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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgctactacctcctattctgattactgtgtttgagattgtatctactatctttctcccatgcctttcatttcacactgaaagaggaatcccct...

Basic information

species Oryza sativa
transcript LOC_Os09g27420.2
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g27420.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G824944_T01 (Zea mays), 5'ss of exon 4
CCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgctactacc-tcctattctgattactgtgtttgagatt-gtatctactatctttctcccatgcctttcatttcacactgaaagaggaatcccct
   |||||| ||||||||||| || |||||| ||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| || || |||||||| ||| |   ||| | |  |     ||  | | ||||    |  ||    ||       || | || |   |   || ||                  
---TCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGTAtc-ttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacaggct-----------

upper sequence: LOC_Os09g27420.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G824944_T02 (Zea mays), 5'ss of exon 4
CCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgctactacc-tcctattctgattactgtgtttgagatt-gtatctactatctttctcccatgcctttcatttcacactgaaagaggaatcccct
 |||||||| ||||||||||| || |||||| ||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| || || |||||||| ||| |   ||| | |  |     ||  | | ||||    |  ||    ||       || | || |   |   || ||                  
ACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatc-ttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacag--------------

upper sequence: LOC_Os09g27420.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0004g01160.t01 (Vitis vinifera), 5'ss of exon 4
CCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatcct------------tgctactacctcctattctgattactgtgtttgagattgtatctactatctttctcccatgcctttcatttcacactgaaagaggaatcccct
 ||  |||| ||||| |||||||| ||   | | || |||||||| || ||| ||||||| ||||  || ||||| ||||| ||||||||||| |||||||||  ||            | ||   |  |    |||| ||||||   |      || ||  |  |    | ||   |  | |    ||| || ||||              
GCCATTGAAGTTTTTATATCCTTTGGATATTAGTATCAAGGAGAAAATAGAGGCAATAGCCAAGTCGTACGGTGCCAGCGGTGTTGAATACTCAGAACAGgtagactcttttagtaaagttctggcattttactttctaattacttgatgaattgttataaattttgaagtcctattagacttcaattttgactctgatt------------

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|86513763|gb|CI156396.1|CI156396
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGGCGGAGAAGCAG              
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCT-----------GAA-CAGgtatccttgc ...
EST: gi|58689176|gb|CK077863.1|CK077863
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAG                         G
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgc ... ggagaagcag-
EST: gi|58689176|gb|CK077863.1|CK077863
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAG                         G
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgc ... ggagaagcag-
EST: gi|58689176|gb|CK077863.1|CK077863
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAG                         G
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgc ... ggagaagcag-
EST: gi|58689176|gb|CK077863.1|CK077863
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAG                         G
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgc ... ggagaagcag-
EST: gi|58689176|gb|CK077863.1|CK077863
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAG                         G
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgc ... ggagaagcag-
EST: gi|87010814|gb|CI312506.1|CI312506
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGGCGGAGAAGCAG              
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCT-----------GAA-CAGgtatccttgc ...
EST: gi|86436750|gb|CI118472.1|CI118472
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGGCGGAGAAGCAG              
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCT-----------GAA-CAGgtatccttgc ...
EST: gi|88956425|gb|CI092686.1|CI092686
EST:     GGTGCTAGCGGCGTTGAATACTCTGAACAG                         ATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCG
genomic: GGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgc ... ggagaagcagATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCG
EST: gi|86517665|gb|CI157871.1|CI157871
EST:     AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGGCGGAGAAGCAG              
genomic: AGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCT-----------GAA-CAGgtatccttgc ...

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: 47 (upstream exon), 73 (downstream exon)
Score: 3

CCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGTCAATAGCTAAGTTCTATGGTGCTAGCGGCGTTGAATACTCTGAACAGgtatccttgc ... ggagaagcagATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCGAAAACTCAGTACTCGTTTTCGCATGTTCCATCCATGAAGGGCGCGCCGT




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