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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggcactacatgttcaactttaacattgtttataacagtggtattcttacacactgtcttctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G006507_T03 (Zea mays), 5'ss of exon 11
ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggcactacatgttcaactttaacattgtttataacagtggtattcttacacactgtcttctgcag
|||||||||||| |||||||| |||||||||||  |||||||||||||||| |||||||||||||||||| |    | | | ||| | |    | |  |||| || ||  || |||| ||||| |||||  |  |||||
ATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAGgtgaa----cgcaatatgctaatgcattagtttgtcta-aagtgtagtatgcttacccactgcttcatgcag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G119725_T03 (Zea mays), 5'ss of exon 10
ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggcactacatgttcaactttaacattgtttataacagtggtattcttacacactgtcttctgcag
||||||||| || |||||||| |||||||| ||  |||||||||||||||| ||||||||||||||||||  ||  ||   ||||     | |||   |||| |  |   |  |||| ||||  ||||    | |||||
ATTTGTTGAGATTATGGCAACAGTGTTCTCCAGAAATGCATGGCGCTGTGTATGGCATATGATTCAGgtgaggtaacatggcatgcaagtcattagt-ttgtctgaagtgg-agtatgcttatgcacttctatatgcag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtg---gagtggcactac----------atgttcaactttaacattgtttataacagtggtattctta----cacactgtcttctgcag--------------------------------------------------------------------------------
 |||||||| || |||||| | || || ||||| || |||||||| ||||| |||||||||||||||||    |  |  |  ||           | | ||    || ||||     | |   |||| |||  |      ||  ||  |||||                                                                                   
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 5'ss of exon 11
ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtg-gcactacatgttcaactttaacattgtttataaca---gtggtattcttacaca-ctgtcttctgcag-----------------------
|||||| ||||| |||||  | || |||||| |||| || ||||| ||||| |||||||||||||||||    |      |  | | | |  ||      |    ||  ||   ||   |  | | |||| || |  ||| ||                        
ATTTGTGGAAATTATGGCCCCTGTCTTCTCTCGGGAAGCTTGGCGTTGTGTGTGGCATATGATTCAGgtatcctttatcttttaggattatattgctttctacacatggcacatgttacaagcatgcacatcttttctcttcaagttattcttctgttatctcatag

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|29673249|gb|CB669524.1|CB669524
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|29616239|gb|CB621251.1|CB621251
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|29641724|gb|CB646731.1|CB646731
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|29641418|gb|CB646425.1|CB646425
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|58596057|gb|CK006585.1|CK006585
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|29676039|gb|CB672314.1|CB672314
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|38475807|gb|CF959940.1|CF959940
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|33795503|gb|CF323621.1|CF323621
EST:     CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
EST: gi|27577797|gb|CB000492.1|CB000492
EST:     CCTTCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG                         AATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG
genomic: CAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTG

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: 67 (upstream exon), 54 (downstream exon)
Score: 22

ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtggagtggc ... tcttctgcagAATGACTTGGTCCATGGATGGGGTCTTGATTTCGCTCTAAGGAAATGTGTGGAG




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