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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggctttcagtttcagagtttctgttcaatcttgctgtttttgacatttatgttatagattttgtattttccttgcagGTTGTTCAGAAAGCACTTGATGATGCAAATGTGTCAGAAAATGATCTTTCAGCAGTGGCTGTCACCGTAGGACCAGGACTTAGTTTATGCCTCAGAG

Basic information

species Oryza sativa
transcript LOC_Os12g29990.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g29990.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G130605_T01 (Zea mays), 3'ss of exon 3
gtttggctttcagtttcag---agtttctgttcaatcttgctgtttttgacatttatgttatagat---tttgtattttccttgcagGTTGTTCAGAAAGCACTTGATGATGCAAATGTGTCAGAAAATGATCTTTCAGCAGTGGCTGTCACCGTAGGACCAGGACTTAGTTTATGCCTCAGAG
|| || |||   |  |||    ||  ||||     | |||| ||  | ||||| |||| ||        ||  ||||| |  | ||||||||||| || || ||||| ||||||||  ||||||||| ||||||||| ||||| ||||| ||| | ||||||||||||||| ||||||| ||||
gtgtgacttcttggatcaacatagggtctgcatccttttgcggtgct-gacatatatgctaattgcctgttcttatttgctatccagGTTGTTCAAAAGGCTCTTGACGATGCAAAATTGTCAGAAAGTGATCTTTCTGCAGTCGCTGTGACCATTGGACCAGGACTTAGTCTATGCCTTAGAG
















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|58678884|gb|CK067571.1|CK067571
EST:     GCGTCGCTCCGAAGATGGCCGAGGAAGCTCATTCTCTTGCGATTGATCAG                         GTTGTTCAGAAAGCACTTGATGATGCAAATGTGTCAGAAAATGATCTTTCA
genomic: GCGTCGCTCCGAAGATGGCCGAGGAAGCTCATTCTCTTGCGATTGATCAGgtttggcttt ... ttccttgcagGTTGTTCAGAAAGCACTTGATGATGCAAATGTGTCAGAAAATGATCTTTCA
EST: gi|29616287|gb|CB621299.1|CB621299
EST:     GCGTCGCTCCGAAGATGGCCGAGGAAGCTCATTCTCTTGCGATTGATCAG                         GTTGTTCAGAAAGCACTTGATGATGCAAATGTGTCAGAAAATGATCTTTCA
genomic: GCGTCGCTCCGAAGATGGCCGAGGAAGCTCATTCTCTTGCGATTGATCAGgtttggcttt ... ttccttgcagGTTGTTCAGAAAGCACTTGATGATGCAAATGTGTCAGAAAATGATCTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcaatcttgctgtttttgacatttatgttatagattttgtattttccttgcagGTTGTTCAGAAAGCACTTGATGATGCAAATGTGTCAGAAAATGATCTTTCAGCAGTGGCTGTCACCGTAGGACCAGGACTTAGTTTATGCCTCAGAG
               ttttgac  putative branch site (score: 3)
                                    ttttgtattttcctt  putative PPT
                    acatttatgttataga  TA-rich tract