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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCTTGACATTGCAAATGTTCATTGCATGCCAAGGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccactcttctcttaacactccctttggaattttgtggtgtaatttaatgattatatctaattagtgtattccatatattttaaattagcag

Basic information

species Oryza sativa
transcript LOC_Os04g56530.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G084586_T01 (Zea mays), 5'ss of exon 4
CACCTTGACATTGCAAATGTTCATTGCATGCCAAGGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccactcttctct----taacactccctttggaattttgtggtgt---aattt-----aatgattatatctaattagtgtattccata--tattttaaattagcag
|||| ||||||||||||||||  |||||||||||||||||||||| ||||| || ||| |||||||||| |||||||||||||||  ||||   |  |   |     ||   | |||    | |||| | ||||   |||||     |||| ||  |||||| || | || |  | |  ||||||||||||||||
CACCCTGACATTGCAAATGTTTGTTGCATGCCAAGGGATCCCTGTTTTGGTAAGCTTTATGGAGCCTGACTATGCAAAATACAGgcaagtctgatggttgttggtacaattattcctccatatttttcttgtgtgttaatttgtttaaatggttggatctaactaatatactgaaaaaatattttaaattagcag

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G017654_T01 (Zea mays), 5'ss of exon 18
CACCTTGACATTGCAAATGTTCATTGCATGCCAAGGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccactcttctct----taacactccctttggaattttgtggtgtaatttaatgattatatctaattagtgtattccatatattttaaattagcag
|||||||||||||||||||||||||||||| |||||||||||||| ||||| || ||| |||||||||| |||||||||||||||  ||||  ||  |   |    |||   | |||    | |||| |  ||||  ||||| ||| ||  |  ||   | |                       
CACCTTGACATTGCAAATGTTCATTGCATGTCAAGGGATCCCTGTTTTGGTAAGCTTTATGGAGCCTGACTATGCAAAATACAGgcaagtctgcttgttgttgatataattattcctccatatttttcttctgta--ttaattatt-taaatgcttgtagcag----------------------

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv01s0011g02270.t01 (Vitis vinifera), 5'ss of exon 18
CACCTTGACATTGCAAATGTTCATTGCATGCCAAGGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtg---agtccactcttctcttaacactccctttggaattttgtggtgtaatttaatgattatatctaattagtgtattccatatattttaaattagcag--
| ||||||||||||||||||||||||| ||    || || ||||| || ||| | ||||||||| |||||||||  |  |||||||    ||| || | | || | ||        | |      |  |  |  | |  ||  || | | |   ||   |  | |  |   |  |||     |   
CTCCTTGACATTGCAAATGTTCATTGCTTGTGGTGGAATACCTGTTTTAGTGGGCTTTCTGGAGGCTGATTATGTGAGGTACAGgtatgtagttcattgtgctatgaatgaatgaatcgcttgactaggaagggagtggat--ttttgtttttctatgattctgctgagcatggaaacagatatgt

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|29622112|gb|CB627123.1|CB627123
EST:     GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAG                         GGGAAATGGTTCATCTTGCAATCGA
genomic: GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccac ... aaattagcagGG-AAATGGTTCATCTTGCAATCGA
EST: gi|58678203|gb|CK066890.1|CK066890
EST:     GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAG                         GGAAATGGTTCATCTTGCAATCGATGGCATATGGCAGGTCTTCAAACTCCA
genomic: GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccac ... aaattagcagGGAAATGGTTCATCTTGCAATCGATGGCATATGGCAGGTCTTCAAACTCCA
EST: gi|29641026|gb|CB646033.1|CB646033
EST:     GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAG                         GGAAATGGTTCATCTTGCAATCGATGGCATATGGCAGGTCTTCAAACTCCA
genomic: GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccac ... aaattagcagGGAAATGGTTCATCTTGCAATCGATGGCATATGGCAGGTCTTCAAACTCCA
EST: gi|29641522|gb|CB646529.1|CB646529
EST:     GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAG                         GGAAATGGTTCATCTTGCAATCGATGGCATATGGCAGGTCTTCAAACTCCA
genomic: GGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccac ... aaattagcagGGAAATGGTTCATCTTGCAATCGATGGCATATGGCAGGTCTTCAAACTCCA

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: 72 (upstream exon), 69 (downstream exon)
Score: 21

CACCTTGACATTGCAAATGTTCATTGCATGCCAAGGGATCCCTGTATTGGTGAGTTTTCTGGAGCCTGATTATGCAAAATACAGgtgagtccac ... aaattagcagGGAAATGGTTCATCTTGCAATCGATGGCATATGGCAGGTCTTCAAACTCCAGCATTCGACTCCAAGAAATGACTTCTGTCGCATAGCGGCAAAAAACGGG




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