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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagtgttctctgctgtttcttcagcgttttcattctctggctccttcaactttctagtatatcactttttttccgttcactgtgatttttaattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGCACGCTACATTAACATAAACAG

Basic information

species Oryza sativa
transcript LOC_Os06g08005.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07905.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G000393_T02 (Zea mays), 3'ss of exon 8
gaagtgttctctgctgtttcttcagcgttttcattctctggctccttcaactttctagtatatcacttttttt-----ccgttcactgtgatttttaattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGCACGCTACATTAACATAAACAG
|  |||  |||     | |    |  ||||  | | | |   ||     ||| | || |   |     ||||      | | |    || |||  |||    |||||||||||| || ||||| ||| |||||||||||||||| || |||||||| |||||||| |||||||| ||
ggggtggactc----atgtgacaaaagtttctagtttttcattcaagatactctgtaatgccttttcattttcaatgactgattcacgttattcataaaaa-cagGTATTTTCGACACGCTTCTGGTTCTTTGTTTATCCTCTCAAAAAATTTGGCTCGCTACATCAACATAAATAG
















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|88512797|gb|CI440303.1|CI440303
EST:     GAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88262435|gb|CI366209.1|CI366209
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88263201|gb|CI366975.1|CI366975
EST:     AGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: AGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|27577598|gb|CB000293.1|CB000293
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|86435305|gb|CI106538.1|CI106538
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88995023|gb|CI036598.1|CI036598
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|86422330|gb|CI059903.1|CI059903
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88834412|gb|CI077695.1|CI077695
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88995018|gb|CI036593.1|CI036593
EST:     ATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: ATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88971772|gb|CI389009.1|CI389009
EST:     GTTTGGAGATTCAAAAAC                         GTATTTTCCCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|89184707|gb|CI007132.1|CI007132
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|89181971|gb|CI113477.1|CI113477
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|86251665|gb|CI016954.1|CI016954
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|29687001|gb|CB683276.1|CB683276
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|86840814|gb|CI335020.1|CI335020
EST:     TGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCCCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: TGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88690259|gb|CI734338.1|CI734338
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88218395|gb|CI218244.1|CI218244
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|86525598|gb|CI165804.1|CI165804
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88974780|gb|CI023076.1|CI023076
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|218479405|gb|FG961659.1|FG961659
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|300215905|gb|HO088531.1|HO088531
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCC
EST: gi|58688376|gb|CK077063.1|CK077063
EST:     GGTC-ACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|218501509|gb|FG952275.1|FG952275
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATAAACGCCATGCTTCCGGTGCTTTGTATATCCTCTCTAACAATATGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88829021|gb|CI073891.1|CI073891
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|86525653|gb|CI165859.1|CI165859
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88273878|gb|CI394284.1|CI394284
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
EST: gi|88830007|gb|CI074679.1|CI074679
EST:     GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAAC                         GTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC
genomic: GGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGC

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: 74 (upstream exon), 70 (downstream exon)
Score: 81

GGGTCAACAATGGTATGAACCTGAATGGTGGAAGTTTGGAGATTCAAAAACgtgagtaaac ... taattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGCACGCTACATTAACATAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaactttctagtatatcactttttttccgttcactgtgatttttaattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGCACGCTACATTAACATAAACAG
                                          ttttaat  putative branch site (score: 81)
                                         ttttt  CT-rich tract
             tatatcacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtgttctctgctgtttcttcagcgttttcattctctggctccttcaactttctagtatatcactttttttccgttcactgtgatttttaattctcagGTATTTTCGCCATGCTTCCGGTGCTTTGTTTATCCTCTCTAACAATTTGGCACGCTACATTAACATAAACAG

- - - - - -tgctgtt
- - - - - - - - - -cttcagc
- - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - -ggctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatt