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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcttttggtactgtaatatttatggcctgacatattattacttgtttcttctctgtgacatatatgtttagtaattttaatccccaagctaactttgctagtgttctggaaatacttcaatatgtgctgttctcacaccaggtttctgttattccagAGTACTGCTGATGACAATATTATGGATTTGATTCAGAGACACATTATATACCATTATCATGATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g49940.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49940.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G466139_T01 (Zea mays), 3'ss of exon 6
gtattcttttggtactgtaatatttatggcctgacatat-tattacttgtttc--ttctctgtgacatatatgtttagtaattttaatccccaagctaactttgctagtgttctggaaatacttcaatatgtgctgtt-----ctcacaccaggtttc-------tgttattc-cagAGTACTGCTGATGACAATATTATGGATTTGATTCAGAGACACATTATATACCATTATCATGATCAG---
|||| |||||| || |||||| ||||  | ||   |||  || |   |  |    | ||  || || |  || ||||  ||| |   |     | ||  || |     | |||||    | ||| | ||| |  | |      || ||||    ||||       | |||||| |||||| |||||||||| || |||||||||||||||||||| |||||||| |  || |  |||||||||   
gtatccttttgatattgtaatcttta--gtctagtatagatactctataatgagatgcttagtaac-tgcatttttaaaaatctcttttgttta-cttgctatatatattttctgcgt-tgcttgagtattttttttaacaaactaacactgcttttcccgtaatttttattcgcagAGTGCTGCTGATGATAACATTATGGATTTGATTCAGAGGCACATTATCTTTCACTCACATGATCAGGAG
















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|29622214|gb|CB627225.1|CB627225
EST:     AAAACAGCGTTAACACAAGATTTTCCCTCCTTGCTCATTTGATTGCCCAG                         AGTACTGCTGATGACAATATTATGGATTTGATTCAGAGACACATTATATAC
genomic: AAAACAGCGTTAACACAAGATTTTCCCTCCTTGCTCATTTGATTGCCCAGgtattctttt ... gttattccagAGTACTGCTGATGACAATATTATGGATTTGATTCAGAGACACATTATATAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctggaaatacttcaatatgtgctgttctcacaccaggtttctgttattccagAGTACTGCTGATGACAATATTATGGATTTGATTCAGAGACACATTATATACCATTATCATGATCAG
                           ttctcac  putative branch site (score: 2)
                                        tttctgtt  putative PPT
       aaatacttcaatat  TA-rich tract