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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttttgatattttgttttgggattctttcacttccaaataataagcatgttaagtttgacatgattgcgtgttgttactcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAGTTCTTGAGAAAAATTTCCCAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g61710.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 4
gtatatttttgatattttgttttggg-attctttcacttccaaataataagcatgttaagtttgacatgattgcg--tgttgttactcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAGTTCTTGAGAAAAATTTCCCAAAG
       |||||| |  || ||||||  | |    |  |||   |  | |   |  |||   | | | ||||||   |||| || ||| | | |||| |||||||| |||||||||||||||||||||||||||||||||||||||||||||||| | ||||| ||||| || ||||||
------gtttgatttagtgctttgggtgtacaaatatatccttctgttcatgtttataaaaataa-aggattgctgctgttatttctcctgt-tagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG

upper sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------gtatatttttgatattttgttttgggattctttcac---ttccaaataataagcatgt-----taagtttgacatgattgcgtgttgttactcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAGTTCTTGAGAAAAATTTCCCAAAG
                                                           || | |||||  ||   | |||   ||| | |    |  ||| |  |  |    |     ||  ||  |    |  | |   | ||  | || || ||| |||||||| |||||||| ||||| |||||||| ||| | ||||||||||| ||||  | | ||||    || |||||||||
gtgtgttcattagttcattagaaatgtgctgctaaggacatgcaaatttacctctaagttaatgttgatcattatatctggttctctattagagatgacaatttgtccgttgatggcaatagattaaaaggaaaagagcaatattttttttttgcagGTTCTGGACTATCAAGCTCTGCAGCGTTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCAAAG

upper sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------gtatatttttgatattttgttttgggattctttcacttccaaataataagcatgttaagtttgacatgattgcgtgttgtt-actcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAGTTCTTGAGAAAAATTTCCCAAAG
                                                                           ||||| || ||| | |  |   |       ||         ||   ||  |  | ||     | |          || || | |  | |  ||| |||||||| |||||||| |||||||||||||| ||| | ||||||||||| ||||  | | ||||    || ||||| |||
gtgtgttcattagttttgaattagaatggtgctgctaaggacatgtaaatttacctctaagttaatgttgatcattatatctt-gatctctattagagatgacaatttgtccgttgatggcaataaattaaaaggaaaaagagcaataatttatttatttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG

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|29681135|gb|CB677410.1|CB677410
EST:     GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAG                         GATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAGgtatattttt ... tcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|29681133|gb|CB677408.1|CB677408
EST:     GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAG                         GATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAGgtatattttt ... tcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|58695416|gb|CK084103.1|CK084103
EST:     GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAG                         GATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
genomic: GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAGgtatattttt ... tcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTA
EST: gi|40493179|gb|BX900637.1|BX900637
EST:     GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAG                         GATCTGGACTTTCAAGCTC
genomic: GGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAGgtatattttt ... tcttatgtagGATCTGGACTTTCAAGCTC

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: 73 (upstream exon), 66 (downstream exon)
Score: 23

ATACAAGGGAGTTTATGAGTATTGTAGGTCAAAAGGGATAGATATGGGTGGACCTGTTGGCCTTGATGTAGTTGTTGATGGCACAGTTCCTACAGgtatattttt ... tcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAGTTCTTGAGAAAAATTTCCCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaataataagcatgttaagtttgacatgattgcgtgttgttactcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAGTTCTTGAGAAAAATTTCCCAAAG
                    gtttgac  putative branch site (score: 23)
                                         ttactctt  putative PPT
                ttaagttt  TA-rich tract