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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgctaatatatatttcagtctcactgataatttcagtctttagttatttctagtgtgcttcatctgtcagtgtttggtaatgtgagcctgtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g07090.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07090.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G003096_T04 (Zea mays), 3'ss of exon 1
ctgctaatatatatttcagtctcactgataatttcagtctttagttatttctagtgtgcttcatctgtca--------gtgtttggtaatgtgagcctgtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAAG
       | ||  ||  ||   ||  | |||||  ||   |||  |  ||  ||| |  |||||||||||        || ||  || || ||| ||||| |||||||||||||||||||| |  |||||||  |||||||||| |||||||||||||||
------ttgtaggttgtagctgca--gctaattatagctcttaagttattgaagtctatttcatctgtcaacaactcggtattcagtcatatgaacctgtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAAG
















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|88576663|gb|CI670808.1|CI670808
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|88305014|gb|CI566068.1|CI566068
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|86596621|gb|CI286534.1|CI286534
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|88403452|gb|CI573175.1|CI573175
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|117230125|gb|CT846221.1|CT846221
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTATCTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|88349839|gb|CI634374.1|CI634374
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|88403396|gb|CI573119.1|CI573119
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|55413991|gb|CV726367.1|CV726367
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|13420770|gb|AU174860.1|AU174860
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|88355634|gb|CI628918.1|CI628918
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|29641053|gb|CB646060.1|CB646060
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
EST: gi|88329864|gb|CI651537.1|CI651537
EST:     CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAA                         GTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA
genomic: CCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAA

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: 72 (upstream exon), 62 (downstream exon)
Score: 32

CTGCTACCCGCCTCTCGCCGCCTCGCCTCCACGCACCCACTACCCCTTCTCCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctcc ... gtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttctagtgtgcttcatctgtcagtgtttggtaatgtgagcctgtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAAG
                                              taattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgctaatatatatttcagtctcactgataatttcagtctttagttatttctagtgtgcttcatctgtcagtgtttggtaatgtgagcctgtaattgtagGTTGGAAGCTGTGTTAACTATTGGAACTCATCTAATACCACACCCAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
-tgctaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg