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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattagtacatattactgaacccttaagctagctagttacatacagcttcagcttggatgcgccatttagtctctgcaactgaacatttttcttatctaaaacctataaacatgtttcatgtgcacag

Basic information

species Oryza sativa
transcript LOC_Os07g04990.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

upper sequence: LOC_Os07g04990.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G111954_T03 (Zea mays), 5'ss of exon 8
GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattagtacatattactgaacccttaagctagctagttacatacagcttcagcttggatgcgccattt-agtctctgcaactgaacatttttcttatctaaaacctataaacatgtttcatgtgcacag
|||||||| |||| || |||||||||||||| || ||||| |||||||||||||||||||| ||||||||||||||| |||||||||     ||      ||||| |  ||  |||| ||| ||||||   |    |||  || |  | |   || ||||||||||| | |||   ||  |||||| ||| ||  |                    
GTGTTCTGACAGGTAAGTACACTCCAGAAAACCCCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAGgtta-----gtg-----tactgtaaactggagctcgctggttacactga----cagtctg-acacacagcttcagtctctgcaattcaac---ttcgttatctgaaatctgaag-------------------
















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|88368695|gb|CI675516.1|CI675516
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTNCAAC-ACTCA
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTT-CAACCACTCA
EST: gi|88519585|gb|CI447239.1|CI447239
EST:     AACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: AACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|29686327|gb|CB682602.1|CB682602
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|86892489|gb|CI311960.1|CI311960
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|88505384|gb|CI432890.1|CI432890
EST:     GTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGGAGAAAGCTATGGGAA
genomic: GTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATT-GGAGAAAGCTATGGGAA
EST: gi|86862869|gb|CI331708.1|CI331708
EST:     TCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: TCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|86840691|gb|CI333939.1|CI333939
EST:     CCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|29686352|gb|CB682627.1|CB682627
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|29684749|gb|CB681024.1|CB681024
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|29685611|gb|CB681886.1|CB681886
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|29685612|gb|CB681887.1|CB681887
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
EST: gi|86838940|gb|CI330354.1|CI330354
EST:     CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG                         CTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG
genomic: CTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAG

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: 75 (upstream exon), 63 (downstream exon)
Score: 126

GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAGgttatattag ... atgtgcacagCTTCAACCACTCATGAACAGGATCAAGGAGATTGGAGAAAGCTATGGGAAGAACCCAACCCAG




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