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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGATTAGAAAGAAGAGGGTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgaagatatcaacattttcatggttttgctgcgctctagataacaaatgaagaatttaactctgttttcagacaataattcgtagcctactttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g03820.3
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 14
AATGGATTAGAAAGAAGAGGGTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgaagatatcaacattttcatggttttgctgcgctctagataacaaatgaagaatttaactctgttttcagacaataattcgtagcctactttgttgcag
|||||||| ||||||||||| |||||||| || |||||| | ||||||||||| | |||| | ||  ||||| |  | | | |||||| ||||||      |||   |     |  |  |   |   | |||  | |   ||  ||||   || |    || |||||  |   | |||                             
AATGGATTGGAAAGAAGAGGATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgt-agtagtgctacattc-agcatcctcggccatgtttacgctttgctgcgaatcactcgttccgttt--ctgaagatcctaatt----aacttaacctttgctacag-----------------------------

upper sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 14
AATGGATTAGAAAGAAGAGGGTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgaagatatcaacattttcatggttttgctgcgctctagataacaaatgaagaatttaactctgttttcagacaataattcgtagcctactttgttgcag
|||||| | |||||||||||||||||||| ||||||||| | |||||||| || | |||  | ||  ||||  ||   |        ||  |||||   ||| ||  |     ||||    || | | | |  |  |   ||  |  |  | |  |                                                   
AATGGACTGGAAAGAAGAGGGTACAAGGAGGTTGGTTTCCTTAGAGAGGTCGACGAAGTAGTGAGAACAGgcaaatgctattcagcaccctcatcttcattcgtttgttggactatctgt-ttctgaagatcctaattaccttcaacttgctacag---------------------------------------------------
















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|29677971|gb|CB674246.1|CB674246
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|86831376|gb|CI299434.1|CI299434
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|88723315|gb|CI746825.1|CI746825
EST:     GTACAAGGAGGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGC
EST: gi|11442624|gb|BF430527.1|BF430527
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|88244533|gb|CI243655.1|CI243655
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCGATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|29645922|gb|CB650929.1|CB650929
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|58663354|gb|CK052040.1|CK052040
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|2311714|gb|C27869.1|C27869
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGGGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|56157390|gb|D48012.2|D48012
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|58695197|gb|CK083884.1|CK083884
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGC
EST: gi|88981214|gb|CI026944.1|CI026944
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|66928215|gb|CX115063.1|CX115063
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|89198318|gb|CI007378.1|CI007378
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
EST: gi|86900529|gb|CI298364.1|CI298364
EST:     GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAG                         GAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC
genomic: GTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAAC

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), 72 (downstream exon)
Score: 66

AATGGATTAGAAAGAAGAGGGTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagattt ... tttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAACGCAGCGTCGATCCTGTCTTCCAGGAGTTGTTATACTGATGCTGAGAAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGATTAGAAAGAAGAGGGTACAAGGAAGTTGGTTTCTTAAGAGAGGTTGATGCAGTGATCAGTTCAGgtgaagatttcaacattccagcatctcttttcattgatgaagatatcaacattttcatggttttgctgcgctctagataacaaatgaagaatttaactctgttttcagacaataattcgtagcctactttgttgcag

- - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - -  GAGAGG