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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctctctctctctctctctctccgcccgcccctctttacatgattctactctctcctcgatctggtgcttgtttgagtgcctgcgctgatggcctaatgccctccttgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG

Basic information

species Oryza sativa
transcript LOC_Os03g63520.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082976_T01 (Zea mays), 3'ss of exon 1
------gtctctctctctctctctctctctccgcccgcccctctt-tacatgattctactctctcctcgatctggtgcttgtttgagtgcctgcgctgatggcctaatgccctccttgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG
      |  || | |||  || |    ||        |  ||||    ||||   | |   ||||    ||||  | ||| |||  ||||   || ||   | |         ||  ||   ||||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||
gtaccggcttccccctccttcccatgatcaggagattcttctctcgcccatgtcgccaggatctc--taatctcatccttttttttgtgcgcccgttggctggc---------cccggctgtgcagATCATTTCGCCGTATCACCTGTACCTGAACCCGAAGCTCGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTTCTCTACTTCCGCAAGATGG

upper sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 1
---------------------------------------gtctctctctctctctctctctctc-cgcccgcccctctttacatgattctactctctcctcgatctggtgcttgtttgagtg-cctgcgctgatggcctaatgccctc-------cttgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG
                                        |||||||||||||||||||||||| | | | ||| |   ||    ||||| |||| ||  |   ||| |||| |  |   |    ||||||  |  | |    || |        |  ||   ||||||||||||||| || |||||||| || ||||| ||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||
gtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcc--cctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcagATCATTTCGCCGTATCACCTGTACCTTAACCCGAAGCTCGTGGTGCAGCACTACGAGATTTGGCGCCTCGTCACTAACTTCCTCTACTTCCGCAAGATGG
















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|88348838|gb|CI631925.1|CI631925
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|88717592|gb|CI741102.1|CI741102
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|33683871|gb|CF312110.1|CF312110
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTATCACCTGTATCTGAACC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACC
EST: gi|117223453|gb|CT848631.1|CT848631
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|33683707|gb|CF311946.1|CF311946
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|87006538|gb|CI294921.1|CI294921
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|88403631|gb|CI575515.1|CI575515
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|88397381|gb|CI580891.1|CI580891
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|88398700|gb|CI598665.1|CI598665
EST:     CTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: CTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGC-TGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
EST: gi|88354906|gb|CI615787.1|CI615787
EST:     GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAG                         ATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC
genomic: GCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCAC

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: 74 (upstream exon), 54 (downstream exon)
Score: 29

GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctct ... tgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtgcttgtttgagtgcctgcgctgatggcctaatgccctccttgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG
                              gcctaat  putative branch site (score: 29)
                                    tgccctccttgcctc  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctctctctctctctctctctccgcccgcccctctttacatgattctactctctcctcgatctggtgcttgtttgagtgcctgcgctgatggcctaatgccctccttgcctcgcagATCATTTCGCCCTACCACCTGTATCTGAACCCCAAGCTGGTGGTGCAGCACTACGAGATCTGGCGCCTCGTCACCAACTTCCTCTACTTCCGTAAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG