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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttagccttttcttattttcctcaatcttgttttctttatattatcccccttctgtttcccaaggtctatggaatatggataaactgcaactcttgaaccgtttaaaagaccatcatttggaggaaactgagctatccaagtgacaggagcattatttacttaacttgatctgccttttgtatggaatgcag

Basic information

species Zea mays
transcript GRMZM2G033619_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033619_T02 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 18
CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttagccttttcttattttcctcaatcttgttttctttatattatcccccttctgtttcccaaggtctatggaata--tggataaactgcaactcttgaaccgtttaaaagaccatcatttggaggaaactgagctatccaagtgacaggagcattatttacttaacttgatctgccttttgtatggaatgcag
                                      | |||||||||||||||||||| || |||||||||||||||||||| ||| ||||||| ||||||||| |      || || ||||||| ||| ||   || ||| |  |      ||    | |   |||  ||     | |  | | |  |  |||  | ||| |  |||                                                                                         
--------------------------------------ATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctat------ttatttttttccttaatttttccttttttgttctgattaact---atatagaaagaactgcaacacaactagttgcagagcag-tattggaatgtt-----------------------------------------------------------------------------------------

upper sequence: GRMZM2G033619_T02 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os03g49420.4 (Oryza sativa), 5'ss of exon 8
CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttagccttttcttattttcctcaatcttgttttctttatattatcccccttctgtttcccaaggtctatggaata--tggataaactgcaactcttgaaccgtttaaaagaccatcatttggaggaaactgagctatccaagtgacaggagcattatttacttaacttgatctgccttttgtatggaatgcag
                                 ||| || |||||||||||||||||||| || |||||||||||||||||||| ||| ||||||| ||||||||| |      || || ||||||| ||| ||   || ||| |  |      ||    | |   |||  ||     | |  | | |  |  |||  | ||| |  |||                                                                                         
---------------------------------GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAGgtacctat------ttatttttttccttaatttttccttttttgttctgattaact---atatagaaagaactgcaacacaactagttgcagagcag-tattggaatgtt-----------------------------------------------------------------------------------------
















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|16925300|gb|BM078368.1|BM078368
EST:     TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
EST: gi|16926388|gb|BM079456.1|BM079456
EST:     GTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: GTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
EST: gi|5030633|gb|AI714827.1|AI714827
EST:     TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
EST: gi|78105523|gb|DV523941.1|DV523941
EST:     TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
EST: gi|166587713|gb|EG190265.1|EG190265
EST:     GTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: GTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
EST: gi|18166327|gb|BM336166.1|BM336166
EST:     TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
EST: gi|78105524|gb|DV523942.1|DV523942
EST:     TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: TGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
EST: gi|166692936|gb|EG264559.1|EG264559
EST:     GTTTTTGCAGAG                         ATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG
genomic: GTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATG

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 76

CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATGGTTAATCTACTAAGGCAACTTCAGGCAACATTGCCTCCTTCAGTATTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATGGTTAATCTACTAAGGCAACTTCAGGCAACATTGCCTCCTTCAGTATTAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 70

CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATGGTTAATCTACTAAGGCAACTTCAGGCAACATTGCCTCCTTCAGTATTAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 47

CTATTATTTTTTCGTGTAATCAACGTTCAACAGGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAGgtacctttag ... tggaatgcagATATTATGTGCGGGCAAAGATCTAGCAACAGAACAGACTGCCAGCAGGATGGTTAATCTACTAAGGCAACTTCAGGCAACATTGCCTCCTTCAGTATTAG