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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtacatgttgtgctag

Basic information

species Oryza sativa
transcript LOC_Os02g56850.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G806449_T02 (Zea mays), 5'ss of exon 3
GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtaca--tgttgtgctag
||||||||||| |||||||| ||||| ||||||||||| || |||| |||||| ||||||||||||||||||||| |    || |||| | |||   |||||||         |||||  | |  |  |  | | | ||| ||              | || | |       || ||| |||||  |  |||| |||| ||  |     | |||| ||||
GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGACgtaagcatctcc----tagttgttttcgt--gcatttctc-------gtgcttactcaaaacatgcagctattctgcttg------------gtatattaa------ctacattctaaa-tcgacatgttcataatgattttattattgtcctag
















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|88366537|gb|CI612361.1|CI612361
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88314032|gb|CI600034.1|CI600034
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|29670415|gb|CB666690.1|CB666690
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88417483|gb|CI579144.1|CI579144
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTT
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTT
EST: gi|88760896|gb|CI770452.1|CI770452
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88352021|gb|CI626021.1|CI626021
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88337120|gb|CI628206.1|CI628206
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCGAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88430778|gb|CI596892.1|CI596892
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|2443112|gb|C74883.1|C74883
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|38469842|gb|CF953973.1|CF953973
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCAT
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGT-GATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCAT
EST: gi|88723894|gb|CI745591.1|CI745591
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88760244|gb|CI769800.1|CI769800
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88416046|gb|CI594158.1|CI594158
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|426418|gb|D22281.1|D22281
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTNATACGTGGTTGTGTNCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88396564|gb|CI601047.1|CI601047
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|29680732|gb|CB677007.1|CB677007
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88694888|gb|CI738926.1|CI738926
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88726529|gb|CI750184.1|CI750184
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88389287|gb|CI598085.1|CI598085
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88417209|gb|CI576283.1|CI576283
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
EST: gi|88744812|gb|CI768172.1|CI768172
EST:     CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC                         GTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC
genomic: CTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATC

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: 62 (upstream exon), 70 (downstream exon)
Score: 30

GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatct ... gttgtgctagGTGTGTGATACGTGGTTGTGTGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGACgtaagcatctgccgattacttgtctgcgtttacatttctgtcgttgaatgcttgattatgatttaaaccaactctcctcatcccctgggtgagaatgtgagatgttgctgcatcctaaaacccgcatgctcattattgtacatgttgtgctag

- - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG