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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtgatttcccctgctcttgcataatgcatttagcctatttggtcttcatctgcaagtcttatgttctgtcgttgtaataatttgatttcttttgcagACGGTCTTTATAACTTTGAATGGATCTTGGAAACTTGGTGGGTTTGGTTTTGCTCTTTCTGTTGACCAAGCCACAGGCAGTTTGACATCAACACAGCAAT

Basic information

species Oryza sativa
transcript LOC_Os01g42950.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 2
--tctgtgatttcccctgctcttgcataatgcatttagcctatttggtcttcatctgcaagtcttatgttctgtcgttgtaataatttgatttcttttgcagACGGTCTTTATAACTTTGAATGGATCTTGGAAACTTGGTGGGTTTGGTTTTGCTCTTTCTGTTGACCAAGCCACAGGCAGTTTGACATCAACACAGCAAT
  ||||     | ||       |   | |||    | || | ||       ||||    |||  ||   |       |||| ||||   |||||||||| ||||||||||||||||||  || ||||||||||| |||||||||||||||||||||||||| ||||| |||||||||||  ||||||| ||| |||||| ||
aatctgcagaatacctaatgaat--ttgatgttacttgcttgttattatgccatcattgagttctacactagtgtactgtattaatcatatttcttttgtagACGGTCTTTATAACTTCTAACGGATCTTGGAAGCTTGGTGGGTTTGGTTTTGCTCTTTCAGTTGATCAAGCCACAGGTGGTTTGACTTCATCACAGCTAT
















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|58653744|gb|CK042424.1|CK042424
EST:     CTTCATAACAATGCCCATCTTGCCCATCGAGCTATATCACCCGAG                         ACGGTCTTTATAACTTCGAATGGATCTTGGAAACTTGGTGGGTTTGGTTTT
genomic: CTTCATAACAATGCCCATCTTGCCCATCGAGCTATATCACCCGAGgttgaatgca ... tcttttgcagACGGTCTTTATAACTTTGAATGGATCTTGGAAACTTGGTGGGTTTGGTTTT
EST: gi|33678979|gb|CF307218.1|CF307218
EST:     ACTTTCTTCATAACAATGCCCATCTTGCCCATCGAGCTATATCACCCGAG                         ACGGTCTTTATAACTTTGAATGGATCTTGGAAACT
genomic: ACTTTCTTCATAACAATGCCCATCTTGCCCATCGAGCTATATCACCCGAGgttgaatgca ... tcttttgcagACGGTCTTTATAACTTTGAATGGATCTTGGAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcatctgcaagtcttatgttctgtcgttgtaataatttgatttcttttgcagACGGTCTTTATAACTTTGAATGGATCTTGGAAACTTGGTGGGTTTGGTTTTGCTCTTTCTGTTGACCAAGCCACAGGCAGTTTGACATCAACACAGCAAT
                                     atttgat  putative branch site (score: 5)
                                           tttcttttgc  CT-rich tract
                             ttgtaataatttgatt  TA-rich tract