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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttaccgaagctttcccttagtcgtgctgggcgcgcccgcgcgcgcgtgcgtgcgttcgtctctgatctcggtggggagcacacgggggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC

Basic information

species Oryza sativa
transcript LOC_Os02g27360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g27360.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G015441_T01 (Zea mays), 3'ss of exon 1
gtaagttttaccgaagctttcccttagtcgtgctgggcgcgcccgc-gcgcgcgtgcgtgcgttcgtctctgatctcggtggggagcacacgggggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC
                        |||  |  ||      ||   | |   || |   |  | | ||||  ||    || |  |    | ||    | ||||| || |||| ||| ||||| | ||||||| ||||| | ||| |||||||||||||||||||||| |||||||||||||||                     
-----------------------gtaggtgatctaccttggctttcagtatgcttttcttggcttgtct--gactgtggagATGTCTTCCCGCCCAG-CGCAGCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACGGGCAGCGACATCCTC---------------------

upper sequence: LOC_Os02g27360.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G473204_T01 (Zea mays), 3'ss of exon 1
gtaagt--tttaccga----agctttcccttagtcgtgctgggcgcgcccgcgcgcgcgtgc-gtgcgttcgtctctg-atctcggtggggagcacacgggggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC
||| ||  | || |       |||   | |  |   | ||||  |||     |          ||  | |  |||  |  | || |   || |    | | |  |||||| || |||| ||||||||||| ||||||| ||||| | ||| ||||||||||||||||||||||||||||||| ||||| ||||| ||| || ||  ||||
gtaggtgatctatcagcatcggctgcgcgtgtgcgtttctggctgcggtgatgatgatacatagtaggcttctcttggcgtgtctgactggggttt-ctgcgcagcgcagCCTGTACTACACGCGGATTGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTTTGGGTGAACGGCATCAGCTGC

upper sequence: LOC_Os02g27360.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G411333_T02 (Zea mays), 3'ss of exon 1
-----------gtaagttttaccgaagctttcccttagtcgtgctg-ggcgcgcccgcgcgcgcgt-gcgtgcgttcgtctctgatctcggtggggagcacacgggggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC
            | ||  |  |||  ||   |  ||  ||  ||||  ||   |||    |   || |  ||| ||  |    |     |   ||| |    ||  |   | ||| || |||| ||| ||||| | ||||||| ||||| | ||| ||||||||||||||||||||||||||||||| |||||||||||||||||| ||  ||||
gtaggtgacctatcagcctcgccggcgcgcgctgtttttctggctgcagcttccccataggtcagtagtatgcttttcttggcgtgtctgactgggggtcttcgcag---cacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC

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|88673093|gb|CI727208.1|CI727208
EST:     GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCG
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCG
EST: gi|88669996|gb|CI724112.1|CI724112
EST:     GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCANGCGGAT
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGAT
EST: gi|88672198|gb|CI726314.1|CI726314
EST:     GCCGNCATCGACCTCCCC-TCGGCGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCGGATTGGGATCGGCACGCCGGNGAAGCGCTACTA
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTA
EST: gi|88673628|gb|CI727741.1|CI727741
EST:     GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCGGATTGGGATCGGCACGCC
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCC
EST: gi|88673735|gb|CI727848.1|CI727848
EST:     GCCGCCATCGACCTCCCCCTCGGNGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCGGATTGGGATCGGCACG
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACG
EST: gi|29664886|gb|CB661161.1|CB661161
EST:     GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGT
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGT
EST: gi|88671690|gb|CI725721.1|CI725721
EST:     GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCG
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCG
EST: gi|88673629|gb|CI727742.1|CI727742
EST:     GNCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCGGATTGGGATCGGCACGC
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGC
EST: gi|88673072|gb|CI727187.1|CI727187
EST:     GCCGCCATCGACCTCCCCCTCGGNGGCAGCGGCCTCGCCACCGAGACCGG                         GCTCTACTTCACGCGGATTGGGATCGGCACGCC
genomic: GCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCC

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), 52 (downstream exon)
Score: 6

ACCTCTCGGCGCTCCGGGAGCACGACGGACGCCGCCACGGCCGCCTCCTCGCCGCCATCGACCTCCCCCTCGGCGGCAGCGGCCTCGCCACCGAGACCGGgtaagtttta ... gggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcgcgtgcgtgcgttcgtctctgatctcggtggggagcacacgggggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC
                   ctctgat  putative branch site (score: 6)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttaccgaagctttcccttagtcgtgctgggcgcgcccgcgcgcgcgtgcgtgcgttcgtctctgatctcggtggggagcacacgggggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA