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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattttctacaaccacatgcacattgccctggatgatctgtatataagcttctgatcaatcgatttaccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAACAACTTCACTCCACCTGGATCACTTACTGCTTTCATCGGCCAACCGAGAT

Basic information

species Oryza sativa
transcript LOC_Os06g47350.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G415846_T01 (Zea mays), 3'ss of exon 4
gtattattttctacaaccacatgcacattgccctggatg-atctgtatataagcttctgatcaatcgatttaccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAACAACTTCACTCCACCTGGATCACTTACTGCTTTCATCGGCCAACCGAGAT
||||  ||    |     | || || | |   |||  |  || | | | | || |||||||  |||  | |  | |  ||||||| |||||||| || |   | ||||| |||||||||||||||||||| || ||||||||||||||| | || | |  || ||| |   | || || |
gtatacttcctcagttgtatatccagagttttctgcttttatgtttgtttgagtttctgatggatctgtgt-tcgtgtagGCTGCTGTGGCAGACCAATATCTCAGAGAATGTTTGCAGATGCTTGTGAATAATTTCACTCCACCTGGACCCCTCATTCGTTACATTGAGGAGCCAAGGT
















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|29681086|gb|CB677361.1|CB677361
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29685786|gb|CB682061.1|CB682061
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29624118|gb|CB629129.1|CB629129
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29636778|gb|CB641787.1|CB641787
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|58598402|gb|CK008930.1|CK008930
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTATGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29676281|gb|CB672556.1|CB672556
EST:     CTTGAACCGCGATACAAGGGATGCTCTTTTGTCATTAATCACCCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAA
genomic: CTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACC-AGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAA
EST: gi|29676742|gb|CB673017.1|CB673017
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC

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: 74 (upstream exon), 75 (downstream exon)
Score: 92

ATATTTACGATGTCTATCTGGTACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAACAACTTCACTCCACCTGGATCACTTACTGCTTTCATCGGCCAACCGAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgccctggatgatctgtatataagcttctgatcaatcgatttaccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAACAACTTCACTCCACCTGGATCACTTACTGCTTTCATCGGCCAACCGAGAT
                             ttctgat  putative branch site (score: 92)
                  tgtatataa  TA-rich tract