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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTCTGACAGGTAAGTACACTCCAGAAAACCCCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAGgttagtgtactgtaaactggagctcgctggttacactgacagtctgacacacagcttcagtctctgcaattcaacttcgttatctgaaatctgaagatgcgccatgtcatgtatgtacag

Basic information

species Zea mays
transcript GRMZM2G111954_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111954_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g04990.1 (Oryza sativa), 5'ss of exon 8
GTGTTCTGACAGGTAAGTACACTCCAGAAAACCCCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAGgtta-----gtg-----tactgtaaactggagctcgctggttacactga----cagtctg-acacacagcttcagtctctgcaattcaac---ttcgttatctgaaatctgaagatgcgccatgtcatgtatgtacag
|||||||| |||| || |||||||||||||| || ||||| |||||||||||||||||||| ||||||||||||||| |||||||||     ||      ||||| |  ||  |||| ||| ||||||   |    |||  || |  | |   || ||||||||||| | |||   ||  |||||| ||| ||  | |     |||||    | || ||||
GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattagtacatattactgaacccttaagctagctagttacatacagcttcagcttggatgcgccattt-agtctctgcaactgaacatttttcttatctaaaacctataaa-----catgtttcatgtgcacag
















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|18170355|gb|BM340195.1|BM340195
EST:     CCCCTACTGGTCCTCGAGCAGACACATACACCCCTGAGTTCCTCGCCAAG                         CTCCAACCACTTATGAACAGGATTAAAGAGATCGGAGCAAGCTATGGCAAG
genomic: CCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAGgttagtgtac ... gtatgtacagCTCCAACCACTTATGAACAGGATTAAAGAGATCGGAGCAAGCTATGGCAAG
EST: gi|148936270|gb|EC880348.2|EC880348
EST:     CCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAG                         CTCCAACCACTTATGAACAGGATTAAAGAGATCGGAGCAAGTTATGGCAAG
genomic: CCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAGgttagtgtac ... gtatgtacagCTCCAACCACTTATGAACAGGATTAAAGAGATCGGAGCAAGCTATGGCAAG
EST: gi|211142180|gb|FL083863.1|FL083863
EST:     CTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCACCAAG                         CTCCAACCACTTATGAACAGGATTAAAGAGATCGGAGCAAGCTATGGCAAG
genomic: CTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAGgttagtgtac ... gtatgtacagCTCCAACCACTTATGAACAGGATTAAAGAGATCGGAGCAAGCTATGGCAAG

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: 38 (upstream exon), 49 (downstream exon)
Score: 591

GTGTTCTGACAGGTAAGTACACTCCAGAAAACCCCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAGgttagtgtac ... gtatgtacagCTCCAACCACTTATGAACAGGATTAAAGAGATCGGAGCAAGCTATGGCAAGAGTCCAACCCAG




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