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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctgattcatttaaatttctgttatctcaagggtgaaataacag

Basic information

species Oryza sativa
transcript LOC_Os11g36440.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G108457_T01 (Zea mays), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctga-ttcatttaaatttctgttatctcaagggtgaaataacag--------------
|| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||  || || |||   || | || |   |||  | |||||||  | |||||||||||||      | |||||||              
TGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATGgtaagttcaa-gcttgatcttctggatctccattccaaattcatttggacttctgttatctcagtatcaatataacaggtcttgtgcgatag

upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G108457_T02 (Zea mays), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctga-ttcatttaaatttctgttatctcaagggtgaaataacag
|| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||  || || |||   || | || |   |||  | |||||||  | |||||||||||||      | |||||||
TGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATGgtaagttcaa-gcttgatcttctggatctccattccaaattcatttggacttctgttatctcagtatcaatataacag

upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G106531_T01 (Zea mays), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctgattcatttaaatttctgttatctcaagggtgaaataacag
|| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||  |||      ||    ||  ||   |||  ||||||||  ||||||||||||| || |   | |||||||
TGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATGgtaagttcaatcttaatcttctggatcttcatttcaaattcatttggatttctgttatcttaatgccaatataacag

upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G106531_T02 (Zea mays), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctgattcatttaaatttctgttatctcaagggtgaaataacag--------------
|| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||  |||      ||    ||  ||   |||  ||||||||  ||||||||||||| || |   | |||||||              
TGTTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATAAATGCAAGCATGgtaagttcaatcttaatcttctggatcttcatttcaaattcatttggatttctgttatcttaatgccaatataacaggtcttgtgcgatag

upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G34060.1 (Glycine max), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctgattcatttaaatttctgttatctcaagggtgaaataacag-----------------------
|| ||||| ||||||||||||||||| ||||| ||||| ||||| |||||   ||||||||          |  || |   | | || |   |  |||| | | |||||  || |   |  |   |    | |                        
TGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATGgtaatctcttcatttatctttttcattctttcagttctttcaatcatatttcatttcttaaattgtctaggagagaaggattcatgcttgcattcattgc

upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G10990.1 (Glycine max), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtgga--atgcatgactctcagaattttg---cttctgattcatttaaatttct---gttatctcaagggtgaaataacag---------------
|| ||||| ||||||||||||||||| ||||| ||||| ||||| |||||   ||||||||       ||  ||   | |||   ||||    ||| | ||    ||  ||||||    || |||    |  ||     ||                
TGTTTTATAGTGAGCACAGTCAATGCTTTGCAGACACCAATGATCAATGCTGCCATGgtaatctattcatttatctttttcattcttttagttcttttaatcttattgcatttcttaaattgtctaggagaggaggattcatgcttgcattcattgt

upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G06820.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctgattcatttaaatttctgttatctcaagggtgaaataacag
|| || |||||||||||||||||||| ||||| || || ||||| |||||||| |||||| |     ||  |     |  |   | | ||  || | |  || | ||| | || ||| | |  |  ||  ||||
TGTTTCATTGTGAGCACAGTCAATGCTTTGCAGACGCCAATGATCAATGCAAGTATGgtaggattcttgtttttgcatttggtgtctactcgtgttaccctttattttattttttcttatgtcttcaaggacag

upper sequence: LOC_Os11g36440.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0032g00800.t01 (Vitis vinifera), 5'ss of exon 5
TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaatgcatgactctcagaattttgcttctgattcatttaaatttctgttatctcaagggtgaaataacag
|| ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| |||||||||||     |   || || |     | |   || | |||  ||    || |||  ||||      |   |      
TGTTTTATAGTGAGCACAGTTAATGCTTTGCAGACACCAATGATCAATGCGAGCATGgtaagcttt-taattgccttttgttctctctatttttatttcttagctttcctgaaatcttgtttcttccag-----

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|58668037|gb|CK056723.1|CK056723
EST:     TTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATG                         GTCTTGTGCGATAGGCACTTCGGGGGAATTAACTATCCAGTTGGTGGTGTT
genomic: TTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaa ... gaaataacagGTCTTGTGCGATAGGCACTTCGGGGGAATTAACTATCCAGTTGGTGGTGTT




















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: 60 (upstream exon), 49 (downstream exon)
Score: 12

TGCTTTATTGTGAGCACAGTCAATGCCTTGCAAACACCCATGATTAATGCAAGCATGgtaagtggaa ... gaaataacagGTCTTGTGCGATAGGCACTTCGGGGGAATTAACTATCCAGTTGGTGGTGTTGGTGGTATTGCTATGTCCTTGGCAGATGGGCTTGTTGACAAAGGCAGTG




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