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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaatgaggattttgaagcataaaatagtttttttttgcattgtaatttaacactgtgttctgtaaacatctttacatcaacatatggtatagt...

Basic information

species Oryza sativa
transcript LOC_Os06g40730.1
intron # 12
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 12
lower sequence: GRMZM2G092895_T01 (Zea mays), 5'ss of exon 12
GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataa-atgaggatt--ttgaagcataaaatagtttttttttgcattgtaatttaacactgtgttctgtaaacatctttacatcaacatatggtatagt
|||||||||||||||||||| |||||||| ||||||||||||  | |||| |  |||| ||||||||||||| || || ||   |  |  ||        ||| | |     | |  ||  |   || ||   | |||   | ||  |  || | | |  |           
GATTTTCTTTTGGATGAAAACCATAACCTTACTGAGATGGACGGTAACACAGGAGAGTGTCATTTAGAGgtagaagaagatattgcctagtttgtttgagaaaaaataacgatctttatgatttctttacttggagtta-atgaattttctttccttattag----------
















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:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88665861|gb|CI716017.1|CI716017
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|58595357|gb|CF993665.1|CF993665
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGGCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88671997|gb|CI726113.1|CI726113
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|89172448|gb|CI721507.1|CI721507
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88671150|gb|CI725266.1|CI725266
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88674443|gb|CI728556.1|CI728556
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88672670|gb|CI726786.1|CI726786
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88675398|gb|CI729511.1|CI729511
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88673380|gb|CI727493.1|CI727493
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88671674|gb|CI725790.1|CI725790
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88667182|gb|CI719318.1|CI719318
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88909100|gb|CI718408.1|CI718408
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88677007|gb|CI731120.1|CI731120
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88674048|gb|CI728161.1|CI728161
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|58656512|gb|CK045192.1|CK045192
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88908563|gb|CI713121.1|CI713121
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88673085|gb|CI727200.1|CI727200
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88954834|gb|CI720249.1|CI720249
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88593829|gb|CI713783.1|CI713783
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88668460|gb|CI722022.1|CI722022
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88594800|gb|CI714758.1|CI714758
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88673190|gb|CI727304.1|CI727304
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
EST: gi|88669516|gb|CI723434.1|CI723434
EST:     ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAG                         GATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC
genomic: ATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAAC

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: 69 (upstream exon), 63 (downstream exon)
Score: 15

GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaa ... ccttttgtagGATAAATCTCACAGGCAAAATGAGGAGTGCTGCTCATACACAAGTTCAAACCGAGAGAGCTGGGGAAGATGTTCTTCCTTGGGGGCAGCGAGTGATGGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTCTTTTGGATGAAAATCATAACCTCACTGAGATGGACACTCACACTGCTGAGTCTCATTTAGAGgtaaaataaatgaggattttgaagcataaaatagtttttttttgcattgtaatttaacactgtgttctgtaaacatctttacatcaacatatggtatagt

- - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - -  GATGGA