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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT

Basic information

species Oryza sativa
transcript LOC_Os04g52370.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 5
gtaatgtcttttaacc-acaattttactctcttttttaatttcgt------ttcacatctttaccct--gaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT
|||||   ||  ||||    || ||    |  ||| | |  || |      |||| ||  | || ||   ||| |   ||||||||||||| || | |||||| || |  || || |||||||||||||| ||||||||||| ||||    |||||||||||||||||||| ||||| |||||||||| |
gtaatagtttcaaacctgtcatcttctagttatttattacctcttcttctcttcagattatcacactcaaaaaatgttaataacttgcagGCCCGAGTAACACTGTGCTGATCCACTGGTATATAATGACAAGCCCCTTCACAGATGCTTCCACTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCT

upper sequence: LOC_Os04g52370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT
|||| ||  ||   |    ||| |  |   | |||  ||||| ||| ||||  |  || |   |||| |  | |||||||||  ||  |      || || ||||||||||| || ||||| || || || || |||||  |||| |||||||| || ||||||| ||||||||||||| |
gtaaggttattctgc----attctgtt---tgtttgtatttcatttgacatgctgcccttattatttta--ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT
















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|58674987|gb|CK063674.1|CK063674
EST:     AGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATA                         GTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCA
genomic: AGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATAgtaatgtctt ... taacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCA
EST: gi|396941374|gb|HO188583.1|HO188583
EST:     AGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATA                         GTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCA
genomic: AGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATAgtaatgtctt ... taacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT
                                          aaataac  putative branch site (score: 2)
                                   aaatttgaaataactt  TA-rich tract