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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaatttgcatgcttttctgtttggaaggaagtggcattgattcttgaaaccaagtgtgacatatatatatacatgttgtgatatatttgtatgattgcag

Basic information

species Oryza sativa
transcript 13114.m00108
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01014.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G04660.2 (Glycine max), 5'ss of exon 6
GGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaatttgcatgcttttctgtttggaaggaagtggcattgattcttgaaaccaagtg-tgacatatatatatacatgttgtgatatatttgtatgattgcag
||  || |||||||||||||||||||||||||  | |||||||| |   | ||||| |  || || || || ||||||||  ||||| |  | || |||||||||| |  ||      ||||| | |||      |  | |   | | |||    |  || || || ||| |    ||   | |     | | |||      || |||
GGTGTGCTGCCTCCATTTGTTCCATTTGCTCAGGCATTTGCAGCTGTACTTACTGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTAAAGgtgactttgtttattgcccttttgtattttccct-acttcgttctcagtct---gattaaatgatggcatctcccaatggttctatcttttttttttctctctttcag

upper sequence: LOC_Os03g01014.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G40650.4 (Glycine max), 5'ss of exon 6
GGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaatttgcatgcttttctgt-ttggaaggaagtggcattgattcttgaaaccaagtgtgacatatatatatacatgttgtgatatatttgtatgattgcag
||  || |||||||||||||||||||||||||| | ||||| || |   | || || |  || || || || ||||||||  ||||| |  | || |||||||||| |  ||    | |  || | | ||      |  | |   | | |||    |  ||   || | | |    ||    ||| ||   | ||       || |||
GGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTAAAGgtgactttg-ttaatttccccttttatattttccctactttgttctcagtct---gattaacgatggcctctcctaatg---gttctgtctttttctctctctttcag

upper sequence: LOC_Os03g01014.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv02s0012g01220.t01 (Vitis vinifera), 5'ss of exon 6
GGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaatttgcatgcttttctgtttggaaggaagtggcattgattcttgaaaccaagtgtg-acatatatatatacatgttgtgatatatttgtatgattgcag
||  || ||||||||||||| |||||||| ||  |||||||||| |  ||||| || ||||| || || || ||||||||||||||| |  | || ||||||   |   ||       |||||       | |   | |    |   ||| |  |      | |  |  | | | | | ||  |                        
GGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAAAGgttgattatatcaaacctcttttaaacaatgtacctaatcatttcatttcctacactttgatttacaagtttctttttccacatcag---------------------

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|14980697|gb|BI305375.1|BI305375
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGCGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|13165324|gb|AU174121.1|AU174121
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|86906380|gb|CI294503.1|CI294503
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|14980567|gb|BI305245.1|BI305245
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGNGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|33679460|gb|CF307699.1|CF307699
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|58609210|gb|CK037243.1|CK037243
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGT
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGT

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: 69 (upstream exon), 69 (downstream exon)
Score: 38

GGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG




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