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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaagcaaacacttcatcttgttctgtaatgctatgtgggaaggagtggtgatgctgaatgctagcctgatttttctttttgcttctattgctgcatattatttgtagGATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTGTTCGTCAAGTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g57330.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57330.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G471805_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------gtaagagaagcaaacacttcatc----------ttgttctgtaatgctatgtgggaaggagtggtgatgctgaatgctagcctgatttttctttttgcttctattgctgcatattatttgtagGATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTGTTCGTCAAGTTCTTG
                                                                    | || ||||  | ||  | ||||          |     |    | || | |  |  | ||| | ||  || |||| | |  |||| |   ||| |  | |   ||           |   ||||||| ||||| |||||||| || |||||||||||||||||||| |||||||| ||||||||||||
gtgaggagaagtggagaactggagtagcaccagatgaatctcgcttcttaaagagattttgcatttaagaaaaagaattagactttgcatcagaaggcggatcaacttcatcttcttttttagctgtagttgcgaaacttaatggtggg-tgatctgaatttcttttgcctctggc--------ctgacagGATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTG

upper sequence: LOC_Os02g57330.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G013981_T03 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------gtaagagaagcaaacacttcatcttgttctgtaatgctatgtgggaaggagtggtgatgctgaatgctagcctgatttttctttttgcttctattgctgcatattatttgtagGATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTGTTCGTCAAGTTCTTG
                                                                          |  ||  || |      ||| |||  |||      ||||    |  | || ||  || || |||| | |  |||| |   ||||  ||| | || |||      | ||  ||||||| ||||| |||||||  || |||||||||||||||||||| |||||||| |||||||| |||
gtgacgagaactagagtagcaagatgaatcttgcctcttaaaaaaagtttcttttaagaaaaaataattgggctttggattaggaggtggatcaacttcatctt-----ctattcaagctgtagcggccatacttaatggtggg-tgatctgaatttt--cttttgtttctgg-----aattacagGATCCAAACTCCAAGCACCATGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTTTTG
















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|27576395|gb|CA999089.1|CA999089
EST:     CGTCCGCGATTTCGCTGGAGTTGCTGGGCCATCGGCTGCACATTTCTCAG                         GATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTG
genomic: CGTCCGCGATTTCGCTGGAGTTGCTGGGCCATCGGCTGCACATTTCTCAGgtaagagaag ... ttatttgtagGATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgaatgctagcctgatttttctttttgcttctattgctgcatattatttgtagGATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTGTTCGTCAAGTTCTTG
           gcctgat  putative branch site (score: 4)
              tgatttttcttttt  TA-rich tract