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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgacagaattatcatttttaggcttgtcaaaagtaagaaatgtgatcattttgtgtgttgactgatctattttcctttcgcagTGATCTTGGAAATGCACAACTGTCAGGTGCATTGGTTCCCCAGCTTGGGCAGTTGAAAAATCTGCAATATCT

Basic information

species Oryza sativa
transcript LOC_Os04g38480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G870959_T01 (Zea mays), 3'ss of exon 2
gtaagtttttgacagaattatcatttttaggcttgtcaaaagtaagaaatgtgatcattttgtgtgttgactgatctattttcctttcgc-agTGATCTTGGAAATGCACAACTGTCAGGTGCATTGGTTCCCCAGCTTGGGCAGTTGAAAAATCTGCAATATCT
|||||||   ||   ||| ||| | || |  ||       ||    ||   ||| ||||| |  | |||     ||| ||| ||||| || ||||||||||||||||||||||| |||||| ||||||| || ||||||||||| ||||||||| ||||||||||
gtaagtt---gatcaaat-atcttgttcattctcccttggaggtgaaagactgaccattt-gaatattg-----tctgtttcccttttgctagTGATCTTGGAAATGCACAACTATCAGGTCCATTGGTGCCACAGCTTGGGCAATTGAAAAATATGCAATATCT
















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|44670533|gb|CR283967.1|CR283967
EST:     TGCACATGGTTCCATGTAACTTGTAACCCTGACAACAGCGTGATCAGAGT                         TGATCTTGGAAATGCACAACTGTCAGGGGCATTGGTTCCCCAGCTTGGGCA
genomic: TGCACATGGTTCCATGTAACTTGTAACCCTGACAACAGCGTGATCAGAGTgtaagttttt ... cctttcgcagTGATCTTGGAAATGCACAACTGTCAGGTGCATTGGTTCCCCAGCTTGGGCA
EST: gi|58588679|gb|CF986987.1|CF986987
EST:     TGCACATGGTTCCATGTAACTTGTAACCCTGACAACAGCGTGATCAGAGT                         TGATCTTGGAAATGCGCAACTGTCAGGGGCATTGGTTCCCCAGCTTGGGCA
genomic: TGCACATGGTTCCATGTAACTTGTAACCCTGACAACAGCGTGATCAGAGTgtaagttttt ... cctttcgcagTGATCTTGGAAATGCACAACTGTCAGGTGCATTGGTTCCCCAGCTTGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagtaagaaatgtgatcattttgtgtgttgactgatctattttcctttcgcagTGATCTTGGAAATGCACAACTGTCAGGTGCATTGGTTCCCCAGCTTGGGCAGTTGAAAAATCTGCAATATCT
                               gactgat  putative branch site (score: 3)
                                     tctattttcctttcgc  CT-rich tract
                                    atctatttt  TA-rich tract