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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactttcctgaatactggttttcccaaatgattcctgttaagtatccccgtgtaattcctgcagaatttctaactttctactctttggtacgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG

Basic information

species Oryza sativa
transcript LOC_Os04g40310.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 2
---------cactttcctgaatac-tggttttcccaaatgattcctgttaagtatccccgtgtaattcctgcagaatttctaactttctactctttggtacgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG
           |||| |||  | | |  ||||| | |||| ||| |   || || | || || | |    | |  || | |   |||| |   |||      ||||||||||||| || || ||||||||||||||||| |||||||||||||||||||||| ||||||||| ||  | ||||||||||
tcatcacatttcttttctgctttcctaattttctcgaatgcttctttgcaaata-caccatggatta---ggattatctgtgggtttcaatctttt------ttttgtagGTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATTGTTGGAGGGACGGGCATCATGCCTGGAG

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 2
----cact-ttcctgaatactggttttcccaaatgattcctgttaagtatccccgtgtaattcctgcagaatttctaactttctactctttggtacgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG
    |||| || || | || |    || |   |   |   |  || |  ||     |   ||||  |     || ||       | | | ||  | |||||| |||| || || || || ||||| ||||| ||||| ||||| ||||| |||||||||||||| ||||| || ||||||||||
acttcactgttgctaagtattaacctttcattactgtatgtagta-gcgtcttttggcttttccccc----cttttataacagcaatttatgaaatgttttgcagGTAACGCCGAATCTCTATGGGAATTTAGTTGCAAACACTGCTGCTGGTATTGCTGGAGGCACAGGAGTCATGCCTGGAG
















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|29687051|gb|CB683326.1|CB683326
EST:     ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG                         GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST: gi|29662276|gb|CB658551.1|CB658551
EST:     ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG                         GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST: gi|87018960|gb|CI256845.1|CI256845
EST:     ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG                         GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST: gi|29662277|gb|CB658552.1|CB658552
EST:     ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG                         GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
EST: gi|29687448|gb|CB683723.1|CB683723
EST:     ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATG                         GTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATT

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: 60 (upstream exon), 71 (downstream exon)
Score: 18

TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt ... cgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccgtgtaattcctgcagaatttctaactttctactctttggtacgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG
                      ttctaac  putative branch site (score: 18)
                   aatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactttcctgaatactggttttcccaaatgattcctgttaagtatccccgtgtaattcctgcagaatttctaactttctactctttggtacgttttgtagGTTACACCAAACCTTTATGGCAATTTGGTTGCTAACACGGCTGCAGGTATTGCTGGAGGGACAGGTGTTATGCCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - -tcctgaa
- - - - - - - - - - - - - - - attcctg
- - - - - - - - - - - - - - - - - - - - - - - -ccgtgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgcag