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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacctcttaaattgttctattgcctcatggtgttaagtgacatgaagtcaatactccatagctacagtgtaactagagaaattttcttgcagAGGCTGTTCAACGTTCTGCTTTTATTGCCGAAGCAGAGGGCACAACAACTATTGAACCCACCCATCTGGAGCGTGTATTGCCACAACTTCTTTTGGACTT

Basic information

species Oryza sativa
transcript LOC_Os04g40550.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G100263_T01 (Zea mays), 3'ss of exon 4
gtatgtacctcttaaattgttctattgcctcatggtgttaagtgacatgaagtcaatactccatagctacagtgtaactagagaaattttcttgcagAGGCTGTTCAACGTTCTGCTTTTATTGCCGAAGCAGAGGGCACAACAACTATTGAACCCACCCATCTGGAGCGTGTATTGCCACAACTTCTTTTGGACTT
           | ||| ||    ||  |  || | |  | | || |  ||||  |   |   |    |  ||| ||||| |     || | ||||||||||| ||||||| ||||||||||| || ||||| ||||      |   ||||||||||||||| || |||||||| ||||| || || || ||||||||
----------gtaaaactgc---atcactgcaagctaatca-tgtcgggaagcgatcgcatta----tgtagtttaactggtttt-ttctgttgcagAGGCTATTCAACGCTCTGCTTTTATCGCTGAAGCGGAGGATGGTGCTGTTATTGAACCCACCCACCTAGAGCGTGTGTTGCCGCAGCTGCTCTTGGACTT

upper sequence: LOC_Os04g40550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G02820.1 (Glycine max), 3'ss of exon 5
gtatgtacctcttaaattgttctattgcctcatggtgttaagt---gacatgaagtcaatactccatagctacagtgtaactagagaaattttct-----tgcagAGGCTGTTCAACGTTCTGCTTTTATTGCCGAAGCAGAGGGCACAACAACTATTGAACCCACCCATCTGGAGCGTGTATTGCCACAACTTCTTTTGGACTT
||   ||| |||||||             |     | ||  ||   |||   || |    |    ||   || | | |    | | || ||||||     ||||||||||||||||||| |||||  |||||| |||||||||||  | |     || ||||| || ||| |||||  | |  | || ||  | ||||| || ||
gttcatacatcttaaaagagaaacacatttgggattctttggtcatgactataactttgcatataatctttataatctcgaca-acaacttttctgttgatgcagAGGCTGTTCAACGTGCTGCTACTATTGCAGAAGCAGAGGGTGCTAGTCAAATAGAACCTACTCATTTGGAGATTATTCTCCCTCAGTTACTTTTAGATTT


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacatgaagtcaatactccatagctacagtgtaactagagaaattttcttgcagAGGCTGTTCAACGTTCTGCTTTTATTGCCGAAGCAGAGGGCACAACAACTATTGAACCCACCCATCTGGAGCGTGTATTGCCACAACTTCTTTTGGACTT
                             gtgtaac  putative branch site (score: 3)
                                            ttttcttgc  putative PPT
                                         aaattttctt  TA-rich tract