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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagtccttagctttgttacattatatgcctggatgaataactgtttcttattcgtgccctttttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGATCTGAGCACTCCTGTCCAGATATCCAAGAGAGTAGTATATCCACATGTA

Basic information

species Oryza sativa
transcript LOC_Os01g73880.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G002616_T01 (Zea mays), 3'ss of exon 4
gtgagtagtcctta-gctttgttacattatatgcctggatgaataa------ctgtttcttattcgtgccctttttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGATCTGAGCACTCCTGTCC-AGATATCCAAGAGAGTAGTATATCCACATGTA
||||| ||  |||| || |   |   ||| ||| || | | | |||      |  ||||| | |  |||||||||  | || ||||||||||||| |||||||||||||| || |||||||| ||||| ||||||||      ||    ||| ||| |        |||||     ||| |||  
gtgagcagggcttaagcctccctttgtta-atgtcttgtttagtaagctgcaccatttctgactt-tgcccttttgtgctgcagGACGATGCAAAGAAGATGGACAAAGGCCTGAAGAACCGTTACACGGTTTGATCCTGATGCTGGAATCCCAGAGAGTTGTAGCAGTAGCTGGCCCAAATGC-
















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|88567613|gb|CI498330.1|CI498330
EST:     ACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: ACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88551571|gb|CI481639.1|CI481639
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|86544785|gb|CI184991.1|CI184991
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88990171|gb|CI107597.1|CI107597
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88288752|gb|CI517883.1|CI517883
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88973113|gb|CI717642.1|CI717642
EST:     AAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88529129|gb|CI456611.1|CI456611
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|86854076|gb|CI252067.1|CI252067
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88560717|gb|CI491406.1|CI491406
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88562713|gb|CI493430.1|CI493430
EST:     ACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGTTCTCAAGAACCGCTACACAGTTTGA
genomic: ACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88539299|gb|CI466400.1|CI466400
EST:     AGTGGAAAGTATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGTTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88424017|gb|CI689716.1|CI689716
EST:     AGTGGAAAGTATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAA
EST: gi|14571254|gb|BI118622.1|BI118622
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|58680307|gb|CK068994.1|CK068994
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|58692941|gb|CK081628.1|CK081628
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCCAAAAAGATGGACCAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|8527831|gb|AU092646.1|AU092646
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88540755|gb|CI468824.1|CI468824
EST:     AGTGGAAAGTATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|14571263|gb|BI118631.1|BI118631
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACSATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88213475|gb|CI213324.1|CI213324
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|86543932|gb|CI184138.1|CI184138
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88524848|gb|CI453801.1|CI453801
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88578465|gb|CI687398.1|CI687398
EST:     AGTGGAAAGTATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|58686020|gb|CK074707.1|CK074707
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88548459|gb|CI476833.1|CI476833
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|87034065|gb|CI187427.1|CI187427
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|10794861|gb|AU108827.1|AU108827
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|88323665|gb|CI558686.1|CI558686
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|86529829|gb|CI170035.1|CI170035
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|8858103|gb|AU095421.1|AU095421
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
EST: gi|86527733|gb|CI167939.1|CI167939
EST:     AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCAT                         GACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA
genomic: AGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGA

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: 75 (upstream exon), 75 (downstream exon)
Score: 92

ATAAGCATTGGGAAGCAGTGGAAAGAATTTCTGGATTACAAGGACTCGATTGGGTTCATTGTTCATgtgagtagtc ... ttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGATCTGAGCACTCCTGTCCAGATATCCAAGAGAGTAGTATATCCACATGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattatatgcctggatgaataactgtttcttattcgtgccctttttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGATCTGAGCACTCCTGTCCAGATATCCAAGAGAGTAGTATATCCACATGTA
                 gaataac  putative branch site (score: 92)
                          tttcttattcgtgccc  putative PPT
                          tttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagtccttagctttgttacattatatgcctggatgaataactgtttcttattcgtgccctttttggttgtagGACGATGCAAAAAAGATGGACAAAGGTCTCAAGAACCGCTACACAGTTTGATCTGAGCACTCCTGTCCAGATATCCAAGAGAGTAGTATATCCACATGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA