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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcaagttatgcatgactgtggataggtcaactaaaatatctatctgttcacatccttgcaataaactttgtcactagttattttctgtcttatgagttattacttcgtagCTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTGGAAACAG

Basic information

species Oryza sativa
transcript LOC_Os03g18080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18080.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G047894_T04 (Zea mays), 3'ss of exon 4
gtaagtatcaagttatgcatgactgtggataggtcaactaaaatatctatctgttcacatccttgcaataaactttgtcactagttattttctgtcttatgagttattacttcgtagCTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTGGAAACAG
     | |   ||||| |  || |||   ||  | |  | | |||   ||       |     || |||   | |           || |   |   ||     ||| | |  ||||||||||||||||||| |||||| |||||||| |||||||||| ||||| ||||| |||
---tttcttttgttatactggattgtatctaactga--tgagatagaaata---atgcgatgatggaatgctcctca---------atgtaaagctataaacactatgattatgtagCTTGCAGAGGGCATCCAAGTTGGCTGCTGGGAGGGTACATAAACCACTATGGAAGCAG
















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|88298501|gb|CI563496.1|CI563496
EST:     AAACTACTCATGGGCTTTATTACTCTTATGACAGGGATTTGACACTTGAA                         CTTGCAGAGGGCATCAAAAGTTGCCTGCTGGGCGGGTACATAAGCCAACT
genomic: AAACTACTCATGGGCTTTATTACTCTTATGACAGGGATTTGACACT-GAAgtaagtatca ... tacttcgtagCTTGCAGAGGGCATCAAA-GTTGCCTGCTGGGCGGGTACATAAGCCA-CT
EST: gi|117222519|gb|CT845898.1|CT845898
EST:     GAAACTACTCATGGGCTTTATTACTCTTATGACAGGGATTTGACACTGAA                         CTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTG
genomic: GAAACTACTCATGGGCTTTATTACTCTTATGACAGGGATTTGACACTGAAgtaagtatca ... tacttcgtagCTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTG
EST: gi|29624693|gb|CB629704.1|CB629704
EST:     GAAACTACTCATGGGCTTTATTACTCTTATGACAGGGATTTGACACTGAA                         CTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTG
genomic: GAAACTACTCATGGGCTTTATTACTCTTATGACAGGGATTTGACACTGAAgtaagtatca ... tacttcgtagCTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTG

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: 47 (upstream exon), 65 (downstream exon)
Score: 23

AAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACTCATGGGCTTTATTACTCTTATGACAGGGATTTGACACTGAAgtaagtatca ... tacttcgtagCTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTGGAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaataaactttgtcactagttattttctgtcttatgagttattacttcgtagCTTGCAGAGGGCATCAAAGTTGCCTGCTGGGCGGGTACATAAGCCACTCTGGAAACAG
                                            ttacttc  CT-rich tract
                   tagttatttt  TA-rich tract