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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAACTGGCAAAGAGAACATACAATGCAAGACATCCTGATCGGCTTAAAAAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttccatatctctgcttcagtgaatttgatctacagcctcgtcgttttcccttaagcttataaaccgcaaccaaaatttgagttttaaaacttaat...

Basic information

species Oryza sativa
transcript LOC_Os03g50440.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G090172_T01 (Zea mays), 5'ss of exon 4
GGTAACTGGCAAAGAGAACATACAATGCAAGACATCCTGATCGGCTTAAAAAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttccatatctc--tgcttcagtgaatttgat----------ctacagc--ctcgtcgt--tttcccttaagcttataaaccgcaaccaaaatttgagttttaaaacttaat-------------------------------------------------------------------
|| || ||| |||| |||||||||||| | |||||||||| | ||||||||| |||||||||  |||||||||| || |||||  | ||||| ||||| |||| || |     |||  | || ||||   ||  ||          ||  |||  || |  ||  | |  ||| |   |   || |    |||| | | || | | ||  |  ||                                                                    
GGCAAGTGGGAAAGGGAACATACAATGGAGGACATCCTGAGCAGCTTAAAAAGGGAGATGTCAACTCCTCAGAACCGCAGGCTGTACCAACCTCATGAAGgtatttccttctgctcattactccagtaccttatatgctgacaatgctgtagctacttgaagtaatctttcttgaatatccgaaaccttgccaagactagattgtcaagccaaaaacataactcgcaaatcttggaaaatgattagcaagcacccctagttgataatttttttttatcgccag

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G090172_T02 (Zea mays), 5'ss of exon 4
GGTAACTGGCAAAGAGAACATACAATGCAAGACATCCTGATCGGCTTAAAAAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttccatatctc--tgcttcagtgaatttgatctacagcctcgtcgttttcccttaagcttataaaccgcaaccaaaatttgagttttaaaacttaat
|| || ||| |||| |||||||||||| | |||||||||| | ||||||||| |||||||||  |||||||||| || |||||  | ||||| ||||| |||| || |     |||  | || ||||   ||  ||      |   |  ||     ||| |  | ||    |   |  |         ||   ||   ||  
GGCAAGTGGGAAAGGGAACATACAATGGAGGACATCCTGAGCAGCTTAAAAAGGGAGATGTCAACTCCTCAGAACCGCAGGCTGTACCAACCTCATGAAGgtatttccttctgctcattactccagtaccttatatgc-tgacaatgctgtagctacttgaagtaatctttcttgaatatccgaaaccttgccaagactag-
















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|86509985|gb|CI152618.1|CI152618
EST:     CAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTTC
genomic: CAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTG-TC
EST: gi|15852518|gb|BI805314.1|BI805314
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAA-GAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|27545659|gb|CA763865.2|CA763865
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|88484619|gb|CI421890.1|CI421890
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|88242402|gb|CI242251.1|CI242251
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|88200708|gb|CI200558.1|CI200558
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|86845255|gb|CI340364.1|CI340364
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|88997021|gb|CI389687.1|CI389687
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|58592031|gb|CF990339.1|CF990339
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|89194551|gb|CI116988.1|CI116988
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
EST: gi|58691622|gb|CK080309.1|CK080309
EST:     AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATG                         GCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA
genomic: AAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCA

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), 73 (downstream exon)
Score: 38

GGTAACTGGCAAAGAGAACATACAATGCAAGACATCCTGATCGGCTTAAAAAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttcca ... ctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCATCATGTAAGAGATGCGAATTGCAATGTACAGTATTATTAAATTGAGTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAACTGGCAAAGAGAACATACAATGCAAGACATCCTGATCGGCTTAAAAAAGGAGATGTCTGCTCCTCAGAATCGTAGGCTCCATCAACCCCATGATGgtaatttccatatctctgcttcagtgaatttgatctacagcctcgtcgttttcccttaagcttataaaccgcaaccaaaatttgagttttaaaacttaat

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC