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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatattgtagtggtccttttgtaaggctgacatatactgaacttgtcgttactctggtccccatgtcttctgtgattaagtatttgaggagactt...

Basic information

species Oryza sativa
transcript LOC_Os06g39640.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G079080_T02 (Zea mays), 5'ss of exon 19
GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatattgtagtggtccttttgtaaggctgacat-atactg----aacttgtcgttactc--tggtccccatgtcttctgtgattaagtatttgaggagactt
|||| ||||||||||| ||||| ||||||||| | ||||||||||||||||||||||| ||||||||||| ||||||| | || ||| |      || || ||| | || || |   ||    | | || | ||||    | |     || |  |     |      ||||| |       
GAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaaaagtaatgtgga----tttgtggaagaccgatattactttgtgcaatcctgacattacatgttagctggaatattctaccgtacctgtcatttgtgagtg---

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 19
lower sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 18
GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatattgtagtggtcc-----ttttgtaaggctgacat-atactgaacttgtcgt----tactctggtccccatgtcttctgtgattaagtatttgaggagactt
|||||||||||||||| ||||| ||||||||| ||||||||||||||||||||||||| ||||||||||| ||||||||| |  ||| || | |      || || ||  ||||||| | | |  | |||   |    |||  |  |   | |||| | | |  ||    || ||         
GAACTGTTGTTGATTCTAAGATATGCCACCCAACAGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaagagtgatgtggtagactgaaatttgtggaatcctgacattacattttagttggaatattctaccgtactgaacctgtcattt-tagttggtcatatg---------

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA10G38770.1 (Glycine max), 5'ss of exon 20
GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaaga-atattgtagtggtccttttgtaaggctgacatatactgaacttgtcgttactctggtccccatgtcttctgtgattaagtatttgaggagactt----
| |||||||||||| | || |||||||| ||| |||| |||||||| || ||||| ||||||||||| || ||||||  | ||| | |  |   |    |   |       || || ||   || |  ||||     |    ||   || || ||   |  |||     ||        
GGACTGTTGTTGATACCAAAATCTGCCATCCAACAGAATTTGATTTTTATCTCTGCAGCCATGCTGGCATCCAGgtagaagatagttttctttcctcccttctatatcaggatttattg---ttataattaca--aatgagaattggttatgggaaagaaaattgtcatagttcaaaac

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA20G28970.1 (Glycine max), 5'ss of exon 20
GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatattgtagtggtccttttgtaaggctgacatatactgaacttgtcgttactctggtccccatgtcttctgtgattaagtatttgaggagactt-
| ||||| |||||||| || |||||||| ||| |||| |||||||| || ||||| ||||||||||| || |||||| ||| || ||  |  | |  |       ||  ||     |    || |  | ||    |       || |   |  |  || | ||  |     | | 
GGACTGTCGTTGATTCCAAAATCTGCCATCCAACAGAATTTGATTTTTATCTCTGCAGCCATGCTGGCATCCAGgta-gaagatagttttttttccctcccttctctaccaggatttattattataatcacagatgagaattggtttatgggaaagaaattttccatagttcata

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 19
lower sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 18
GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatattgtagtggtccttttgtaaggctga-catatactgaacttgtcgttactctggtccccatgtcttctgtgattaagtatttgaggagactt
| ||||| || ||||| ||||| ||||| ||| | |||||||| |||||||| || |||||||| || |||||||||||   || |        | ||||||    ||  ||||    ||  || | |||||                                           
GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaagttgatggagccctggcctttgtagctttgctcatacgacgagattat-gttacag-----------------------------------------

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|163920974|gb|EG710111.1|EG710111
EST:     GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|86435965|gb|CI107198.1|CI107198
EST:     TGTAGCCATGCTGCAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: TGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|87016539|gb|CI273749.1|CI273749
EST:     AGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: AGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|29636941|gb|CB641950.1|CB641950
EST:     GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|86594915|gb|CI258169.1|CI258169
EST:     TCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: TCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|29674861|gb|CB671136.1|CB671136
EST:     GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|88906357|gb|CI375429.1|CI375429
EST:     GCCACCCATCAGAGTTTGATTTGTACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|8404400|gb|AU091754.1|AU091754
EST:     GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|86431420|gb|CI085031.1|CI085031
EST:     TGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: TGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|86477748|gb|CI120381.1|CI120381
EST:     GCCACCCATCAGAGTGTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|29636972|gb|CB641981.1|CB641981
EST:     GCCACCCATCAGAGTTTGATTTATACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
EST: gi|27576993|gb|CA999687.1|CA999687
EST:     GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAG                         GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC
genomic: GCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTC

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: 60 (upstream exon), 74 (downstream exon)
Score: 5

GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatat ... agttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTGTTGTTGATTCAAAGATCTGCCACCCATCAGAGTTTGATTTCTACCTCTGTAGCCATGCTGGAATTCAGgtaagaatattgtagtggtccttttgtaaggctgacatatactgaacttgtcgttactctggtccccatgtcttctgtgattaagtatttgaggagactt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA