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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcctatgaacatctctatggttgctagtgttccttattgctcggattgaaacctcttaatttttctttgcatcctgtcagAGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAGTTGAATCAAACTATGGCAATCATGCCAATGACATCAAGTGGTCCAGTACC

Basic information

species Oryza sativa
transcript LOC_Os12g13170.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13170.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 8
gtgtgcctatgaacatctcta--tggttgctagtgttccttattgctcggattgaaacctcttaatttttctttgcatcctgtcagAGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAGTTGAATCAAACTATGGCAATCATGCCAATGACATCAAGTGGTCCAGTACC
|| ||  | || |||| || |  ||| | ||  | || | | || || | | |  | | | ||      | ||||||| |  | ||| ||||||||||||| |||||||||||||||||  | |||  ||| ||| ||||| ||| ||||||||||| |||| ||  |||||||||| |||| | |
gtatgtatgtggacatatcaacttggcttcttcttttgcatttttct-gaactttatcattttgggccat-tttgcattcaattagATGTTCGAAGTTCCCGGAATGGTGTATCACGTTTGCAATCTGAGGGAAAATTGAACCAAGCTATGGCAATCTTGCCCATACCATCAAGTGGCCCAGCAAC

upper sequence: LOC_Os12g13170.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G074373_T01 (Zea mays), 3'ss of exon 9
gtgtgcctatgaacatctctat--ggttgctagtgttccttattgctcggattgaaacctcttaatttttctttgcatcctgtcagAGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAGTTGAATCAAACTATGGCAATCATGCCAATGACATCAAGTGGTCCAGTACC
|| ||  |||| |||| ||||   || | ||  | || | | || || | | |  | | | ||  |     |||||||    | ||| || ||||||||||||||||||| ||||||||| |||||  ||| ||| || || ||| |||||||||||||||| ||| |||||||||| |||||| |
gtatgtgtatggacatatctactaggcttcttcttttgcatttttct-gaactttatcatgtttgtgccaatttgcata--attagACGTACGAAGTTCCCAGAATGGTGCATCACGTTCTCCATCTGAGGGAAAATTTAACCAAGCTATGGCAATCATGCCCATGCCATCAAGTGGCCCAGTAAC
















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|33796386|gb|CF324060.1|CF324060
EST:     GATTCACATCACAAGGAAAGTGGACAAGAGCAAGATGGAG                         AGGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAG
genomic: GATTCACATCACAAGGAAAGTGGACAAGAGCAAGATGGAGgtgtgcctat ... atcctgtcagAGG-TTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAG
EST: gi|86879567|gb|CI327191.1|CI327191
EST:     GATTCACATCACAAGGAAAGTGGACAAGAGCAAGATGGAG                         AGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAGT
genomic: GATTCACATCACAAGGAAAGTGGACAAGAGCAAGATGGAGgtgtgcctat ... atcctgtcagAGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgttccttattgctcggattgaaacctcttaatttttctttgcatcctgtcagAGGTTCGAAGTTCCCAGAATGGTGTATCACGTTCACCATCCCAGGCAAAGTTGAATCAAACTATGGCAATCATGCCAATGACATCAAGTGGTCCAGTACC
                            tcttaat  putative branch site (score: 3)
                                  tttttctttgcatcct  CT-rich tract
                            tcttaatttttcttt  TA-rich tract