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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGACCATCAAGAAGAAACTAATCCGCAAAGCTCTTGACATGATTAGAAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagttctctgtggatcacaggtcatatactgttatttatgatgtaattctcacataatcttctgtactcag

Basic information

species Oryza sativa
transcript LOC_Os06g50300.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 13
CTGAAGACCATCAAGAAGAAACTAATCCGCAAAGCTCTTGACATGATTAGAAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagttctc--------tgtggatcacaggtcatatactgt-tatttatgat-gtaattctca---cataatcttctgtactcag
|||||||| ||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||||||||| ||||||||||||||    ||  |        |||| ||  || |||| || || | ||||| | ||   ||| || |    |  | |  ||||| ||||
CTGAAGACTATCAAGAAGAAGCTGATCCGCAAAGCTCTTGACATGATTAGGAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaatgtctttccccccctgctgtgaat-gcaagtcacatgctctatatttgtcattacaatgctaaaagtaggaacaactgtaatcag

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 11
CTGAAGACCATCAAGAAGAAACTAATCCGCAAAGCTCTTGACATGATTAGAAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaaca---agttctctgtgg--atcacaggtcatatactgt-tatttatgatgtaattctcacataa--tcttctgtactcag
|| ||||||||||||||||| || ||||||||||| ||||||||||| || ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| |    ||| || |  |  |   || |||| ||||| | || ||||  |  || |     | |   | |||| || ||||
CTCAAGACCATCAAGAAGAAGCTGATCCGCAAAGCCCTTGACATGATCAGGAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgggttttccgcagtgaatgcaagtcacatactctgtaattatctttaaagtactgaaaagatttttctctaatcag
















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|58693264|gb|CK081951.1|CK081951
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|58684599|gb|CK073286.1|CK073286
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|33800491|gb|CF326115.1|CF326115
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|58685726|gb|CK074413.1|CK074413
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|58689260|gb|CK077947.1|CK077947
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|29627895|gb|CB632906.1|CB632906
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTTCAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|14192100|gb|AU184311.1|AU184311
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|55410371|gb|CV722747.1|CV722747
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
EST: gi|29659228|gb|CB655503.1|CB655503
EST:     AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAG                         ATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT
genomic: AAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCT

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), 74 (downstream exon)
Score: 158

CTGAAGACCATCAAGAAGAAACTAATCCGCAAAGCTCTTGACATGATTAGAAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagtt ... ctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCTGGAATGAGTTTGGAAAATCAGTCAAGTTGGGCATCATTGAAGACGCAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAGACCATCAAGAAGAAACTAATCCGCAAAGCTCTTGACATGATTAGAAAACTTGCTGAGGAAGATCCTGATGAGTACAGCAACAAAGATAAGACAGgtaacaagttctctgtggatcacaggtcatatactgttatttatgatgtaattctcacataatcttctgtactcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA