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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttagttatagtgatgagattcatttgggcaagttatttggcaattctttttacatgttctatcgctggcataacttttcactgtttcatgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCACTACGACATCCTTCCAGTGGCTCACCAACTTTTAGTAGCGGCAGCCCTT

Basic information

species Oryza sativa
transcript LOC_Os12g07450.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07450.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G096070_T01 (Zea mays), 3'ss of exon 11
---tggttagttatagtgatgagattcatttgggcaagttatttggcaatt--ctttttacatgttctatcgctggcataacttttcactgtttcatgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCACTACGACATCCTTCCAGTGGCTCACCAACTTTTAGTAGCGGCAGCCCTT
      |   | |   |||  || || |  | | ||||||    |||| ||  |||   ||||| | ||| |||||||||| |||||  |||| ||||||  |||||||| ||||| |||||||||||||||||| |||||||||||| |||||||||||| |||||||| |||| |||||| || ||||| ||||| |||||||
atacaatgcttaaacatgacaagctttaaattg-caagtt----ggcattttgcttgcaacatgatttattgctggcataaattttcgttgttgcatgcttgtagGACACCCAACTACTTCTGTGGGACCTGGCACTGGATGAGATTGTTGTCCCACTACGGCATCCTTCAAGTGCCTCACCTACGTTTAGCAGCGGGAGCCCTT

upper sequence: LOC_Os12g07450.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 11
--tggttagttatagtgatgagattcatttgggcaagttatttggcaattctttttacatgttctatcgctggcataacttttcactgtttcatgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCACTACGACATCCTTCCAGTGGCTCACCAACTTTTAGTAGCGGCAGCCCTT
  |  | | |  |     |      | ||| |   |  |   | |||  | |||| |  ||||  ||      || |     | |   | |   |    |||||||||||| ||||||| |||||||||| | ||||||||||||  || ||  | |||| ||||||  |||| || |||||||  |||   || ||||  |
tatattcattcctgaaatttcccaaccttttgtttatgtgcgttgca--ttttttaaattgttacatataatacaaatgcactaaagatatttggtggttagGACACACAATTGCTTCTATGGGACCTGGAAATGGATGAGATTGTGGTACCCTTGCGACGTCCTTCTGGTGGATCCCCAACTTACAGTGCTGGAAGCCAGT

upper sequence: LOC_Os12g07450.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA03G33740.1 (Glycine max), 3'ss of exon 10
tggttagttatagtgatgagattc--atttgggcaagt-tatttggcaattctttttacatgttctatcgctggcataacttttcactgtttcatgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCACTACGACATCCTTCCAGTGGCTCACCAACTTTTAGTAGCGGCAGCCCTT
   ||    | |    || | ||   |||||    | | | ||| ||  |||      | ||||   ||         |  |   |   |||  || ||  |||| |||||| |||||||||||||||||| | |||| |||||||  || ||  |  | |  ||  |  |||| || || ||||  ||||  || ||||  |
caatttaagaaaaaagtgtggttgtaatttgtatgaatgtgttttgcc-ttccaagctcgtgtttggtcaaattttggaactaagaaattttggtgatc--agGATACACAATTGCTTCTGTGGGACCTGGAAATGGACGAGATTGTAGTGCCCTTGAGGCGGCCACCTGGTGGATCCCCGACTTACAGTACTGGAAGCCAGT

upper sequence: LOC_Os12g07450.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 11
tggttagttatagtgatgagattcatttgggcaagttatttg---gcaattctttttacatg-ttctatcgctggcataacttttc--actgtttcatgctc-ctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCACTACGACATCCTTCCAGTGGCTCACCAACTTTTAGTAGCGGCAGCCCTT
     |  |  | |  ||| |||  |     |   || |||    ||| | | |||| ||   || |||   |   | || |   |  |   | |  || |   |||||||||||| ||||||| |||||||||| | ||||||||||||  || ||  | |||| ||||||  |||| || |||||||  |||   || ||||  |
-----atattcattcctgaaatt--tcccaaccttttgtttatgtgcattgcatttttcaaacttttatatataatacaaatgcactaaagatattttggtggttagGACACACAATTGCTTCTATGGGACCTGGAAATGGATGAGATTGTGGTACCCTTGCGACGTCCTTCTGGTGGATCCCCAACTTACAGTGCTGGAAGCCAGT

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|29670875|gb|CB667150.1|CB667150
EST:     CTGATGGAACAGGAGAAAATACCGTGTATCGTTTTGGTTCTGTTGGTCAG                         GACACACAACTGCTTCT
genomic: CTGATGGAACAGGAGAAAATACCGTGTATCGTTTTGGTTCTGTTGGTCAGgtatcacaaa ... atgctcctagGACACACAACTGCTTCT
EST: gi|29665681|gb|CB661956.1|CB661956
EST:     CTGATGGAACAGGAGAAAATACCGTGTATCGTTTTGGTTCTGTTGGTCAG                         GACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCA
genomic: CTGATGGAACAGGAGAAAATACCGTGTATCGTTTTGGTTCTGTTGGTCAGgtatcacaaa ... atgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCA
EST: gi|33822326|gb|CF336974.1|CF336974
EST:     GATGGAACAGGAGAAAATACCGTGTAT-GNNTTTGGGTTCTGTTGGTCAG                         GACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTTGCTGTCCC
genomic: GATGGAACAGGAGAAAATACCGTGTATCGT-TTTGG-TTCTGTTGGTCAGgtatcacaaa ... atgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATT-GCTGTCCC
EST: gi|58685449|gb|CK074136.1|CK074136
EST:     CTGATGGAACAGGAGAAAATACCGTGTATCGTTTAGGTTCTGTTGGTCAG                         GACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCA
genomic: CTGATGGAACAGGAGAAAATACCGTGTATCGTTTTGGTTCTGTTGGTCAGgtatcacaaa ... atgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctttttacatgttctatcgctggcataacttttcactgtttcatgctcctagGACACACAACTGCTTCTGTGGGACCTGGCATTGGATGAGATTGCTGTCCCACTACGACATCCTTCCAGTGGCTCACCAACTTTTAGTAGCGGCAGCCCTT
                         gcataac  putative branch site (score: 3)
                                              tgctcct  putative PPT
                           ataactttt  TA-rich tract