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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcaaaatgtgttctgatctacttcaccaaatggactcaaatttaagtttcttaattatctttgtgttgttgttaaccagttatacaatttttttctagGTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTGCCATATCAAGTATATGGCAATGGAAAGACTGGATCAGAG

Basic information

species Oryza sativa
transcript LOC_Os09g21780.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 2
-agtcaa--aatgtgttctgatctacttcaccaaatggactcaaatttaagtttcttaattatctttgtgtt-gttgttaaccagttatacaatttttttctagGTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTGCCATATCAAGTATATGGCAATGGAAAGACTGGATCAGAG
   ||||  ||||||||||||  |   |  | | |   |||   |  | || | |||| |||| || | ||| | |||| ||||| ||| || | |||| |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||| || ||||| ||||| |||||||||||| | 
tcatcaatcaatgtgttctgaattgagttgctacacatact---agctgagctgctta-ttattttcgggttagatgttgaccagatatgcattcttttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTACCATATCAGGTGTATGGAAATGGGAAGACTGGATCACAA

upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G055917_T02 (Zea mays), 3'ss of exon 2
agtcaaaatgtgttctgatctacttcaccaaatggact-caaatttaagtttcttaattatctttgtgtt-gttgttaaccagttatacaatttttttctagGTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTGCCATATCAAGTATATGGCAATGGAAAGACTGGATCAGAG
 |      | ||   |||  | || |||  | | |    | ||  | || | |||| | || || | ||| | |||| ||||| | |||| || ||| |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| || ||||||||||| |||| ||||||  ||
cggtgcgttctgaattgagttgctgcacatactagctgactaagctgagctgctta-taattttcgggttagatgttgaccagatgtaca-ttctttcctagGTATAAATATGAAAATGAGCAGGTTATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTACCGTATCAGGTGTATGGCAATGGGAAGATTGGATCTCAG

upper sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G055917_T01 (Zea mays), 3'ss of exon 2
agtcaaaatgtgttctgatctacttcaccaaatggactcaaatttaagtttcttaattatctttgtgttgttgttaaccagttatacaatttttttctagGTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTGCCATATCAAGTATATGGCAATGGAAAGACTGGATCAGAG------------------------------------------
                                                                     | |||| ||||| | |||| || ||| |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| || ||||||||||| |||| ||||||  ||                                          
---------------------------------------------------------------------gatgttgaccagatgtaca-ttctttcctaggtataaatatgaaaatgagcaggttattgatgctgcttcaactgatgcaagctcacccttaccgtatcagGTGTATGGCAATGGGAAGATTGGATCTCAGTTGCCAACTCGAGGAACATATGATCAGCTATTAGAAAGACAG

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|29687679|gb|CB683954.1|CB683954
EST:     CATAAAGAAACAGACAAGATTGACATACGTGCTGATGCAGAACTTTTGAG                         GTATAGATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAG
genomic: CATAAAGAAACAGACAAGATTGACATACGTGCTGATGCAGAACTTTTGAGgtactaccat ... ttttttctagGTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAG
EST: gi|58665932|gb|CK054618.1|CK054618
EST:     CATAAAGAAACAGACAAGATTGACATACGTGCTGATGCAGAACTTTTGAG                         GTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAG
genomic: CATAAAGAAACAGACAAGATTGACATACGTGCTGATGCAGAACTTTTGAGgtactaccat ... ttttttctagGTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttcttaattatctttgtgttgttgttaaccagttatacaatttttttctagGTATAAATATGAAAATGAGCAGGTCATTGATGCTGCTTCAACTGATGCAAGCTCACCCTTGCCATATCAAGTATATGGCAATGGAAAGACTGGATCAGAG
                          tgttaac  putative branch site (score: 2)
                                            tttttttct  putative PPT
                                    ttatacaatttttttc  TA-rich tract