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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagtgatcatactcatttgagttcacgcacaatgtcattctgttcttagttatcaaatgtttgtccacagaaataaaaaaaatattccatgatctttttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os03g17930.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G015730_T03 (Zea mays), 3'ss of exon 11
gtacgagtgatcatactcatttgagttcacgcacaatgtcattctgttcttagttatcaaatgtttgtccacagaaataaaaaaaatattccatgatctttttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG
| | | | || |||| | ||| | | || ||| | || || ||| ||||| | | ||||||||||| ||||||||| | | | ||||| |||| |||||||| |||||||| ||||| | ||||||||||| |||||| ||||||| |||||| | ||||| |||
--------------gtatgctctacataatgctcaatattattgtat-ctactttacttgtcaatagttgactgaagtaaaac---tctcgtatgatcttttt-catcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG

upper sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G31830.1 (Glycine max), 3'ss of exon 11
----gtacgagtgatcatactcatttga---gttcacgcacaatgtcattctgttcttagttatcaaatgtttgtccacagaaataaaaaaaatattccatgatctt--tttgca-tcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG
| | | ||| || ||| | ||||| | || |||||| | | || | | || || || | | || | | || | | || | || || |||||||| || || ||||| || |||||||| ||| ||||| |||||||||||| |||||| || |||||| | || | |||| |||| |||
gtaaacataatttatcttatatcttttatttgttcaag-actcagtcatttt-tgctgaatcatatcttggatgaactctaaagtcctctgtctttttctttattgtggttaacaatcagATGGCAAAATCAATCAAGGAACTCAAGAAGGAGAATCAATTCTTGAAGAGTAAATCTGAGAAGTCTGATGTTACACTCATAGAGTTAGTTGATGAG
















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|33809158|gb|CF330463.1|CF330463
EST:     TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|88955373|gb|CI091465.1|CI091465
EST:     TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|38479504|gb|CF963613.1|CF963613
EST:     TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|86436064|gb|CI107297.1|CI107297
EST:     GAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: GAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|88219408|gb|CI218968.1|CI218968
EST:     TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|29639434|gb|CB644443.1|CB644443
EST:     TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|86499080|gb|CI141713.1|CI141713
EST:     TCACCAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|58675688|gb|CK064375.1|CK064375
EST:     TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
EST: gi|88263669|gb|CI366570.1|CI366570
EST:     AGAT-GAAAAG                         ATGGTGAACGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAG
genomic: AGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAA-GCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAG
EST: gi|86425721|gb|CI070818.1|CI070818
EST:     TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAG                         ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT
genomic: TCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGT

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: 57 (upstream exon), 60 (downstream exon)
Score: 28

GATGCCCTCACAAAAAGCAATGAAGTCTTTGAGACATACAAGAAGGAGATGGAAAAGgtacgagtga ... tttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaatgtttgtccacagaaataaaaaaaatattccatgatctttttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG
                                         tctttttgc  CT-rich tract
 aaataaaaaaaatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgagtgatcatactcatttgagttcacgcacaatgtcattctgttcttagttatcaaatgtttgtccacagaaataaaaaaaatattccatgatctttttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG