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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattgtgtctaagttcaagtgttcaactgctgtaaaatatgaagtcttgttacttttacattacaatttgtctcactcactcttttggtttacctgcagGACGTATCACACCTGAGAGTGTCATTTACAGCTTTGGTACCTTGCTTTTGGATGTTCTTAGTGGGAAGCATATTCCTCCTAGCCAT

Basic information

species Oryza sativa
transcript LOC_Os04g58750.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58750.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 6
caattgtgtctaagttcaagtgttcaactgctgtaaaatatgaagtcttgttacttttacattacaatttgtctcactcac-------tcttttggtttacctgcagGACGTATCACACCTGAGAGTGTCATTTACAGCTTTGGTACCTTGCTTTTGGATGTTCTTAGTGGGAAGCATATTCCTCCTAGCCAT
  ||| |||   || |    ||| |||   |  || | |||    |  | |||   | | | | |      || || ||         ||||||| ||||| |||||||||||| || ||||| |||||||| ||||||||||| ||||||||  | ||||||||||||||||||||||||||||| ||||||
-tattttgttatagat----tgtacaagatcattagattatct--ttgtattaacatcaaagttctcaacatcgcattcctgcaaatgtcttttgttttacatgcagGACGTATTACTCCTGAAAGTGTCATATACAGCTTTGGAACCTTGCTGATTGATGTTCTTAGTGGGAAGCATATTCCTCCGAGCCAT
















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|33675914|gb|CF304153.1|CF304153
EST:     AAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGAGAACTG                         GACGTATCACACCTG
genomic: AAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGAGAACTGgttggtacct ... ttacctgcagGACGTATCACACCTG
EST: gi|29624788|gb|CB629799.1|CB629799
EST:     AAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGAGAACTG                         GACGTATCACACCTGAGAGTGTCATTTACAGCTTTGGTACCTTGCTTTTGG
genomic: AAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGAGAACTGgttggtacct ... ttacctgcagGACGTATCACACCTGAGAGTGTCATTTACAGCTTTGGTACCTTGCTTTTGG
EST: gi|58603429|gb|CK013957.1|CK013957
EST:     TTACTCCTCCAGAGTACATGAGAACTG                         GACGTATCACACCTGAGAGTGTCATTTACAGCGTTTGGTACCTTGCTTTTG
genomic: TTACTCCTCCAGAGTACATGAGAACTGgttggtacct ... ttacctgcagGACGTATCACACCTGAGAGTGTCATTTACAGC-TTTGGTACCTTGCTTTTG
EST: gi|58656214|gb|CK044894.1|CK044894
EST:     AAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGAGAACTG                         GACGTATCACACCTGAGAGTGTCATTTACAGCTTTGGTACCTTGCTTTTGG
genomic: AAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGAGAACTGgttggtacct ... ttacctgcagGACGTATCACACCTGAGAGTGTCATTTACAGCTTTGGTACCTTGCTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgttacttttacattacaatttgtctcactcactcttttggtttacctgcagGACGTATCACACCTGAGAGTGTCATTTACAGCTTTGGTACCTTGCTTTTGGATGTTCTTAGTGGGAAGCATATTCCTCCTAGCCAT
                             cactcac  putative branch site (score: 2)
                                            tttacct  putative PPT
         ttttacattacaattt  TA-rich tract