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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcctcttttgtgctaatctgttgattcatcacctttttttttttgcctcatgggattttgcgttgattcctgattctgtcctttctgacgttaaaaaaccattttcactgttgcagACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC

Basic information

species Oryza sativa
transcript LOC_Os01g13770.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 7
gtttgtgcctcttttgtgctaatctgttgattcatcacctttttttttttgcctcatgggattttgcgt-tgattcctgattctgtcctttctgacgttaaaaaaccattttcactgttgcagACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC
                                                          |  | |||  |  ||||     |  |||| |  |   | ||  |  | | |||      ||||||||||| |||||||||||||| ||||||||||| || ||||||||||| || ||||| |||||||| || |||||||||
----------------------------------------------------------gtctgttgtttacgatttgctctcttgtcttaaccatccttcta--atcgtttctggcattgcagACTGACATGGATAGCACCAACGTGTATGCTTACATTTCAATAATTGCTCTCATTGTTTGCATTCCGCCTGCAGTGATC

upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 7
gtttgtgcctcttttgtgctaatctgttgattcatcacctttttttt---tttgcctcat----gggattttgcgttgattcctgattctgtcctttctgacgttaaaaaaccattttcactg-------------ttgcagACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC
|||     || || ||  ||   |||||  ||| |     |  | ||   |    | ||     | |    |   ||||     | |  | |||| | |  |   ||||  |   ||  | ||             ||||||||||| ||||| || || ||| | ||||||||||| || || ||||| || ||||| ||||||||||| ||  | || 
gttatcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTCATTGTCTGCATTCCACCGGCTCTCATT
















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|29616222|gb|CB621234.1|CB621234
EST:     TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATG                         ACTGATATGGATAGCACCAATGTGTATGCTTATAT
genomic: TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATGgtttgtgcct ... actgttgcagACTGATATGGATAGCACCAATGTGTATGCTTATAT
EST: gi|29661884|gb|CB658159.1|CB658159
EST:     TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATG                         ACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTT
genomic: TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATGgtttgtgcct ... actgttgcagACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTT
EST: gi|325493498|gb|JG458022.1|JG458022
EST:     TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATG                         ACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTT
genomic: TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATGgtttgtgcct ... actgttgcagACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTT
EST: gi|29657881|gb|CB654156.1|CB654156
EST:     TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATG                         ACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTT
genomic: TCTCTAACATCTCATTCACTTACCGGAGCATTTATTCCAAGAAAGCTATGgtttgtgcct ... actgttgcagACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgattcctgattctgtcctttctgacgttaaaaaaccattttcactgttgcagACTGATATGGATAGCACCAATGTGTATGCTTATATCTCAATAATTGCCCTTATTGTGTGCATTCCACCAGCAGTGATC
                     ttctgac  putative branch site (score: 2)
                                        ttttcact  putative PPT
                             ttaaaaaaccatttt  TA-rich tract