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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataaccgcctcttgacgtggggaagttccacgtactttgtatagatcatctcgtttacaatccccatacttggaacaatcattttgttgatgttgcatggatggcgtttcgctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g13730.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13730.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G590033_T01 (Zea mays), 5'ss of exon 16
CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatata-------accgcctctt-------gacgtggggaagttccacgtactttgtatagatcatctcgtttacaatccccatacttggaacaatcattttgttgatgttgcatggatggcgtttcgctgcag
||||||||| | || |||| ||| ||||| ||||  |||||| | ||||||||||| ||||| || || ||||||||||||||||| ||||||  ||          ||||| |       | | ||||||| |   |  |   |  | |  |  ||| | || |     |  | | |       ||   | | | | | |  | |  || |    |   | |||
CTTCTTCCACGGGAGCGCAAAAAGCAAGAGTACCAGGATGCTTTGAAGGAGCGGTACAAGCATCTCCCAGAAGTCAAGCGGATTGTAAGgtaagctatggtggtgttgcctcctctgccgaggcatggggaaatcaaaactctctctttttcacaatcgcattgatgtctcttacagtacagggtatatatgtatggctttgtcgttaattg----ttattacag
















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|218501280|gb|FG957978.1|FG957978
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|218494779|gb|FG960743.1|FG960743
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAA
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAA
EST: gi|109712958|gb|CI105566.1|CI105566
EST:     AGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACATGGCGGCCAACTTAAGGCGAAC
genomic: AGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|86260043|gb|CI065916.1|CI065916
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|89185133|gb|CI049679.1|CI049679
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|86488699|gb|CI131332.1|CI131332
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|89185840|gb|CI047709.1|CI047709
EST:     AGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCCATCTACAAGGCGGCCCACTTAAGGCGAAC
genomic: AGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|86430787|gb|CI083210.1|CI083210
EST:     TAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTNACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: TAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|86430767|gb|CI083190.1|CI083190
EST:     GCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|88347170|gb|CI631250.1|CI631250
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|58682639|gb|CK071326.1|CK071326
EST:     CCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: CCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|88305455|gb|CI630617.1|CI630617
EST:     CTGTCAAGGAGCGGTATAAGCACCCTCTCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAACCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: CTGTCAAGGAGCGGTATAAGCACCTTC-CCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|58690597|gb|CK079284.1|CK079284
EST:     GGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCTATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|89192699|gb|CI049997.1|CI049997
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|89193061|gb|CI050359.1|CI050359
EST:     AGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: AGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|89184500|gb|CI047065.1|CI047065
EST:     TAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: TAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|88828815|gb|CI073685.1|CI073685
EST:     TATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATGTACAAGGCGGCCAACTTAAGGCGAAC
genomic: TATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|89184749|gb|CI048305.1|CI048305
EST:     AAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: AAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|88385229|gb|CI630330.1|CI630330
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|88841233|gb|CI080687.1|CI080687
EST:     GCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|86435192|gb|CI106425.1|CI106425
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|86431397|gb|CI085008.1|CI085008
EST:     CGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: CGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|87035464|gb|CI190086.1|CI190086
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|87040354|gb|CI194976.1|CI194976
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATTTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|218502449|gb|FG965484.1|FG965484
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCC
EST: gi|86255866|gb|CI068315.1|CI068315
EST:     TAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: TAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|3759655|gb|C96913.1|C96913
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|88348688|gb|CI631382.1|CI631382
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCACGCGGATTGTGAG                         GCATAGGCACTTACCTAAGNCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
EST: gi|88351589|gb|CI628809.1|CI628809
EST:     GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAG                         GCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC
genomic: GCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAAC

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: 56 (upstream exon), 73 (downstream exon)
Score: 21

CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataac ... ttcgctgcagGCATAGGCACTTACCTAAGCCAATCTACAAGGCGGCCAACTTAAGGCGAACGATGATTGAAGCAGAAAACCGTAAAGAAGAAAGGAGGCGTGCGCACAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTTCCAAGAGAACGCAGAAAACAAGAATACCTAGATGCTGTCAAGGAGCGGTATAAGCACCTTCCCGAAGTCAAGCGGATTGTGAGgtaatataaccgcctcttgacgtggggaagttccacgtactttgtatagatcatctcgtttacaatccccatacttggaacaatcattttgttgatgttgcatggatggcgtttcgctgcag

- - - - - - - - - - - - - - - - - - - - - -  AAGGAG