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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccgcctttatctagttctctttttcgtcaagctattttctttttgacatcttgatcagatttcttatgcttgttctgtttgtatatgtattctctgcagTGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g40620.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 5
gccgcctttatctagttctctttttcgtcaagctattttctttttgacatcttgatcagatttcttatgcttgttctgtttgtatatgt---attctctgcagTGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAG
   |  ||  |  |  |      |     ||   ||   | ||   |  |  ||||| | |   ||||| || |  | ||||||    |   ||| | |||||  ||||| ||||| |||||||||||||||||||||||||| ||||| ||||| ||||||
--agtgttggtacaccttgtcactggtctaaagcatccaccttaccat-tgctgatcggctagtttatgtttctaatatttgtaaccatcttattatatgcagCACCAACCATAATCATTGCACATGAATTCTATGATGCCTTACCAATCCATCAGTTTCAG

upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G498418_T01 (Zea mays), 3'ss of exon 3
gccgcctttatctagttctctttttcgtcaagctattttctttttgac-atcttgatcagatttcttatgcttgttctgtttgtatatgtattctctgcagTGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAG
   ||||||    |  | | ||| |  |||| ||  ||  |    |   |    |    |   | ||||| || |  | ||||||  | | || | ||||| |||||| ||||| || || |||||||||||||||||||| ||||| ||||| ||||||
-ttgccttttgtcaactttgtttcttttcaatcttcttgatggggggggaggggggggggggcttttatgtttctcatatttgtaactatcttatgtgcagCGCCAACCATAATCATAGCGCATGAATTCTATGATGCCTTACCAATCCATCAGTTTCAG

upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0066g02600.t01 (Vitis vinifera), 3'ss of exon 5
gccgcctttatctagttctctttttcg--tcaagctatttt---ctttttgacatcttgatcagatttcttatg-cttgttctgtttgtatatgtattctctgcagTGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAG
        |||  || | |  |||  |  ||| |   ||     | | ||     ||||| |     | || |  |||    ||  | | | ||   | | | |||||||||| || |||||||| ||||| || ||||||||  | ||| ||||||||||||||
-------gtatggagatattctttctgagtcatgtccttacaaacctcttatgtgcttgagccatccttttgtctcttaacttgcatctgtttgctctttttccagTGCCAACAATCATTATTGCCCATGAGTTTTATGATGCTCTACCAGTTCATCAATTTCAG

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|25800535|gb|CA756496.1|CA756496
EST:     TGGAGCCCCTGTACACTGGCATGCTTCCCTTGAACAGGTTCCTTCAGGAT                         TGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATC
genomic: TGGAGCCCCTGTACACTGGCATGCTTCCCTTGAACAGGTTCCTTCAGGATgtatggagtt ... ttctctgcagTGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATC
EST: gi|29644655|gb|CB649662.1|CB649662
EST:     TGGAGCCCCTGTACACTGGCATGCTTCCCTTGAACAGGTTCCTTCAGGAT                         TGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATC
genomic: TGGAGCCCCTGTACACTGGCATGCTTCCCTTGAACAGGTTCCTTCAGGATgtatggagtt ... ttctctgcagTGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatcttgatcagatttcttatgcttgttctgtttgtatatgtattctctgcagTGCCAACTATAATTATTGCACATGAATTCTATGATGCCTTGCCAATTCATCAATTTCAG
                                           tattctct  CT-rich tract
                                 tttgtatatgtatt  TA-rich tract