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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCGCCGTACCTGCGCAAGGTGGACCTCGAGGCCTACTCCGGCTACGACCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctcttcttcttcatcatctctcgatccatctgattctgttggttgttcgagcaattgacgggaggaaagttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g08320.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08320.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G004696_T01 (Zea mays), 5'ss of exon 2
GGCGCGCCGTACCTGCGCAAGGTGGACCTCGAGGCCTACTCCGGCTACGACCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctcttcttcttcatcatc----tctcgatccat--ctgattctg---ttggttgttcgagcaattgacg------ggaggaaagttgcag-----------------------------------------
|||||||| |||||||| |||||||||||  |||| ||| |||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| || ||  || |     || || |     |||| | | |   |  | |||    |  ||     |||  ||  |       ||  ||  ||| | |                                         
GGCGCGCCCTACCTGCGGAAGGTGGACCTGCAGGCGTACGCCGGCTACGACCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgctaccgtcccaccaccaccccctcgcttcgtgcttcctcctgggtctaatttccgcagcgctttgctctgtttggtcgagcgttccggctgacggagggtttttttttttggtttggatgcgcgcgcag
















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|87026433|gb|CI252387.1|CI252387
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCCCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAATGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88242594|gb|CI242443.1|CI242443
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|94362956|gb|CI053117.1|CI053117
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86542731|gb|CI182937.1|CI182937
EST:     TTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACCCGGTGAACGGGACGG
genomic: TTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|22307664|gb|BQ908886.1|BQ908886
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCCGGTGAACGGGACG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACG-CGGTGAACGGGACG
EST: gi|88955604|gb|CI091893.1|CI091893
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88207580|gb|CI207429.1|CI207429
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88850081|gb|CI091376.1|CI091376
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86531401|gb|CI171607.1|CI171607
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88849381|gb|CI089289.1|CI089289
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTTGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86512640|gb|CI155273.1|CI155273
EST:     TCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: TCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|15849694|gb|BI797970.1|BI797970
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|89170448|gb|CI039725.1|CI039725
EST:     CCAGCTCCTCCGCGCGCTGCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88845667|gb|CI008664.1|CI008664
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88205398|gb|CI204784.1|CI204784
EST:     CCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGGAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88242921|gb|CI240772.1|CI240772
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86526139|gb|CI166345.1|CI166345
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86424642|gb|CI063403.1|CI063403
EST:     TTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: TTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88237189|gb|CI237038.1|CI237038
EST:     CCAGCTCCTCCGCGCGCTGCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86593437|gb|CI264316.1|CI264316
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|87014717|gb|CI269424.1|CI269424
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88244233|gb|CI243355.1|CI243355
EST:     CGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86252743|gb|CI010225.1|CI010225
EST:     CCAGCTCCTCCGCGCGCTNCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86522134|gb|CI162340.1|CI162340
EST:     CCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|87013760|gb|CI269259.1|CI269259
EST:     CAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|87014558|gb|CI284070.1|CI284070
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|29685212|gb|CB681487.1|CB681487
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88975839|gb|CI024090.1|CI024090
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86824408|gb|CI262940.1|CI262940
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88205307|gb|CI204693.1|CI204693
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|88836932|gb|CI008368.1|CI008368
EST:     CCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|86507819|gb|CI150452.1|CI150452
EST:     TTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: TTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|87020583|gb|CI263446.1|CI263446
EST:     CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCC                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG

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: 57 (upstream exon), 73 (downstream exon)
Score: 20

GGCGCGCCGTACCTGCGCAAGGTGGACCTCGAGGCCTACTCCGGCTACGACCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctctt ... aaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTGCCGACGTACGAGGACAAGGACGGCGACTGGATGCTCGTCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGCGCCGTACCTGCGCAAGGTGGACCTCGAGGCCTACTCCGGCTACGACCAGCTCCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCCgtaagctcttcttcttcatcatctctcgatccatctgattctgttggttgttcgagcaattgacgggaggaaagttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC