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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacttcgagctttgtcattcgatctggatgtgaacttttattttaagtctcatagcttgtctttctttcattatgtagGAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAAATGACTCAGTATCGGATAAGAATGAGGAAGCTTCAACTGAAAGTGAG

Basic information

species Oryza sativa
transcript LOC_Os07g16950.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g16950.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 3
gtatgcacttcgagctttgtcattcgatctggatgtgaactttta--ttttaagtctcatagcttgtctttctttcattatgtagGAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAAATGACTCAGTATCGGATAAGAATGAGGAAGCTTCAACTGAAAGTGAG
|||||||  || ||||     || |  | |     | || |||    | ||  |||| ||   || |   | |||  | ||  ||||||||||||| ||| ||||||||||||| || || ||||| ||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||
gtatgcatctctagctaacgtatactgtttctccttaaaatttagagtatttggtctaattttttttggcttttttgtcattaagGAATTTTGGCCTAAGCTACTTGTGCACAAGATCAAACAGCGGCTGACAAAAATGACTCAATATCGTATAAGAATGAGGAAACTTCAACTGAAAGTGAG

upper sequence: LOC_Os07g16950.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0030g01480.t01 (Vitis vinifera), 3'ss of exon 13
-------------gtatgcacttcga--gctttgtcattcgatctggatgtgaacttttatttta----agtctcatagcttgtctttctttcattatg-tagGAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAAATGACTCAGTATCGGATAAGAATGAGGAAGCTTCAACTGAAAGTGAG
                |||| ||  |  |  || |  ||   |||  ||   |  ||||     |     ||  | ||   | | ||| |||  || |   ||   |||||||| ||||| ||||| |||||||  |||||||| || || ||||||||||||   || ||  | ||||||||||||  | |||||   ||
gtattctacttctccttgcaatttcatagggtttttgtttcctctttatcgaagtttttggaggacaccggttgcttaatctatatttatttggttttaacagATGTTTTGGCCGAAGTTGCTTGTTCACAAAACAAAGCAGCGTCTCACTAAAATGACTCAGATGCGAATTCGCATGAGGAAGCTTGCATTGAAAACAAG

upper sequence: LOC_Os07g16950.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g09220.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtatgcacttcgagct--ttgtcattcgatctggatgtgaacttttatttta----agtctcatagcttgtctttctttcattatg-tagGAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAAATGACTCAGTATCGGATAAGAATGAGGAAGCTTCAACTGAAAGTGAG
                |||| ||  |  |  || |  ||   |||  ||   |  ||||     |    |||  | ||   | | ||| |||  || |   ||   |||||||| ||||| ||||| |||||||  |||||||| || || ||||||||||||   || ||  | ||||||||||||  | |||||   ||
gtattctacttctccttgcaatttcatatggtttttgtttactcttcatcgaagtttttggaggacaccagttgcttaatctatatttatttggttttaacagATGTTTTGGCCGAAGTTGCTTGTTCACAAAACAAAGCAGCGTCTCACTAAAATGACTCAGATGCGAATTCGCATGAGGAAGCTTGCATTGAAAACAAG

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|427797|gb|D23935.1|D23935
EST:     GAAATTATGAGAAAGCAATGGAAGTCATCAATAAGCATCTT                         GAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAA
genomic: GAAATTATGAGAAAGCAATGGAAGTCATCAATAAGCATCTTgtatgcactt ... cattatgtagGAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggatgtgaacttttattttaagtctcatagcttgtctttctttcattatgtagGAATTTTGGCCCAAGTTACTTGTGCACAAAATTAAGCAGCGCCTGACAAAAATGACTCAGTATCGGATAAGAATGAGGAAGCTTCAACTGAAAGTGAG
                                cttgtctttctttcat  CT-rich tract
       tgaacttttattttaa  TA-rich tract