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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggagtactgttttccctttaattttttctgcgggtgctagcttgctatttgagtagctgcagaaccatcaagaagctaatgcaacttttgcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACTGCC

Basic information

species Oryza sativa
transcript LOC_Os01g13730.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13730.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 10
----gggagtact-gttttccctttaattttttctgcgggtg-----ctagcttgctatttgagtagctgcagaaccatcaagaagctaatgcaacttttgcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACTGCC
    |  | | || |||||     | ||  |    |    |      ||||||| ||| ||  ||| || | | |  |   | |  || | | |   |||||||||||||||||||||||| ||| |||||||||||||||| |||||||||||||||||||| 
gtcagtcaattctcgtttttagaatcatgatagacgtacatttttttctagctt-ctaattttgtatctactgtatgacatacagtctgacgtatgatttgcttatgcagACAAGGTGCAATTCAGTATGCTGGAACCCTAGAGAGCCTATGAACTTCACTGCT
















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|218494779|gb|FG960743.1|FG960743
EST:     CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAG                         ACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACT
genomic: CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAGgtttgttgaa ... gcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACT
EST: gi|58676735|gb|CK065422.1|CK065422
EST:     CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAG                         ACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACT
genomic: CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAGgtttgttgaa ... gcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACT
EST: gi|58676759|gb|CK065446.1|CK065446
EST:     CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAG                         ACAAGGTGCAACTCAA
genomic: CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAGgtttgttgaa ... gcttatgcagACAAGGTGCAACTCAA
EST: gi|58666954|gb|CK055640.1|CK055640
EST:     CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAG                         ACAAGGTGCAA
genomic: CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAGgtttgttgaa ... gcttatgcagACAAGGTGCAA
EST: gi|58665877|gb|CK054563.1|CK054563
EST:     CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAG                         ACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACT
genomic: CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAGgtttgttgaa ... gcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACT
EST: gi|3759655|gb|C96913.1|C96913
EST:     CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAG                         ACAAGGTGCAACTCAATATGCTGGAACCCTAGGGANCCTATGAACTTCACT
genomic: CACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAGgtttgttgaa ... gcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACT

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: 64 (upstream exon), 54 (downstream exon)
Score: 22

TGATCGGAGTATAACACTTTATGATCTACGCATGTCATCCCCTGCTAGAAAGCTAATCATGAAGgtttgttgaa ... gcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttgagtagctgcagaaccatcaagaagctaatgcaacttttgcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACTGCC
                             agctaat  putative branch site (score: 22)
                                        cttttgctt  putative PPT
                                      aactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggagtactgttttccctttaattttttctgcgggtgctagcttgctatttgagtagctgcagaaccatcaagaagctaatgcaacttttgcttatgcagACAAGGTGCAACTCAATATGCTGGAACCCTAGGGAGCCTATGAACTTCACTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - -tactgtt
- - - - - - - - - - - - -tttctgc
- - - - - - - - - - - - - - - - -ggtgcta
- - - - - - - - - - - - - - - - - - - - gcttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taatgca