 (Selaginella moellendorffii), 3'ss of exon 3
gttagatttcaacttgattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGT
        | |  |||  |   ||    |||| ||   |  |   ||     ||  ||| ||  |  |||||||| || || ||||| ||||||||| ||||||| ||| |||| |||||||| ||||| ||||| |||| ||| |||||||||||||| ||||| ||||
-------gtaagtttgtcttcgctcctttttcctccacgatgttgacactctgttcgtt-tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGT

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|163927773|gb|EG710541.1|EG710541
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|2428687|gb|C73150.1|C73150
EST:     GGAGGTGCTGCTGATTGTCAATTTTGGGCATAGGAACTTGGGCATTCAAG                         TGCCGACTCCATTGAGCTCGCGAACAAGCGGAGGATTCTCTATT
genomic: GGAGGTGCTGCTGATTGTCAATTTTGG-CATAGGAACTTGGGCAT-CAAGgttagatttc ... tgcttttcagTGCCGACTCCAT-GAGCTCGCGAACAAGCGGAGGAT-CTCTATT
EST: gi|58663124|gb|CK051810.1|CK051810
EST:     GAGG-GCTGCTGATTGTCAA-TTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: GAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|58597702|gb|CK008230.1|CK008230
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|58600214|gb|CK010742.1|CK010742
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|58595565|gb|CK006093.1|CK006093
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|86830088|gb|CI290291.1|CI290291
EST:     CAGGAGGTGCTGCTGATTGTCACTTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCAT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCAT
EST: gi|29669742|gb|CB666017.1|CB666017
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|29669743|gb|CB666018.1|CB666018
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|87023733|gb|CI286484.1|CI286484
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|1631791|gb|C19520.1|C19520
EST:     GGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: GGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|218491233|gb|FG953090.1|FG953090
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|58604003|gb|CK014531.1|CK014531
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|58600793|gb|CK011321.1|CK011321
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|58586566|gb|CF984874.1|CF984874
EST:     AGGAGGTGCTGCTGATTGTCGAAGTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: AGGAGGTGCTGCTGATTGTC-AATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|88402829|gb|CI613277.1|CI613277
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCA
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCA
EST: gi|58592922|gb|CF991230.1|CF991230
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|58604785|gb|CK015313.1|CK015313
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|8858107|gb|AU095425.1|AU095425
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|218499941|gb|FG967251.1|FG967251
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|55411406|gb|CV723782.1|CV723782
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|10931155|gb|AU161429.1|AU161429
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
EST: gi|33801628|gb|CF326686.1|CF326686
EST:     CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAG                         TGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT
genomic: CAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCT

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: 75 (upstream exon), 74 (downstream exon)
Score: 89

AACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagatttc ... tgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGT
                             aactaaa  putative branch site (score: 89)
                                             tgcttttc  putative PPT
                             aactaaaa  TA-rich tract