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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgtatcgcttatatatgcattagtaaggagttgttcaatttgagctgctgtattttatgcatatgatacctgatatggacag

Basic information

species Oryza sativa
transcript LOC_Os01g74190.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G095663_T01 (Zea mays), 5'ss of exon 4
TGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttg---tatcgcttata-tatgcattagtaaggagttgttcaatt-tgagctgctgtattttatgcatatgatacctgatatggacag-
 ||||| ||||| | ||  ||||| |||||||| ||||||||||| ||||| ||||| || ||| |||| || || |||||||| || |||||||||||||||||  ||   |||  | |||| ||  ||    |||    || ||   |    || | || ||| ||||  | || ||   |  ||   |    
AGCAGAACTACTTCGTATGTGTGGAGGTGGTTACCATGTGAACCTGATTCCCTATAACCCAATTGAAGGCTCCGAGTACAAGAGACCTTACAGAAAAGTGgtatgtgtgctttatgtcctataataaacaaatataaactattatttcgtaaccagttact-tatcttatttacattat-tatactacaaattag

upper sequence: LOC_Os01g74190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G395039_T01 (Zea mays), 5'ss of exon 6
TGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttg---tatcgcttata-tatgcattagtaaggagttgttcaatt-tgagctgctgtattttatgcatatgatacctgatatggacag-
 ||||| ||||| | ||  ||||| |||||||| ||||||||||| ||||| ||||| || ||| |||| || || |||||||| || |||||||||||||||||  ||   |||  | |||| ||  ||    |||    || ||   |    || | ||| || ||||  | |  ||   |  |    |    
AGCAGAACTACTTCGTATGTGTGGAGGTGGTTACCATGTGAACCTGATTCCCTATAACCCAATTGAAGGCTCCGAGTACAAGAGACCTTACAGAAAAGTGgtatgtgtgctttatgtcctataataaacaaatataaactattatttcgtaaccagttactg-atcttatttacactat-tatactgcaaattag

upper sequence: LOC_Os01g74190.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G168412_T01 (Zea mays), 5'ss of exon 8
TGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttg---tatcgcttata-tatgcat-tagtaaggagttgttcaatttgagctgctgtattttatgcatatgatacctgatatggacag-
 ||||| ||||| | ||  ||||| |||||||| ||||||||||| ||||| ||||| || ||| |||| || || |||||||| || |||||||||||||||||| ||   |||  | ||||  |  ||  ||| ||  | |  |||      || | ||| || ||||  | |  ||   |  |    |    
AGCAGAACTACTTCGTATGTGTGGAGGTGGTTACCATGTGAACCTGATTCCCTATAACCCAATTGAAGGCTCCGAGTACAAGAGACCTTACAGAAAAGTGgtatgcgtgctttatgtcctataacaaacaaatagaaactattatttcgtaaccagttactg-atcttatttacactat-tatactgcaaattag

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|86868308|gb|CI331968.1|CI331968
EST:     CTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGGT
genomic: CTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGC-GT
EST: gi|86826053|gb|CI362477.1|CI362477
EST:     CAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|8860133|gb|AU097451.1|AU097451
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|87015982|gb|CI279734.1|CI279734
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|33684141|gb|CF312380.1|CF312380
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|88829806|gb|CI004844.1|CI004844
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACTGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|8859557|gb|AU096875.1|AU096875
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACTGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86261467|gb|CI017209.1|CI017209
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86852974|gb|CI324676.1|CI324676
EST:     AGAGGCCCTACAGAAAAGT-                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: AGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|88529133|gb|CI456616.1|CI456616
EST:     CCCTACAGAAAANTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|89193096|gb|CI050394.1|CI050394
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|88838957|gb|CI012833.1|CI012833
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86879494|gb|CI327165.1|CI327165
EST:     CCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         TTTCAAGCGTTTGTTGATGGGCTAGAAGCTCGGAAGATAACCTTAAGCGTT
genomic: CCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|88219718|gb|CI219278.1|CI219278
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86429578|gb|CI076259.1|CI076259
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86260731|gb|CI000179.1|CI000179
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|33381455|gb|CF196798.1|CF196798
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGNNNCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|8858615|gb|AU095933.1|AU095933
EST:     CTTATAATCCGATTCAAGGTTCTGAATNCAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATANCCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86540664|gb|CI180870.1|CI180870
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86850815|gb|CI338791.1|CI338791
EST:     ATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: ATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86597829|gb|CI276615.1|CI276615
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86498774|gb|CI141407.1|CI141407
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86489905|gb|CI132538.1|CI132538
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|88227884|gb|CI227364.1|CI227364
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
EST: gi|86251798|gb|CI018990.1|CI018990
EST:     CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTG                         GTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT
genomic: CTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTT

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: 70 (upstream exon), 19 (downstream exon)
Score: 5

TGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgt ... atatggacagGTTCAAGCGTTTGTTGATGCGCTAGAAGCTCGGAAGATAACCGTAAGCGTTCGACAAACCCGTGGGCTTGATGCTAATGCCGCTTGCGGACAACTAAGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGATTCAAGGTTCTGAATACAAGAGGCCCTACAGAAAAGTGgtatgcttgtatcgcttatatatgcattagtaaggagttgttcaatttgagctgctgtattttatgcatatgatacctgatatggacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG