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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctatatctatttagcattgcacatccctgatatcccattttcttgaaaccttttgctacatgggaattcgacggtttcctgatattccacatgtttcagCACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGCCTAACTTCAGTTTTCGACGAGTACCAGCATTTTGCAGCGGCGAAGGCGA

Basic information

species Oryza sativa
transcript LOC_Os02g53160.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G126765_T01 (Zea mays), 3'ss of exon 4
gtagctatatctatttagcattgcacatccctgatatcccattttcttgaaaccttttgctacatgggaattcgacggtttcctgatattccacatgtttcagCACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGCCTAACTTCAGTTTTCGACGAGTACCAGCATTTTGCAGCGGCGAAGGCGA
             |  ||| |  | | | || |||   ||| |      |    |||   | || |  |   |  |   |  |   | ||   |   |||||||||||||||||||||||||| || |||||||| ||| ||||||| ||||||||  | || || ||||||||||||| ||| || || |||||||||||||
------------gtaaagcctctcgcgttccagatggtccagtcc----agcattttccttccacgatagcacttcccctgacgagtgtttttc---tttcagCACCGGACTGGCTGCGTCGTCGGATGCCTGAGGAAGCTGCAGAAGTGGTGCCTGTCCTCCGTGTTCGACGAGTACCTGCACTTCGCGGCGGCGAAGGCGA

upper sequence: LOC_Os02g53160.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G084086_T01 (Zea mays), 3'ss of exon 4
gtagctatatctatttagcattgcacatccctgatatcccattttcttgaaac--cttttgctacatgggaattc---gacggtttcctgat-attccacatgtttcagCACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGCCTAACTTCAGTTTTCGACGAGTACCAGCATTTTGCAGCGGCGAAGGCGA
| |    | |    ||    |||      |     |||    || |  || ||  ||   | | |||  |  |||   |||| |  |  ||  | |     | |||||||| || |||||||||||||| ||||||||||| ||| ||||||| ||||||||  |||| || ||||||||||||| ||| || || |||||||||||||
gcaagcctgttgcgttccagttggttcagctcagcatcttgcttccacgatactactacagttgcatctggtttccctgacgctgacgcgacgagtgtttttctttcagCATCGCACTGGCTGCGTCGTCGGGTGCCTGAGGAAGCTGCAGAAGTGGTGCCTGTCTTCGGTGTTCGACGAGTACCTGCACTTCGCGGCGGCGAAGGCGA
















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|86597430|gb|CI282554.1|CI282554
EST:     ACGTAAGGAATCAACCGGTGCTCATCCACTGCAAGAGAGGCAAG                         CACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGC
genomic: ACGTAAGGAATCAACCGGTGCTCATCCACTGCAAGAGAGGCAAGgtagctatat ... catgtttcagCACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGC
EST: gi|88528195|gb|CI454415.1|CI454415
EST:     ACGTAAGGAATCAACCGGTGCTCATCCACTGCAAGAGAGGCAAG                         CACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGC
genomic: ACGTAAGGAATCAACCGGTGCTCATCCACTGCAAGAGAGGCAAGgtagctatat ... catgtttcagCACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaccttttgctacatgggaattcgacggtttcctgatattccacatgtttcagCACCGGACTGGCTGCGTCGTTGGGTGCCTGAGAAAGTTGCAGAAATGGTGCCTAACTTCAGTTTTCGACGAGTACCAGCATTTTGCAGCGGCGAAGGCGA
                                tcctgat  putative branch site (score: 3)
                                   tgatatt  TA-rich tract