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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcccctacttgcatgttaatgttgccagcactaaaaaccagcaacaattgcatctcgtctgatttctgtggcactgcgaaaaactggatttttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCTACAGTCGCAGCTGCAAACGAGCTGTACAAGGTCGCGAAATCGCTTGGGC

Basic information

species Oryza sativa
transcript LOC_Os01g39270.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G848696_T02 (Zea mays), 3'ss of exon 10
gtagcccctacttgcatgttaatgttgccagcactaaaaaccagcaacaattgcatctcgtctgatttctgtggcactgcgaaaaact-----------------ggatttttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCTACAGTCGCAGCTGCAAACGAGCTGTACAAGGTCGCGAAATCGCTTGGGC
||||| ||||||||| |||  ||    | |||| |||  | |||   || |||| ||| | ||||  |       |||| | | | ||                   |    ||||||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||  || |||||||| || |
gtagcacctacttgcttgtccattcatctagcagtaacgaacagttccatttgcgtctggcctgacctaatcacgactgagcagagctcctgccactaatgaaacaaacaactcatggcagGACTTGAGGCTCGCATTGGCCCTGGCGGAATCGGTGTCCCAGTCCATTCCTACAGTTGCAGCTGCGAACGAGCTGTACAAGGCTGCAAAATCGCTCGGCC
















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|88504657|gb|CI432163.1|CI432163
EST:     TGGTTAAAGGTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCANAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|38471985|gb|CF956116.1|CF956116
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|89182128|gb|CI012062.1|CI012062
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88289242|gb|CI553218.1|CI553218
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88510436|gb|CI437942.1|CI437942
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGATGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88981451|gb|CI027069.1|CI027069
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|16576901|gb|BI804197.1|BI804197
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88978167|gb|CI384649.1|CI384649
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTTTCCCACTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88476694|gb|CI413965.1|CI413965
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88472231|gb|CI409502.1|CI409502
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGATGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88383777|gb|CI545928.1|CI545928
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|88971438|gb|CI017752.1|CI017752
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|86838955|gb|CI330366.1|CI330366
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
EST: gi|38471057|gb|CF955188.1|CF955188
EST:     TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAG                         GATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT
genomic: TGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCT

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: 66 (upstream exon), 75 (downstream exon)
Score: 14

TTCACAAGGTGCTATCAGTGCTCCCATGTTCTCCCTCAAGGGCCCTTCCATGGTTAAAGCTGCATACCCTACTGCTTTTCCTCTGAAGCATCAGCAGAAGgtagccccta ... ttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCTACAGTCGCAGCTGCAAACGAGCTGTACAAGGTCGCGAAATCGCTTGGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcatctcgtctgatttctgtggcactgcgaaaaactggatttttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCTACAGTCGCAGCTGCAAACGAGCTGTACAAGGTCGCGAAATCGCTTGGGC
          gtctgat  putative branch site (score: 14)
                                          tttttcat  putative PPT
                                         atttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcccctacttgcatgttaatgttgccagcactaaaaaccagcaacaattgcatctcgtctgatttctgtggcactgcgaaaaactggatttttcatggcagGATTTGAGGCTCGCATTGGCCCTGGCAGAATCGGTGTCCCAGTCTATTCCTACAGTCGCAGCTGCAAACGAGCTGTACAAGGTCGCGAAATCGCTTGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC