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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccatcaaatcatcaattgccacttaactgaaaatgcttatctgcattttctgttgcctgttcttgtgcttagaatgttattattctagatattcactaaaattgagcacatttgcttttctttccccacagGACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAACGTTGACCTATCTTTAACAAATGATGATCTACATAAGATCTTTGGTGACT

Basic information

species Oryza sativa
transcript LOC_Os02g31290.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtaaccatcaaatcatca-att--gccacttaactgaaaatgcttatc-----tgcattttctgttgcctgttcttgtgcttagaatgttattattctagatattcac-taaaattgagcacatt--tgcttttctttcccca---------cagGACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAACGTTGACCTATCTTTAACAAATGATGATCTACATAAGATCTTTGGTGACT
                                          |     |  | | |||| |||  |    ||   | |  ||  | ||      ||| ||   || |   ||   ||||| |||   ||  ||  ||||  || |  |  | |   |  |    ||  || | || ||  | |           ||||||||||||||||||||||||| |||||||| ||  ||||  | |||||| ||||   |||| |  | ||||||||||| | | | || |||||    |
gtatgttgagcatgttcaaaaaatcttgctgcacacatgatattgttttacagttatcatattcagtgttttgtgttagcattatcattgacaatgctttggatgctatttgggtttgtgttta--ttgaaatggttctgcatgtcaaggtgatgctttgttgtttgatgttctttttaactcggtgttatgttagGACAATCCTTCGGAGAAAGATATCAACCAGGGTACCCTTGTGGTATTTAACCTTGATTCATCTGTTTCCAATGATGATCTTCGTCAAATTTTTGGCATTT
















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|29628170|gb|CB633181.1|CB633181
EST:     ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAG                         GACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
genomic: ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAGgtaaccatca ... ttccccacagGACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
EST: gi|29644611|gb|CB649618.1|CB649618
EST:     ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAG                         GACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
genomic: ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAGgtaaccatca ... ttccccacagGACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
EST: gi|29628253|gb|CB633264.1|CB633264
EST:     ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAG                         GACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
genomic: ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAGgtaaccatca ... ttccccacagGACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
EST: gi|29629461|gb|CB634470.1|CB634470
EST:     ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAG                         GACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
genomic: ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAGgtaaccatca ... ttccccacagGACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAAC
EST: gi|58605539|gb|CK033572.1|CK033572
EST:     ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAG                         GACAATCCTTCGGAGAAAGATATTAACCAGGGAGGCTATTGTACTTTTTAA
genomic: ACAAGGCACTGAGGCGTAGGAAACTTGACATACATTATTCCATTCCGAAGgtaaccatca ... ttccccacagGACAATCCTTCGGAGAAAGATATTAACCAGGGAA-CTATTGTACTTTTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattattctagatattcactaaaattgagcacatttgcttttctttccccacagGACAATCCTTCGGAGAAAGATATTAACCAGGGAACTATTGTACTTTTTAACGTTGACCTATCTTTAACAAATGATGATCTACATAAGATCTTTGGTGACT
                 cactaaa  putative branch site (score: 2)
                              cacatttgcttttctt  putative PPT
            atattcactaaaatt  TA-rich tract