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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_Os06g47350.1
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|29656148|gb|CB652423.1|CB652423
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29636778|gb|CB641787.1|CB641787
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29676742|gb|CB673017.1|CB673017
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|29678964|gb|CB675239.1|CB675239
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29624118|gb|CB629129.1|CB629129
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
EST: gi|29685786|gb|CB682061.1|CB682061
EST:     ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTG                         GCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC
genomic: ACTTGAACAGCGATACAAGGGATGCTCTTTTGTCATTAATCACCAGATTGgtattatttt ... taccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgccctggatgatctgtatataagcttctgatcaatcgatttaccatccagGCTGCAGTGGCAGATCAGTTCTTAAGAGAGTGTTTGCAGATGCTTGTGAACAACTTCACTCCACCTGGATCACTTACTGCTTTCATCGGCCAACCGAGAT
                             ttctgat  putative branch site (score: 3)
                  tgtatataa  TA-rich tract