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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcag

Basic information

species Zea mays
transcript GRMZM5G814700_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 13
AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaattatt--caattaaataagtgctactgtatcg--tgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcag
|| || || ||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||  || |  | ||       |  |  |||    |  ||||  |    |        ||  ||  | |   |   |   |||||      | || |                                                                
AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagatactatctatagggcctgcccagctgagctggctgcaactgcatcacagccagctgctgcccgaagca---gcaatgccagtggcttgctcctgc-------------------------------------------------------------

upper sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 5'ss of exon 12
AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaattattcaattaaataagtgctactgtatcgtgcagtt-atggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcag
|||||||| |||||||| ||||||||||||||| | | | | ||| |  ||||  ||||||||||| ||||   |  | |  |  |   || |  | | |     ||| || | |||  |  ||   |||| ||  ||     |      |     ||   | ||  | |   || |                                                     
AATAAATGCAATGTCGGATATGCTTTCATCAACCTTATCGAACCTGAAAATATTGTTCCGTTTTATAAGgtataagctttgtacctttttatgatcaatt----tgtgtagatgatgtatcattgttctttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacag---------------------------------------------------
















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|22542340|gb|BU092793.1|BU092793
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGGTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|33095731|gb|CF055725.1|CF055725
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|67013397|gb|CO442146.1|CO442146
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|26558461|gb|CA830696.1|CA830696
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGCTTAACAGCGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|211008041|gb|FL362435.1|FL362435
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|71307207|gb|DR789770.1|DR789770
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|33093066|gb|CF053060.1|CF053060
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|32867814|gb|CF007496.1|CF007496
EST:     ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: ATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
EST: gi|33091257|gb|CF051251.1|CF051251
EST:     CCAATCCTCAGCATATCATTCCGTTTTATCAG                         AGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA
genomic: CCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCA

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), 49 (downstream exon)
Score: 373

AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 356

AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 503

AATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAGgtgagaatta ... cgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC