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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgtttcaattgtataaatgattttaattattccttttcacatgttttcatatttcaatctgttgctatttgatctggttgccag

Basic information

species Zea mays
transcript GRMZM2G080044_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080044_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g11140.1 (Oryza sativa), 5'ss of exon 4
GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgtttcaattgtataaatgattttaat---tatt-------------ccttttcacatgttttcatatttcaatctgttgctatttgatctggttgccag
||  | ||||||||||||||||| | |||||||||||| ||||||||||| ||||| ||||||||||||| |   |||| || | || ||||  |  || |   ||||               || ||| ||| |||||| |||  |  |||     | |||| |||| | |||
GTCATGCTGGTTGATCAATCTGACAGATTTGTATTTAAGCCCATGTTGTATGAGCTCTTGTCAGGAGgtaatgtagtttgaagtataaaaatactgctagtgtatattataatttactggattttatcatatggtttcatgtttttaaatgtgaaactatgatttggtcggcag
















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|76934119|gb|DV173742.1|DV173742
EST:     CGAGCTATTGTCAGGAG                         AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
genomic: CGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
EST: gi|30306789|gb|CD001462.1|CD001462
EST:     ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG                         AAGTGGATATCTGGGAGATAGCTCCATC
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATC
EST: gi|29543792|gb|CB604172.1|CB604172
EST:     ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG                         AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
EST: gi|31998276|gb|CD662009.1|CD662009
EST:     ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG                         AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
EST: gi|211318168|gb|FL216126.1|FL216126
EST:     ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG                         AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGT
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGT

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: 37 (upstream exon), 48 (downstream exon)
Score: 26

GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA


Block sizes: 45 (upstream exon), 38 (downstream exon)
Score: 20

GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA


Block sizes: 43 (upstream exon), 41 (downstream exon)
Score: 9

GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 12

GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA