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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttttactttcatgacgtaactgtacctttgcgtgtgtgttgatatgtttgatttcatgtgcttcatttcttattttgccacgctgctgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAGCAATAGAGGATGCCATTAAAAAGCTTGGAGAATCATCGGACTGAAAGCA

Basic information

species Oryza sativa
transcript LOC_Os01g50960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G112535_T01 (Zea mays), 3'ss of exon 2
tttgttttactttcatgacgtaactgtacctttgcgtgtgtgttgatatgtttgatttcatgtgcttcatttcttattttgccacgctgctga-attgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAGCAATAGAGGATGCCATTAAAAAGCTTGGAGAATCATCGGACTGAAAGCA---
 |  | ||  ||| |||  ||   ||| | | |   ||||||    |     |  |||       ||| | | || |||    ||| |  |   | |||||| || ||| ||||  | |||||||||||||||||| |  || |||| || ||||||||||||||||| |||||||||| ||| |||   |||||||       
atcttctttgttttatgttgtgg-tgtgcttctttttgtgtgccattgctcattgtttatctcttttcttctattctttactaacgtttttcctagtgcagGTATCAGTATGACTTTGGAGCAGTGGGAAGCATTTTGCAATGCTGTACCTGCAATAGAGGATGCCATCAAAAAGCTTGAAGATTCA---GACTGAACTGGTTT

upper sequence: LOC_Os01g50960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G159948_T01 (Zea mays), 3'ss of exon 3
tttgttttactttcatgacgtaactgtacctttgcgtgtgtgttgatatgtttgatttcatgtgcttcatttcttattttgccacg--ctgctgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAGCAATAGAGGATGCCATTAAAAAGCTTGGAGAATCATCGGACTGAAAGCA---
  ||  || || | ||  | |   | ||  ||   |||||      |  || ||   |  |  |   |||||  |  | | | |     |     | |||||| || ||| ||||| | |||||||||||||||||| |  || |||  || || |||||||||||||| |||||||||| ||| |||   |||||| | |    
--tggatttctgtgatctctttgttttatgttgtggtgtgctgcttttcgtgtgtcattgttggtaccattttcttctctactaacatttatcctagtgcagGTATTAGTATGACAATGGAGCAGTGGGAAGCATTTTGCAATGCTGCACCTGCGATAGAGGATGCCATCAAAAAGCTTGAAGATTCA---GACTGAGAACTTGT

upper sequence: LOC_Os01g50960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G112535_T02 (Zea mays), 3'ss of exon 3
tttgttttactttcatgacgtaactgtacctttgcgtgtgtgttgatatgtttgatttcatgtgcttcatttcttattttgccacgctgctga-attgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAGCAATAGAGGATGCCATTAAAAAGCTTGGAGAATCATCGGACTGAAAGCA
 |  | ||  ||| |||  ||   ||| | | |   ||||||    |     |  |||       ||| | | || |||    ||| |  |   | |||||| || ||| ||||  | |||||||||||||||||| |  || |||| || ||||||||||||||||| |||||||||| ||| |||   ||||||     
atcttctttgttttatgttgtgg-tgtgcttctttttgtgtgccattgctcattgtttatctcttttcttctattctttactaacgtttttcctagtgcagGTATCAGTATGACTTTGGAGCAGTGGGAAGCATTTTGCAATGCTGTACCTGCAATAGAGGATGCCATCAAAAAGCTTGAAGATTCA---GACTGA-----

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|33693217|gb|CF321456.1|CF321456
EST:     GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|89181730|gb|CI113236.1|CI113236
EST:     GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88504698|gb|CI432204.1|CI432204
EST:     GGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88490909|gb|CI428181.1|CI428181
EST:     GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCNCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|89181475|gb|CI112981.1|CI112981
EST:     TCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCGTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: TCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGC-TGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88488325|gb|CI425596.1|CI425596
EST:     AAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: AAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88475611|gb|CI412882.1|CI412882
EST:     ACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: ACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|86260041|gb|CI065914.1|CI065914
EST:     GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88531852|gb|CI458369.1|CI458369
EST:     AGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: AGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88514182|gb|CI441688.1|CI441688
EST:     AGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: AGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|218481362|gb|FG954013.1|FG954013
EST:     GAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88481108|gb|CI418379.1|CI418379
EST:     GGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88486473|gb|CI423744.1|CI423744
EST:     GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88512126|gb|CI439632.1|CI439632
EST:     GACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88483344|gb|CI420615.1|CI420615
EST:     GCCCGCCAAAG                         GGATAAGTTTGACAGGTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88504791|gb|CI432297.1|CI432297
EST:     AGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCANTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: AGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88204074|gb|CI203923.1|CI203923
EST:     GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|86506674|gb|CI149307.1|CI149307
EST:     GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: GTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
EST: gi|88512283|gb|CI439789.1|CI439789
EST:     CGGCAAGGAGCTGCCCGCCAAAG                         GGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG
genomic: CGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAG

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: 69 (upstream exon), 74 (downstream exon)
Score: 17

TCGGCCAGGAGGAGGGTGACTCTTCAGGAGTTCAAGGGCAAGACGCTTCTGTCCATCCGAGAGTACTACTTCAAGGACGGCAAGGAGCTGCCCGCCAAAGgtgatgcaca ... tgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAGCAATAGAGGATGCCATTAAAAAGCTTGGAGAATCATCGGACTGAAAGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtttgatttcatgtgcttcatttcttattttgccacgctgctgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAGCAATAGAGGATGCCATTAAAAAGCTTGGAGAATCATCGGACTGAAAGCA
                    ttcatttcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttttactttcatgacgtaactgtacctttgcgtgtgtgttgatatgtttgatttcatgtgcttcatttcttattttgccacgctgctgaattgcagGGATAAGTTTGACAGTTGAGCAGTGGGAAGCATTTCGTGATTCTGTGCCAGCAATAGAGGATGCCATTAAAAAGCTTGGAGAATCATCGGACTGAAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - tttcatg
- - - - - - - - - - - -ctgtacc
- - - - - - - - - - - - - - - -ttgcgtg
- - - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acgctgc