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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttgaatgtttgatctgcatcaccctttacctgttattttttatgaaatcacaagaatcttattactattctgcttgtcctgtggttcag

Basic information

species Oryza sativa
transcript LOC_Os10g35930.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35930.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 5'ss of exon 2
ATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttgaatgtttgatctgcatcaccctttacctgttattttttatgaaatcacaagaatcttattactattctgcttgtcctgtggttcag
||| ||| |||||| |||||||| || ||| | ||||||||||| ||||||||||| || ||||||||| | ||||  ||||  || ||||| |   |||||  ||   | | |   ||||    || |   |  ||  ||| ||| |   |||||  |  ||| ||  |    |||   | | ||  |      
ATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAGgttcgt---attataaaatctctgacatcgaatctct-ctatctttca---aatcatcatgatcataacaagtctctttcttttctcag------

upper sequence: LOC_Os10g35930.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT3G61230.1 (Arabidopsis thaliana), 5'ss of exon 2
ATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtt--tgaatgtttgatctgcatcaccct-ttacctgtta-ttttttatgaaatcacaagaatctt-attactat-tctgcttgtcctgtggttcag
|| || | ||| || ||||||||||| ||| | || ||||||||||||||||| ||||| ||||| ||| | || |  ||||  ||||| ||||   ||||| || |    |||  |   | | | |  | || ||   | |||   | |  |||||    || ||||||   |||| | ||| ||||  || |  | |||
ATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAGgt-tgctaacaaatcctctgttttctttgctctgttttttattaacctctcttgaaaagctaacaatctttgctactttctcttcttggtcttt--tacag

upper sequence: LOC_Os10g35930.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 5'ss of exon 2
ATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttgaatgtttgatctgcatcaccctttacctgttattttttatgaaatcacaagaatcttattactattctgcttgtcctgtggttcag
||| ||| ||| || |||||||||||||| || ||||||||  | |||||||||||||| ||||||||  | ||||  ||||  ||||| ||    |||   ||||  || | |||  | |  |  |    ||     || |   ||      ||  ||  | || | | ||||  | ||       | |     
ATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTT----TCAAACATgtgagacttttt--tttaaaaaatttatttggcattctgggtttctttttcttaatgagctaactcctatggttctgcatgaatag-----

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|88402615|gb|CI598842.1|CI598842
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTGAACAG
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG
EST: gi|88396276|gb|CI598388.1|CI598388
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTGAACAGGCTAA
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAGGCTAA
EST: gi|32948518|gb|BP185090.1|BP185090
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTGAACAG
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG
EST: gi|86479286|gb|CI121919.1|CI121919
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTGAACAG
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG
EST: gi|87021526|gb|CI274133.1|CI274133
EST:     GAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTGAACAG
genomic: GAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG
EST: gi|88400530|gb|CI593605.1|CI593605
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTGA
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGA
EST: gi|88300748|gb|CI589740.1|CI589740
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTG
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTG
EST: gi|4879590|gb|AU063889.1|AU063889
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGA-CTTCCCCTCAG                         GTACAAAGGCAA-CAGTGAACAG
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG
EST: gi|87020814|gb|CI269531.1|CI269531
EST:     TGA-CAGCTATTCAAGGAAACAGGCACCTTCAAGAAG-ACTTCCCCTCAG                         GTACAAAGGCAAACAGTGAACAG
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG
EST: gi|218489691|gb|FG954871.1|FG954871
EST:     TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAG                         GTACAAAGGCAAACAGTGAACAG
genomic: TGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG

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), 23 (downstream exon)
Score: 230

ATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttga ... tgtggttcagGTACAAAGGCAAACAGTGAACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGCAGCTATTCGTCCATGGATGGGGTTCTTTACTGCAAGACCCATTTTGAGCAGCTATTCAAGGAAACAGGCACCTTCAAGAAGAACTTCCCCTCAGgtatgtttgaatgtttgatctgcatcaccctttacctgttattttttatgaaatcacaagaatcttattactattctgcttgtcctgtggttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC