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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaagccttcaagattccttactgttttatttttccgacactattgcttaagcagtttctattggctttacaccctgcattgacaattgctcttatttagATGATAGGAACTTCAACAAGACTGCCTCCAACACAACGCCTTGTTGAGGTAAAAGCAGTTGCTGAGCAATTTCACTTTAAGATATCAACAATATTACTTC

Basic information

species Oryza sativa
transcript LOC_Os02g48380.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48380.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G456238_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------------------gaaagccttcaagattccttactgttttatttttccgacactattgcttaagcagtttctattggctttacaccctgcattgacaat-----tgctcttatttagATGATAGGAACTTCAACAAGACTGCCTCCAACACAACGCCTTGTTGAGGTAAAAGCAGTTGCTGAGCAATTTCACTTTAAGATATCAACAATATTACTTC
                                                                                        |    | ||| |    |||    |||  |  |||  || | || ||||||||||||||||||||||| || |   || ||| |||     ||||  |||||||||||| |||||||| |||||  |||||||||| |||||||| |||||| ||||||||||||| ||||||||||||||||||||||||||  |  ||||||
gtctgatcacattcctttccttatccttaatcaacaagtggcatactaaatcaattatctcataaataaaagacaaactatggctatcataaatccaaaaaaagttaactatttggtgatccaccattgtttcttaagcagtttctattggctttgcatcacccagtgataataaatgtgcttatatttagATGATTGGAACTTCGACAAGGTTGCCTCCAACCCAACGCCTGGTTGAGATAAAAGCAGTTGCCGAGCAATTTCACTTTAAGATATCAACCTTGCTACTTC

upper sequence: LOC_Os02g48380.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G124396_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------------gaaagccttcaagattccttactgttttatttttccgacactattgcttaagcagtttctattggctttacaccctgcattgacaat-----tgctcttatttagATGATAGGAACTTCAACAAGACTGCCTCCAACACAACGCCTTGTTGAGGTAAAAGCAGTTGCTGAGCAATTTCACTTTAAGATATCAACAATATTACTTC
                                                                                        |    | ||| |    |||    |||  |  |||  || | || || |||||||||||||||||||| || | | || ||| |||     ||||  |||||||||||| |||||||| |||||  |||||||||| |||||||| |||||| ||||||||||||| ||||||||||||||||||||||||||  |  ||||||
gtctgatcacatccctttccttatccttaatcaacaagtggcatactaaatcaattatctcacaaataaaagacaaactatggctatcataaatccaaaaaaagttaactatttgctgatccaccattgtttctgaagcagtttctattggctttgcatcatccagtgataataaatgtgcttatatttagATGATTGGAACTTCGACAAGGTTGCCTCCAACCCAACGCCTGGTTGAGATAAAAGCAGTTGCCGAGCAATTTCACTTTAAGATATCAACCTTGCTACTTC

upper sequence: LOC_Os02g48380.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G065044_T02 (Zea mays), 3'ss of exon 4
gaaagccttcaagattccttactgttttatttttccgacactattgcttaagcagtttctattggctttacaccctgcattgacaat----tgctcttatttagATGATAGGAACTTCAACAAGACTGCCTCCAACACAACGCCTTGTTGAGGTAAAAGCAGTTGCTGAGCAATTTCACTTTAAGATATCAACAATATTACTTC
   | ||   || |    | ||||||    |   ||| || | || |||||||||||||||||| |||| || | | |||||| |||    ||||  |||||||||||| |||||||| |||||  |||||||||| |||||||| |||||| ||||||||||||| ||||||||||||||||||||||| ||  |  ||||||
---atccaaaaaaaaagttcactgtta-gctgacccgccaatgtttcttaagcagtttctattgcctttgcatcatccattgataataatgtgcttatatttagATGATTGGAACTTCGACAAGGTTGCCTCCAACCCAACGCCTAGTTGAGATAAAAGCAGTTGCCGAGCAATTTCACTTTAAGATATCGACCTTGCTACTTC

upper sequence: LOC_Os02g48380.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G480620_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------------------gaaagccttcaagattccttactgttttatttttccgacactattgcttaagcagtttctattggctttacaccctgcattgacaat-----tgctcttatttagATGATAGGAACTTCAACAAGACTGCCTCCAACACAACGCCTTGTTGAGGTAAAAGCAGTTGCTGAGCAATTTCACTTTAAGATATCAACAATATTACTTC
                                                                                        |    | ||| |    |||    |||  |  |||  || | || ||||||||||||||||||||||| || | | || ||| |||     ||||  |||||||||||| |||||||| |||||  |||||||||| |||||||| |||||| ||||||||||||| ||||||||||||||||||||||||||  |  ||||||
gtctgatcacattcctttccttatccttaatcaacaagtggcatactaaatcaattatctcataaataaaagacaaactatggctatcataaatccaaaaaaagttaactatttgctgatccaccattgtttcttaagcagtttctattggctttgcatcatccagtgataataaatgtgcttatatttagATGATTGGAACTTCGACAAGGTTGCCTCCAACCCAACGCCTGGTTGAGATAAAAGCAGTTGCCGAGCAATTTCACTTTAAGATATCAACCTTGCTACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttaagcagtttctattggctttacaccctgcattgacaattgctcttatttagATGATAGGAACTTCAACAAGACTGCCTCCAACACAACGCCTTGTTGAGGTAAAAGCAGTTGCTGAGCAATTTCACTTTAAGATATCAACAATATTACTTC
                                cattgac  putative branch site (score: 3)
                                            ctcttattt  putative PPT
                                             tcttattta  TA-rich tract