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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCGGCGGCTGAGACGAAGAGGGGACCGAGCGGCGCCTCCTTCATCCGGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcagcactctttcccactggtggttgagtttgtggagaacgctgcaccgtttcccgtgccgcgcgaggtgtttgtggaaattcccccgaggccc...

Basic information

species Oryza sativa
transcript LOC_Os02g47940.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47940.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 1
GGCGGCGGCGGCTGAGACGAAGAGGGGACCGAGCGGCGCCTCCTTCATCCGGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcagcactctttcccactggtggttgagtttgtggagaac-gctgcaccg---tttcccgtgccgcgcgaggtgtttgtggaaattcccccgaggccc-------------------------------------
| |||||||||| ||| ||||| || | | || ||| | |||||||||||||   ||||||||||  ||||||||||| ||||||||||||||||| ||||||       |   |    || ||     |    | | ||| |||  |   |||||   ||| |  |||  ||||||||| | |  ||||| |||| | ||                                        
GACGGCGGCGGCCGAGGCGAAGGGGCGGCTGACCGGTGACTCCTTCATCCGGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaatacgagccccgccgctaagattctcttgtatggggaaaaggcacaccgacttttgctatgc-acgcgaggtgctcgccgaaatgccccagtggtaacattcgctgtctcgctgaaaacggtaccccttaacag
















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|88716981|gb|CI740491.1|CI740491
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88370256|gb|CI585261.1|CI585261
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88363721|gb|CI609078.1|CI609078
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGACCTTCGAG                         GTGTTGTACGCTCGGCTTGGGGGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88327579|gb|CI646772.1|CI646772
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAA
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAA
EST: gi|29641902|gb|CB646909.1|CB646909
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88303422|gb|CI669070.1|CI669070
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88389725|gb|CI603224.1|CI603224
EST:     GGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGAACACCTCAGGAGTCTCGCCCCGTACCAGCCC-ATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88402807|gb|CI613255.1|CI613255
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88399533|gb|CI606154.1|CI606154
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88591567|gb|CI709607.1|CI709607
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGNTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88362101|gb|CI607101.1|CI607101
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
EST: gi|88693573|gb|CI737148.1|CI737148
EST:     GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAG                         GTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT
genomic: GGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGAT

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: 75 (upstream exon), 70 (downstream exon)
Score: 39

GGCGGCGGCGGCTGAGACGAAGAGGGGACCGAGCGGCGCCTCCTTCATCCGGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcag ... tccttgctagGTGTTGTCCGCTCGGCTTGGGCGTAAACCAGAGGATATAATCAAGTTGGATGCAAATGAAAATCCATATGGTCCACCTCCGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGCGGCGGCTGAGACGAAGAGGGGACCGAGCGGCGCCTCCTTCATCCGGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcagcactctttcccactggtggttgagtttgtggagaacgctgcaccgtttcccgtgccgcgcgaggtgtttgtggaaattcccccgaggccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccccga