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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatcatgagccttgcgacacctgtctttgtttaatggagtatcgttatttcctttcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC

Basic information

species Oryza sativa
transcript LOC_Os06g46310.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G069198_T04 (Zea mays), 3'ss of exon 5
-----------------gtcagtatcatgagccttgcgacacctgtctttgtttaatgg-agtatcgttatttcctt-tcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC
                 || | | |  ||   | | | |  | |  || ||   | ||  | ||     |   |     |   ||  || |||||||  || || ||  |  ||  | | | |||||| || || || ||||||||||| ||||| ||||| ||||  ||||||||  | |||||||||||||| ||||| ||||| |||||||| ||||||||
gttggtattttatgtttgttaatttattgcatccttcaatccttccctgtgagcattgctaatacaacaacaacaaagccttgtgagcattgctaatagtttgtgaaattcctctgtgt-acagGGAAACATCTTGCAGAGCATTGCAGGGCTGAGTATCCCAAGGTCACAAATTTTGTCTTATGGATTCTTGCAGAACTTGCTGTTGTTGCATGTGACATTCC

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 5
gtcagtatcatgagccttgcgacacctgtctttgtttaatggagtatcgttatttcctttcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC
                 || ||   || | |     || |    | |   ||| | ||  ||  |      | || |||   |     | || |  ||    |||| |||||  | || ||||| ||||||  ||||||||||||||   | || |||||  ||||| ||||||| ||| | |||||||||||||| ||||||||
--------------gtatgtgatttctttatccagctattttcat-tgaatatcttctcccaatttattgatcctcatctccaacgttgtttcttaat--tgtagGAAAGCATTTAGCAGAGCACTGCAGAATTGAATATCCAAAGGTGCCTAACTTCATCCTATGGGTTCTTGCTGAAATTGCTGTAGTTGCATGTGACATTCC
















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|33653430|gb|CF276044.1|CF276044
EST:     TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTG                         GGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATT
genomic: TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATT
EST: gi|88692251|gb|CI735826.1|CI735826
EST:     TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTG                         GGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATC
genomic: TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATC
EST: gi|44677020|gb|CR290454.1|CR290454
EST:     TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCCAGACTG                         GGAAGCACCTGACCGAGCATTGCAGAGC
genomic: TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcctttcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC
                     tgctaat  putative branch site (score: 2)
                                       cttttccat  putative PPT
                        taatcattagttaa  TA-rich tract