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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttttctccagttgtgttgatactttctggaagaacctgaattttctctgtttcttcatatcacttatgttttccttcttatgcctacacggctacacctggtagcatttactcttttattctttgttactcaaatttatttggtgacaatctttcttaatgaatgaattttgtttttagGCTTGTGTCTACAAATGTTCGACAATGATCTTTCACTGGGCAATATCGTTGTCACATTCAACTTAGGGAAACCACAGATTGAGAACAAATG

Basic information

species Oryza sativa
transcript LOC_Os10g10170.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g10170.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G018929_T02 (Zea mays), 3'ss of exon 6
gtaagttttttctccagttgtgttgatactttctggaagaacctgaattttctctgtttcttcatatcacttatgttttccttcttatgcctacacggctacacctggtagcatttactcttttattctttgttactcaaatttatttggtgacaatctttcttaatga-atgaattttgtttttagGCTTGTGTCTACAAATGTTCGACAATGATCTTTCACTGGGCAATATCGTTGTCACATTCAACTTAGGGAAACCACAGATTGAGAACAAATG
                                                                               ||  |||| |    |  || |   | |      |||     ||  | |  | ||   |      | |||| |||||||  ||| || ||| ||||   |||| || ||| ||||| || ||||||||| ||| |||| |||| || || |||||  ||||||  |||| || |||||||||||||||||| ||||||||
-------------------------------------------------------------------------------ccgccttaagaac-cttggttctgctt--ctatattggaaattgaactagtcgtcttttgg---tctttgatgacaatgcttcctactgacatga--cttgtcttcagGTTTGTGCCTTCAAATGTTCAACATTGATTTTTCGCTTGGGAATATTATTGTCAACTTCAGCTCAGGGAAACCACAGATTGACAACAAATG
















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|58691402|gb|CK080089.1|CK080089
EST:     AAAAATAGACAGTATTGACCTCAATCCCACAATCGTTGGTTGTCTTACTG                         GCTTGTGTCTACAAATGTTCGACAATGATCTTTCACTGGGCAATATCGTTG
genomic: AAAAATAGACAGTATTGACCTCAATCCCACAATCGTTGGTTGTCTTACTGgtaagttttt ... ttgtttttagGCTTGTGTCTACAAATGTTCGACAATGATCTTTCACTGGGCAATATCGTTG
EST: gi|58695106|gb|CK083793.1|CK083793
EST:     AAAAATAGACAGTATTGACCTCAATCCCACAATCGTTGGTTGTCTTACTG                         GCTTGTGTCTACAAATGTTCGACAATGATCT
genomic: AAAAATAGACAGTATTGACCTCAATCCCACAATCGTTGGTTGTCTTACTGgtaagttttt ... ttgtttttagGCTTGTGTCTACAAATGTTCGACAATGATCT
EST: gi|88405888|gb|CI591283.1|CI591283
EST:     AAAAATAGACAGTATTGACCTCAATCCCACAATCGTTGGTTGTCTTACTG                         GCTTGTGTCTACAAATGTTCGACAATGATCTTTCACTGGGCAATATCGTTG
genomic: AAAAATAGACAGTATTGACCTCAATCCCACAATCGTTGGTTGTCTTACTGgtaagttttt ... ttgtttttagGCTTGTGTCTACAAATGTTCGACAATGATCTTTCACTGGGCAATATCGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactcaaatttatttggtgacaatctttcttaatgaatgaattttgtttttagGCTTGTGTCTACAAATGTTCGACAATGATCTTTCACTGGGCAATATCGTTGTCACATTCAACTTAGGGAAACCACAGATTGAGAACAAATG
                             tcttaat  putative branch site (score: 3)
                                           ttttgttttt  putative PPT
                           tttcttaatgaatgaa  TA-rich tract