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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgttttcctctttaaattttacctggcatgttcttttgtgctcatctctctcactcgtacattccatcacag

Basic information

species Oryza sativa
transcript LOC_Os11g42790.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G037342_T02 (Zea mays), 5'ss of exon 3
GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgttttcct--ctttaaattttacctggc-atgttcttttgtgctcatctctctcactcgtacattccatcacag---
||||||||| ||||||||||| || || || |||||||| ||||||||  ||||||||||  |||| ||| | |||||||| | |||||| ||||| |||| |||   | ||    || |  ||| || ||   || | ||| || | |  |  ||  |   |  |||||  ||| ||    
GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcggtcccaaatttcacttttaacatgattatatgcttctgggtttcttcctgcctaactcacatttgatctcaatag

upper sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 4
GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgttttcct--ctttaaattttacctggc-atgttcttttgtgctcatctctctcactcgtacattccatcacag---
||||||||| ||||||||||| || || || |||||||| ||||||||  ||||||||||  |||| ||| | |||||||| | |||||| ||||| |||| |||   | ||    || |  ||| || ||   || | ||| ||   |  |  ||  |   |  |||||  ||| ||    
GTTCCAAGTGAAGAAGAAACAGTTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTGTAATATCCCTTGgtaggttcggtcccaaatttcacttttaacatgattatatgcttctggatttctgcctgcctaactcacatttgatctcaatag

upper sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G070594_T01 (Zea mays), 5'ss of exon 1
--GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagtt--gttttcctctttaaattttacctggc-atgttcttttgtgctcatctctctcactcgtacattccatcacag---
  ||||||||| |||||||||||||| || || |||||||| ||||||||  ||||||||||  |||| ||| | |||||||| | | |||| ||||| |||| |||  ||  |    || |  ||| || ||   || | ||| ||   |  |  ||  |   |  |||||  ||| ||    
AGGTTCCAAGTGAAGAAGAAACAATTCTTTCGAAACTTCATTACTATTACACTGTTTGGTGCAGTTGGCACCTTGATCTCTTTTACTCTAATATCCCTTGgtaggttcggtcctaaatttcacttttaacatgattatatgcttctggatttctgcctgcctaactcacatttgatctcaatag

upper sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G02560.1 (Glycine max), 5'ss of exon 3
GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaa-----gttgtt---------ttcctctttaaatt---ttacctggca--------tgttcttttgtgctcatctctctcactcgtacattccatcacag--------------------
||| || || ||||||||||||||||||||||| || |||||||| | | | ||||||||  |||| ||  | || || ||| |  |||| || || |||||     ||  |          ||| | | ||||||   ||||   | |        |  | ||| ||  |||   |  |         |||  || | |                     
GTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATAATATCACTAGgtaattgaagtcatcaattaatgcttcttttataaattacattacaaagtagtaacaatttgtatttggtattcagtgcctttgtgtcccaatttgattataaatcttatttattttgaatag

upper sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G38160.1 (Glycine max), 5'ss of exon 3
GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgttttcctctttaaattttacctggcatgttcttttgtg------------ctcatctctctcactc-gtacattccatcacag-------------------------------
||| || || ||||||||||||||||||||||| || |||||||| | | | ||||||||  |||| ||  | || || ||| |  | || || || ||||| |    |      ||||   ||   |   |  ||    |                |||| | |   | || || | ||   |  ||                                
GTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAGgtaattgaagtcttcaattaatgcttcttttataaattaaaatacaaagtagtaacaattcatatttggtagtcagtgctttgtgtttcaatttgtttataaatcttatttattttgattag

upper sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgttttcctct-ttaaattttacctggcatgttcttttgtgctcatctctctcactcgtacattccatcacag---------------
||| || ||||||||||| |||||||| |||||||||||||| |||| ||| |||||||| ||||| || || || || ||   | | || ||  | |||||         |||  | || |   || |  ||   || |  || ||||| | | |   |  |   | |  |                    
GTTTCAGGTTAAGAAGAAGCAATTTTTTCGCAACTTCATGACCATTATGTTATTTGGTGCTATTGGAACTCTCATTTCATTTGTTATCATCTCATTTGgtaaaaaaccaatctcaatcaactcccacatttcaatatcatgagt-ctcatatattttgatgatgtttccggttttgtttttgttatggctag

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|88851589|gb|CI671029.1|CI671029
EST:     GTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCG                         GTTCTCTAGGAC
genomic: GTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgtt ... tccatcacagGTTCTCTAGGAC
EST: gi|29631041|gb|CB636050.1|CB636050
EST:     GTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCG                         GTTCTCTAGGACTAATATCAAGGCTGAACATAGGTTCCCTTGATCTTGGAG
genomic: GTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgtt ... tccatcacagGTTCTCTAGGACTAATATCAAGGCTGAACATAGGTTCCCTTGATCTTGGAG
EST: gi|88431579|gb|CI576770.1|CI576770
EST:     GTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCG                         GTTCTCTAGGACTAATATCAAGGCTGAACATAGGTTCCCTTGATCTTGGAG
genomic: GTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgtt ... tccatcacagGTTCTCTAGGACTAATATCAAGGCTGAACATAGGTTCCCTTGATCTTGGAG

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: 63 (upstream exon), 69 (downstream exon)
Score: 11

GTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCGgtaagttgtt ... tccatcacagGTTCTCTAGGACTAATATCAAGGCTGAACATAGGTTCCCTTGATCTTGGAGATTATCTTG




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