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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaacattaattcattgcgttactagtgcattattttgaaaatcgtggttgttgatagattatataaatgctgtgttgcag

Basic information

species Oryza sativa
transcript LOC_Os10g32550.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 11
GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaacattaattc-attgcgttactagtgcattattttgaaaatcgtggttgttgatagattat-----ataaatgctg--tgttgcag
|| ||||| |||||||| |||||||||||||||||||| ||||||||||| || || |||||||||||||| || ||||||||| ||| |||| ||   ||| | |  |  |  |||  ||  ||  |  |||||  |||||  ||||     ||  ||  ||  ||||||||
GTGACTGTCTCTAAGGATGACACTGTTATTCTTGATGGCGCTGGAGACAAAAAGTCTATTGAAGAGAGGGCAGACCAGgttcgtgcaatattacttttgttgtgctg-tcttaaattgcttctaactttctggtt-ctgataatttatggattatggattatggatgttgcag

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 12
GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa------------cattaattc--attg---cgttactagtgcattattttgaaaatcgtggt---tgttgatagattatataaatgctgtgttgcag--------------
 ||||  | |||||||| |||||||| || |||||||||||||| || |||||| | |||||||| ||   |||||||||  ||   |             |||||||   |||    | ||  | ||| ||| | ||  |  |  || |   | |||||   || ||    |    |||                   
ATAACAATTTCTAAGGATGACACTGTCATCCTTGATGGAGCTGGTGATAAGAAAGCAATTGAAGAAAGAAGTGAGCAGgtctgtttgaatcttccactattattaatttttattctaccattgttggtgtattctgtttcatgtactgatacttattgatgttttttacttgtttcttgtgatgaattttaacaagcag

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 12
GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaacattaattcattgcgttactagtgcattattttga------aaatcgtggttgttgatagattatataaatgctgtgttgcag--------------
 |||| || |||||||| |||||||| |||||||||||||| || ||||||||| |  |||| || ||    ||||||||| |      ||| || ||||  ||  |  ||    |||||  |       |   ||     || ||     |  ||| |  | |||                   
ATAACAGTTTCTAAGGATGACACTGTCATTCTTGATGGAGCGGGTGACAAGAAAGCACTTGAGGAAAGATGCGAGCAGgtttgagttg-atttatacatttggtcccgtgtattctatttccatccaatgatctgtaaggtttaatgatgcacctaacttgtttgtgatgaattttgataaacag

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 10
GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgtt-cgtacaacatta-------attcattgcgttactagtgcatt----attttgaaaatcgtggt-----tgttgatagattata-taaatgct--gtgttgcag-------
|| || || || |||||||||||||||||||||||||| ||||| |||||||||   ||||| || ||   ||| |||||    |  ||| |||       ||  |||| |||| || |  | |    ||     ||||  ||       ||    ||| |  |  ||| ||||  || |||||        
GTTACAGTCTCCAAGGACGACACTGTTATTCTTGATGGGGCTGGCGACAAGAAAGGAATTGAGGAAAGATGTGAACAGgtaatttttaaccttataccctgataaattg-gttagtaataaaatttgtatgcaagaaattatgaagtgtatgaaagtagttcgttctaattgcttggtattgcaactaacag

upper sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 12
GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaacattaattcattgcgttact---agtgcattattttgaaaatcgtggttgttgatagattatataaatg-ctgtgttgcag--------------------------------------------------------------------------------------------
|| ||  ||||||||||||| |||||||| |||||||| ||||| ||||||||  ||||||| ||  ||  ||||||||| | ||  || ||  |       |||| |   | |    |  ||    | || |  |  ||  |   || | |  |||  ||   ||  |                                                                                            
GTTACAATATCTAAGGACGATACTGTTATCCTTGATGGGGCTGGTGACAAGAAGGCCATTGAGGAACGGTGTGAGCAGgtccatattactttcttctcacatgttatttagaatctcctgattctttattctttttctttcttttcttctctggatgattgatctgtcgattggtttttccttcattgcgaagcaaatgccaaattttatatatttttttcatgttgtaattggattcatttggttacattgggatggcag

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|218485224|gb|FG951291.1|FG951291
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTACGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|33795638|gb|CF323689.1|CF323689
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|58675082|gb|CK063769.1|CK063769
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGGTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|27554443|gb|CA998343.1|CA998343
EST:     AATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: AATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|55411061|gb|CV723437.1|CV723437
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|218483700|gb|FG965930.1|FG965930
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|27577977|gb|CB000672.1|CB000672
EST:     AATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: AATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|27576373|gb|CA999067.1|CA999067
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTACGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|58692466|gb|CK081153.1|CK081153
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTACGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|27546502|gb|CA764746.2|CA764746
EST:     TTCTTGATGGAGCTGGAGACAAGAGATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTACGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|55411724|gb|CV724100.1|CV724100
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|58663314|gb|CK052000.1|CK052000
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTC
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTC
EST: gi|58678370|gb|CK067057.1|CK067057
EST:     TGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|25803762|gb|CA759723.1|CA759723
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTACGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|58666161|gb|CK054847.1|CK054847
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
EST: gi|33796275|gb|CF324004.1|CF324004
EST:     TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAG                         ATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA
genomic: TTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTA

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), 73 (downstream exon)
Score: 108

GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaa ... tgtgttgcagATTAGATCTGCAATTGAGCTAAGCACTTCTGATTATGACAAGGAAAAGCTACAGGAGCGGTTGGCAAAGCTCTCCGGAGGTGTTGCTGTTCTAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAACTGTATCTAAGGACGACACTGTTATTCTTGATGGAGCTGGAGACAAGAAATCCATTGAAGAGAGGGCTGAGCAGgttcgtacaacattaattcattgcgttactagtgcattattttgaaaatcgtggttgttgatagattatataaatgctgtgttgcag

- - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG