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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcgcttcgccgcggcgattaacctgcggctttcctttactgtttaagctgcatctgaggggaatttcatttttggtatggatgacgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCC

Basic information

species Oryza sativa
transcript LOC_Os08g41010.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41010.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G107106_T02 (Zea mays), 3'ss of exon 2
gtaggtcgcttcgccgcggcgattaacctgcggctttcc----tttac-tgtttaagctgcatctgaggggaatttc-atttttggt-----atggatgacgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCC
|||||||||| | | | || ||| || ||| | ||| | | ||||||||||||||| ||| || | ||| ||| || | | | || |||| | ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| ||||||||||||| |||||||| ||||||||
gtaggtcgctctggctccgccgctaagttgtctcttgtcgcaccctacgtatctaagctgcatctgagtggatttcccattggtgggggacaataaacggtg-ttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCC

upper sequence: LOC_Os08g41010.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G134770_T02 (Zea mays), 3'ss of exon 2
gtaggtcgct-tcgccgcggcgattaacc-tgcggctttcctttactgttta--agctgcatctgaggggaatttcatt--tttggtatggatgacgac--tcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCC
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gtaggttgctcttgctccgccgcctcgttatctcactctccgtatctatctataagttgcatctgagtgaattcccctcggcgtgggacaataaacctccttctcagGCAGCCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCAAGAACGTTAACTTCGCCTTTCGCACCACTTGCAACATGCGCAACTGCAACCAGTCCAGGCC
















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|58588238|gb|CF986546.1|CF986546
EST:     GTCGACAACCGTAGGCGATCTGCTGGAAAGCGTGCCCGCACCGACG                         GTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACT
genomic: GTCGACAACCGTAGCCAATCTGCTGGAAAGCGTGCCCGCACCGACGgtaggtcgct ... cgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACT
EST: gi|88358394|gb|CI606903.1|CI606903
EST:     GTCGACAACCGTAGCCAATCTGCTGGAAAGCGTGCCCGCACCGACG                         GTGGGCGGCGTGGGGACGAGTGGGTTTGCCCCAGCTGCCAGAACGTCAACT
genomic: GTCGACAACCGTAGCCAATCTGCTGGAAAGCGTGCCCGCACCGACGgtaggtcgct ... cgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACT
EST: gi|88724063|gb|CI749073.1|CI749073
EST:     GTCGACAACCGTAGCCAATCTGCTGGAAAGCGTGCCCGCACCGACG                         GTGGGCGGCGTGAGGACGACTGGGTTTGGCCCAGCTGCCAGAACGTCAACT
genomic: GTCGACAACCGTAGCCAATCTGCTGGAAAGCGTGCCCGCACCGACGgtaggtcgct ... cgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACT
EST: gi|58673635|gb|CK062321.1|CK062321
EST:     GTGCCCGCACCGACG                         GTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAGCGTCAACT
genomic: GTGCCCGCACCGACGgtaggtcgct ... cgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACT

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: 46 (upstream exon), 71 (downstream exon)
Score: 4

GTCGACAACCGTAGCCAATCTGCTGGAAAGCGTGCCCGCACCGACGgtaggtcgct ... cgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttaagctgcatctgaggggaatttcatttttggtatggatgacgactcacagGTGGGCGGCGTGAGGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCC
                      aatttcattttt  TA-rich tract