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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCGAAAACTATTCTCCAGGATGGAAGTATTCCCACTGGGAGATGAAAGGCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggtcacaccatttaatttattaacttcattgatcagtggcacattaattactataatgcttctaggactcttcataaagtagttaatgataaa...

Basic information

species Oryza sativa
transcript LOC_Os12g25710.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g25710.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G094123_T01 (Zea mays), 5'ss of exon 9
CCGCGAAAACTATTCTCCAGGATGGAAGTATTCCCACTGGGAGATGAAAGGCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggtcacaccatt-taatttattaacttcattgatcagtggcacattaattactataatgcttctaggactcttcataaagtagttaatgataaa--
||| ||||| || |||||||| |||||||||||||||||||| |||||||| |||||  | ||||||||||| |||||||||||| |||||||||| |||||||    ||     | |   || | |  |  |||||   | | | | |     |||  | |  |   |||     | |  || || || |     | |    
CCGTGAAAATTACTCTCCAGGTTGGAAGTATTCCCACTGGGAAATGAAAGGTGTTCCATTGAGAATTGAGATTGGTCCAAAAGATCTGGCAAACAAACAGgtacctgagtattttcctcgcaaatcacca--ttcatgtttaaattggat-cacatttttttgttaactcttatcttttatattaattaatgtgccacatgaa

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G38340.1 (Glycine max), 5'ss of exon 10
CCGCGAAAACTATTCTCCAGGATGGAAGTATTCCCACTGGGAGATGAAAGGCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggtcacaccatttaatttattaacttcattgatcagtggcacattaattactataatgct--tctaggactcttcataaagtagttaatgataaa----------
  | || || |||||||| ||||||||||||||  | ||||| |||||||| ||||||||||||||||| || || ||||| ||| | ||||| || |||||    |  |    ||   |  |  || || |    |  |   || ||  ||  || | | | || |  | |   | |   ||| || ||  |     |  |          
TAGAGATAATTATTCTCCTGGATGGAAGTATTCTAATTGGGAAATGAAAGGTGTTCCTCTAAGAATTGAAATTGGGCCAAAGGATTTAGCAAATAAGCAGgtcattaactttgtcctagtgttgcatcaattctcgtatt---tgtcattttgctt-ccacactgttagtttttcagtgaacatcaaataaatctctttggattttgcatag

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G40930.4 (Glycine max), 5'ss of exon 10
CCGCGAAAACTATTCTCCAGGATGGAAGTATTCCCACTGGGAGATGAAAGGCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggtcacaccatttaatttattaacttcattgatcagtggcacattaat-tactataatgcttctag--gactcttcataaagtagtt--aatgataaa---
  | || || |||||||| ||||||||||||||| ||||||| |||||||| ||||||||||||||||| || || ||||| ||| | ||||| || ||||| ||         ||| |   ||||| || |    |  |           |     ||| | |   ||  ||   || |   |||||    ||  |||  |  |   
TAGAGATAATTATTCTCCTGGATGGAAGTATTCCAACTGGGAAATGAAAGGGGTTCCTCTAAGAATTGAAATTGGGCCAAAGGATTTAGCAAATAAGCAGgt-catcaactttgccagt-gttttatcaattctcatatttgtcattttgcttccacactgttagtttttcagtgaacaccaaataaatctctttgaattttgcatag

upper sequence: LOC_Os12g25710.3 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 5'ss of exon 10
CCGCGAAAACTATTCTCCAGGATGGAAGTATTCCCACTGGGAGATGAAAGGCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacaga-ggtcacaccatttaatttattaacttc--attgatcagtggcacattaattactataatgcttctaggactcttcataaagtagttaatg-ataaa----------------------------------------------
  | || |||||||| ||||| ||||||||||| || ||||| ||||| || |||||||| ||||||||||| || ||||||||  | || ||||| ||||||  |    ||  |    |   ||||||  |||   |   ||  ||  |   || || | |||  ||  | |      ||  ||    |    | |  ||                                                 
TAGAGATAACTATTCACCAGGTTGGAAGTATTCACATTGGGAAATGAAGGGTGTTCCTCTTAGAATTGAGATTGGGCCAAAAGACTTAGCTAACAAGCAGgtatgggtaatccaattgctatttttatttcctttcaaccaatttgtttcttctttat-attattgtgtctgttcagtactctatggtatttccatttcattgcttttacttatttactggaagaatgatatattttgttctatccacag

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|29665238|gb|CB661513.1|CB661513
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|29612729|gb|CB617742.1|CB617742
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|218493888|gb|FG946861.1|FG946861
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|29616050|gb|CB621062.1|CB621062
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
EST: gi|29622778|gb|CB627789.1|CB627789
EST:     GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAG                         GCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT
genomic: GCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCT

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), 75 (downstream exon)
Score: 74

CCGCGAAAACTATTCTCCAGGATGGAAGTATTCCCACTGGGAGATGAAAGGCGTTCCTCTAAGAATTGAGATAGGTCCAAAAGATATGGCAAACAATCAGgtacagaggt ... tgcttttcagGCCCGTGTTGTTAGGCGAGACAATGGTGCAAAAGCTGATATTCCTACGGCTGACTTGGTTGAGAAAGTTAATGGGTTACTTGATGAGGTTCAGAAAAACT




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