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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagctatattttcccattgaaaatcaagttcttgatatgtacatatatgccagacatgtctgggataattgacttgatttacattcaaacaattgtag

Basic information

species Oryza sativa
transcript LOC_Os11g03730.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 6
GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagctatattttcccattgaaaatcaagttcttgat------atgtacat-atatgcca---------gacatgtctg-ggataattgacttgatttacattcaaacaattgtag
|||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| |||||||||  |  | |||||  ||| | ||||| ||||   ||      ||||| || ||||              | |  | |  ||||||| |||| ||||  |||  |  | |||||||
GGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTGgtatgctccgtgttttcttatttagaatcaggttcccaatgctaagatgtatatgatatattgcaatatattaatacatttaaggataatggactagatt-gcatg-atgctattgtag

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 19
------------------------------GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagctatattttcccattgaaaatcaagttcttgatatgtacatatatgc--------cagacatgtctgggataattgacttgatttacattcaaacaattgtag
                              ||||||||||| ||||||||||||||||| ||| | ||||| || ||||||||||||||||| || |||||||||  || | ||||| |||| |||||||||||||| || | |  | ||||          || | |||| |  |||| ||||  |   || ||| | | | | |||||
ATTTATAGCTGGTTCTCTCTGTACACACAGGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGGTTTCCTGgtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttga--tagattccatgcga-ctactgtag

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G006130_T01 (Zea mays), 5'ss of exon 7
GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagctatattttcccattgaaaatcaagttcttgatatgtacatatatgc--------cagacatgtctgggataattgacttgatttacattcaaacaattgtag
||||||||||| ||||||||||||||||| ||| | ||||| || |||||||||||||||||||| |||||||||  || | ||||| |||| |||||||||||||| || | |  | ||||          || | |||| |  |||| ||||  |   || ||| | | | | |||||
GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttga--tagattccatgcga-ctactgtag

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G006130_T02 (Zea mays), 5'ss of exon 7
GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagctatattttcccattgaaaatcaagttcttgatatgtacatatatgccagacatgtctgggataattgacttgatttaca---ttcaaacaattgtag
||||||||||| ||||||||||||||||| ||| | ||||| || |||||||||||||||||||| |||||||||  || | ||||| |||| |||||||||||||| || | |  | ||||   |    | ||   |||  || |  |  || | |   | ||  | | |    
GGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTGgtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgt-tcatagatgtttcagatatttgatagattccatgcgact----

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|29672785|gb|CB669060.1|CB669060
EST:     ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
genomic: ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
EST: gi|29644765|gb|CB649772.1|CB649772
EST:     ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
genomic: ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
EST: gi|29646541|gb|CB651548.1|CB651548
EST:     ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
genomic: ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
EST: gi|29632787|gb|CB637796.1|CB637796
EST:     ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATCCATGTGGAGGG
genomic: ACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
EST: gi|29636288|gb|CB641297.1|CB641297
EST:     TATATCTATGATGTTGGACTTAAAACCACAATTCTTGAGATTCCCTG                         GAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG
genomic: TATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGG

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), 75 (downstream exon)
Score: 53

GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTTGTGGAGGGGGAATGGTTAAGGAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG




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