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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagaacatgtagcttattgagctaccattattgtaacatatcacataagggcttattacattaacgcaatagtaattcttttatctctgtgacttgcagGCATTGGACACCTTTAATACAGCAGTTGTCTCACCAATATATTACGTGATGTTTACTTCACTAACAATTTTAGCCAGTGTGATAATGTTTAAG

Basic information

species Oryza sativa
transcript LOC_Os11g09140.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G104147_T02 (Zea mays), 3'ss of exon 6
acagaacatgtagcttattgagctaccattattgtaacatatcacataagggcttattacattaacgcaatagtaattcttttatctctgtgacttgcagGCATTGGACACCTTTAATACAGCAGTTGTCTCACCAATATATTACGTGATGTTTACTTCACTAACAATTTTAGCCAGTGTGATAATGTTTAAG
    ||    ||   |||  ||||    || |  ||   ||  | ||        ||||| |  | || |   | ||   |||  |||| | | ||||||||| |||| || |||||||||||||| ||||||||||||||||||||||||||||| |||||||||||| |||| |||||||||||||| |||
ttgcaattcttactgtatcaagctgatcttctaatactttaaaatatggttaagaattacttgcaagctaagttgatgagttttcctctttaaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG

upper sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 6
acagaacatgtagcttattgagctaccattattgtaacatatcacataagggcttattacattaacgcaatagtaattcttttatctctgtgacttgcagGCATTGGACACCTTTAATACAGCAGTTGTCTCACCAATATATTACGTGATGTTTACTTCACTAACAATTTTAGCCAGTGTGATAATGTTTAAG
  ||  |      || | ||    |   |  |  ||   ||  | ||      | || ||||  | || |   ||||   |||  |||| | | |||||||||||||| || |||||||||||||| ||||||||||||||||| |||||||||||||||||||||||| ||||||||||||||||||| |||
gtagctcgctgttctcactgtatcaagctggtcttattttaaaatatggttaataatcacatgcaagctaagttaatgtgttttactctttaaattgcagGCATTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTATGTGATGTTTACTTCACTAACAATTATAGCCAGTGTGATAATGTTCAAG
















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|33678556|gb|CF306795.1|CF306795
EST:     CCCTAATTGTAGCCACCTGTGTGAGCACCCAGATAAACTATCTAAATAAG                         GCATTGGACACCTTTAATACAGCAGTTGTCTCACCAATATATTACGTGATG
genomic: CCCTAATTGTAGCCACCTGTGTGAGCACCCAGATAAACTATCTAAATAAGgtacatgaag ... tgacttgcagGCATTGGACACCTTTAATACAGCAGTTGTCTCACCAATATATTACGTGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagggcttattacattaacgcaatagtaattcttttatctctgtgacttgcagGCATTGGACACCTTTAATACAGCAGTTGTCTCACCAATATATTACGTGATGTTTACTTCACTAACAATTTTAGCCAGTGTGATAATGTTTAAG
              cattaac  putative branch site (score: 2)
                               ttcttttatctctgt  putative PPT
                       aatagtaattctttta  TA-rich tract