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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgaatcactttgtgtatagtttgtatatatgtacagtctagtatgtgtttgactggggttttacttctgccatcgtatttaactgtacttgtttttttatatttaagtgacagcaataatgcttgttttgaaagctaggctgccttttgtgacacaattgctatatttcattggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG

Basic information

species Zea mays
transcript GRMZM2G115518_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115518_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 4
gtatgcttgaatcactttgtgtatagtttgtatatatgtacagtctagtatgtgtttga--ctggggttttacttctgc-catcgtatttaactgtacttgtttttttatatttaagtgacagcaataatgcttgttttgaaagctaggctgccttttgtgacacaattgctatatttcattggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG
                                               || ||  ||  |  || ||   | | || ||   |   ||  |   | ||| | |    | | ||||          ||| || |||||   ||| ||||||||   |||| ||||| | || ||||   || || |  |||||||| || |||||||| || |||||||  ||||| |||||||||||||| |||||||| || ||||| ||||||||||
-----------------------------------------------gtgtgctttgaaatcttggaactaatttatgtgtagtttacattcgtatacgtatgcagtcacatttgta-------aattatacttgta--gaatgctaggctat-ttttatgacatagtt-ctat---tcttttgtccagAATTTCCTTTTCACAACCAGGGATGAAAATGCTCCCATGAAGTTGATTGATTTTGGTCTCTCTGATTTCATTAGACCAG
















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|31354119|gb|CD438476.1|CD438476
EST:     TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTGGAAGCCAGAG                         AATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
genomic: TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
EST: gi|76284392|gb|DV023960.1|DV023960
EST:     TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAG                         AATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
genomic: TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
EST: gi|31356504|gb|CD440861.1|CD440861
EST:     TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTGGAAGCCAGAG                         AATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
genomic: TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
EST: gi|211371493|gb|FL287192.1|FL287192
EST:     TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAG                         AATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
genomic: TGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGAC
EST: gi|6760508|gb|AW324597.1|AW324597
EST:     GGCCTTCTGTCATTCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAG                         AATTTTCTCTTCACAAC
genomic: GGCCTTCTGTCAT-CTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAAC

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: 33

ATATACAGAAGAAGATGCCAAAGCGATCATTGTACAGATTTTGAGCGTAGTGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

ATATACAGAAGAAGATGCCAAAGCGATCATTGTACAGATTTTGAGCGTAGTGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 165

ATATACAGAAGAAGATGCCAAAGCGATCATTGTACAGATTTTGAGCGTAGTGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 151

ATATACAGAAGAAGATGCCAAAGCGATCATTGTACAGATTTTGAGCGTAGTGGCCTTCTGTCATCTTCAGGGAGTAGTGCATCGTGATTTGAAGCCAGAGgtatgcttga ... attggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgaaagctaggctgccttttgtgacacaattgctatatttcattggcacagAATTTTCTCTTCACAACAAGAGATGAAAGCGCTCCTATGAAGTTGATTGACTTTGGTCTGTCAGATTTTATTAGACCAG
                                         tttcatt  CT-rich tract
                                     tatatttcatt  TA-rich tract