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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAAAACACCAGCATTGATGCTTTGTTGCCTCAATGGTTTACAAGCTTTCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataactgattagtccttttcccctgtgttactgttccagtttccttgtagtttgttgtttgcatgtgattaaagttgttaatttgcaagtgggc...

Basic information

species Oryza sativa
transcript LOC_Os05g03430.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03430.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G155123_T02 (Zea mays), 5'ss of exon 16
---AAGAAAAACACCAGCATTGATGCTTTGTTGCCTCAATGGTTTACAAGCTTTCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataactgattagtccttttcccctgtgttactgttccagtttccttgtagtttgttgtttgca-----tgtgattaaagttgttaatttgcaagtgggc
   |||| |||||||||  | |||||||| |||| | ||    |   ||| || |||||||||||| ||||||| | ||||||| |||||||  ||||| ||||| || | |  ||||||| |  ||       ||    || | |  | |  |   |  |  ||  |||||     ||||||| |||| | | | ||| ||      
ACAAAGAGAAACACCAGTGTGGATGCTTTATTGCATTAAC--CTGGTAAGATT-CAAGTGTTCTATATGATCCAAGTGGGATCTCCATAGAGTTCATCTAATGgtaaggacagatgattagcctcttcatgtgatggatttgctgctatgttttatgaactatttcattgcagtttttgtgattcaagtagctgagttgtaat-----
















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|88477511|gb|CI414782.1|CI414782
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|86481066|gb|CI123699.1|CI123699
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|88513466|gb|CI440972.1|CI440972
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|88284346|gb|CI405792.1|CI405792
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|88235424|gb|CI236626.1|CI236626
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|94362517|gb|CI052383.1|CI052383
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|87015001|gb|CI273399.1|CI273399
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|88196940|gb|CI196642.1|CI196642
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|218484827|gb|FG958208.1|FG958208
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTAACTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|87027311|gb|CI269986.1|CI269986
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|12622265|gb|AU172478.1|AU172478
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|86478846|gb|CI121479.1|CI121479
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|89192803|gb|CI050101.1|CI050101
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
EST: gi|88513083|gb|CI440589.1|CI440589
EST:     TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATG                         GTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG
genomic: TCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTG

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: 65 (upstream exon), 52 (downstream exon)
Score: 35

AAGAAAAACACCAGCATTGATGCTTTGTTGCCTCAATGGTTTACAAGCTTTCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataa ... tttctgttagGTTGGTATAGAAAATTTTCTAACTGGGTATCGAGGCTTAATGTGGCGACTGGAGCAGTTTGTACATTTTTTTTGTTTTGACTTTTACTGGATATAAGGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAAAACACCAGCATTGATGCTTTGTTGCCTCAATGGTTTACAAGCTTTCAAGTGTTCTATTTGATCCAGGAGGGATCTGCATAGAGGACATCTGATGgtgagcataactgattagtccttttcccctgtgttactgttccagtttccttgtagtttgttgtttgcatgtgattaaagttgttaatttgcaagtgggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA