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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACAAAATCAGTGGTTGAATTGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcatcagtggttggtttgcctcaagtacttgagatcttagctgagtatctccatctgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os06g40730.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40730.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G092895_T01 (Zea mays), 5'ss of exon 11
CTACAAAATCAGTGGTTGAATTGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcatcagtggttggtttgcctcaagtacttgagatcttagctgagtatctccatctgaatgcag
||||||||||||| ||||||||||||||||||||||| |||||| | ||| ||||||  ||||||||||||||||||  |||| ||  || | | ||||   |||||||||| ||       || |||||   || |||||
CTACAAAATCAGTAGTTGAATTGCTGACAGAGAGGGTAAATCAGCTATCTGTTAAAAATGATAATGACTTGgtaagtcaatcattgcctgctcttcctcttctacttgagatttt-------taactccactcgagtgcag
















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|88904818|gb|CI712117.1|CI712117
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88665861|gb|CI716017.1|CI716017
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88671997|gb|CI726113.1|CI726113
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|89172448|gb|CI721507.1|CI721507
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88671150|gb|CI725266.1|CI725266
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88674443|gb|CI728556.1|CI728556
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88672670|gb|CI726786.1|CI726786
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88675398|gb|CI729511.1|CI729511
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88673380|gb|CI727493.1|CI727493
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88671674|gb|CI725790.1|CI725790
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88667182|gb|CI719318.1|CI719318
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88909100|gb|CI718408.1|CI718408
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88677007|gb|CI731120.1|CI731120
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88674048|gb|CI728161.1|CI728161
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|58656512|gb|CK045192.1|CK045192
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88908563|gb|CI713121.1|CI713121
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88673085|gb|CI727200.1|CI727200
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88954834|gb|CI720249.1|CI720249
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88593829|gb|CI713783.1|CI713783
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88668460|gb|CI722022.1|CI722022
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88594800|gb|CI714758.1|CI714758
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88673190|gb|CI727304.1|CI727304
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
EST: gi|88669516|gb|CI723434.1|CI723434
EST:     TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTG                         GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT
genomic: TGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACT

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: 51 (upstream exon), 74 (downstream exon)
Score: 16

CTACAAAATCAGTGGTTGAATTGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcat ... ctgaatgcagGATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAAAATCAGTGGTTGAATTGCTGACAGAGAGGGTCAATCAGTTGTCTATTAAAACAGATAATGACTTGgtaagttcatcagtggttggtttgcctcaagtacttgagatcttagctgagtatctccatctgaatgcag

- - - - - - - - - - - - - -  GAGAGG