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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatactgtgataaagttcttcattgcattttcatcatcttagtttattttgagtgccatcatgactcgtacttattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g21940.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 13
gtaaggatactgt-gataaagttctt-cattgc-----------attttcatcatcttagtttattttgagtgccatcatgactcgtacttattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG
|| ||||||   | |||| | ||||| |||||            |||||     | |||  ||  | ||  || |||| | | | | | || |||||||||||||||||||||||||||||||| || ||||||||||||||||| ||||||
gtgaggatatactagatatatttcttgcattgtctaatgcttcgattttgtgtttgttatcttggtctgtatgacatc-taaattggagttgttttgcagGAACATGTATTGCTTTAGCTACCAATCTGGTAAACTGGAGCATCTGATGAAG

upper sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G30430.1 (Glycine max), 3'ss of exon 14
----------gtaaggatactgtgataaagttcttcattgcattttcatcatcttagtttattttg--agtgccatcatgactc-gtacttattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG
          ||||   |  | || | || |  |   |    |    || |||||     |  |||  |    | ||||||  | | |  |    |||||||| ||||| ||||||||||| || || || ||| |||||||||||||||||
ttccaaatcagtaatttttttttgttgaaataatctctaatttgccaattatctttccaaaaattgttatattcttcatgaaactgcaaattgaatgcagGAATATGTACTGCTTTAGCTATCAATCTGGCAAATTGGAGCATCTAATGAAG

upper sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 14
---gtaaggatactgtgataaagttcttcattgcattttcatcatcttagtttattttgagtgccatcatgactcgtacttattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG
    |   || |   |    || ||    |||   ||| ||  |  ||  | |||| |   ||  |     | | | |       |||||||| ||||| ||||||||||| || || || ||| |||||||||||||||||
tttttgttgaaataatctctaatttgccaattatctttccaaaaa-ttgttatattcttcatgaaactgcaaattgaa-------tgcaggaatatgtactgctttagCTATCAATCTGGCAAATTGGAGCATCTAATGAAG

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|86259935|gb|CI065808.1|CI065808
EST:     GCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACAT                         GAACATGTATTGCTTGAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
genomic: GCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACATgtaaggatac ... tattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
EST: gi|163929440|gb|EG713409.1|EG713409
EST:     GCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACAT                         GAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
genomic: GCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACATgtaaggatac ... tattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
EST: gi|3767253|gb|AU031363.1|AU031363
EST:     GTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACAT                         GAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
genomic: GTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACATgtaaggatac ... tattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
EST: gi|88903169|gb|CI088707.1|CI088707
EST:     GCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACAT                         GAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
genomic: GCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACATgtaaggatac ... tattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAA
EST: gi|88264214|gb|CI367988.1|CI367988
EST:     AAAGGAGAATGGATATATTGTGTTGGTGAAGACAT                         GAACATGTATTGCTTTAGCTACCAGGTCCGGTAAAGCTGGAGCATCTAATG
genomic: AAAGGAGAATGGATATATTGTGTTGGTGAAGACATgtaaggatac ... tattttgcagGAACATGTATTGCTTTAGCTACCA-GTCCGGTAAA-CTGGAGCATCTAATG

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: 49 (upstream exon), 74 (downstream exon)
Score: 18

TTGTAAAAAGTTTTTCATCTGGTAAACGGGAAGGGGGAGATTTCCTTGCAGCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACATgtaaggatac ... tattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcatcatcttagtttattttgagtgccatcatgactcgtacttattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG
                                           cttatttt  CT-rich tract
        atcttagtttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatactgtgataaagttcttcattgcattttcatcatcttagtttattttgagtgccatcatgactcgtacttattttgcagGAACATGTATTGCTTTAGCTACCAGTCCGGTAAACTGGAGCATCTAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA