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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgcaaactgaccgagatatactttctaataaatatatactttcatgtgggattgtattgtgcttatagctatggcactaatcactgtactaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCG

Basic information

species Oryza sativa
transcript LOC_Os02g47220.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 9
ctttgcaaactgaccgagatatactttctaataaatatatactttcatgtgggat-tgtattgtgcttatagctatggcacta--atcactgtactaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCG
||      |||      || ||  ||||   | |||    |  |   | |    | ||| |    | ||| ||  ||  | ||  || ||| |  |  |||||||||||||||||||||||||| |||||||||||| || |||||||||||||||||||||||  ||||  |||||||||| ||||||||||| ||||||||
ctagagggacta--tatgacatgatttcatctgaatcagcagctcagttttacttatgtgtgcgccatattgcactgataatagcatgact-tggttgtgcagAGAATCTGTTGGTTAGCAAAGGTGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTCTCATCATTGCCACCATATACAGAATATGTCTCAACTCG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 8
-ctttgcaaactgaccgagatatactttctaataaat-atatactttcatgtgggattgtattgtgcttatagctatggcactaatcactgtactaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCG
 ||     |      |  |   ||      | || || | ||  || | | ||     | |      || ||   ||      |    |  |  |  ||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||| ||||  |||| ||||| ||||||||||| ||||||||
cctaaatgatactttcttgtactagagggcagtatatgacatgattgcgtctgaatcagcagctcagttttactgataatggca--tgccttgattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG
















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|58660884|gb|CK049564.1|CK049564
EST:     TCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG
genomic: TCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTGgtaggttctc ... actaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG
EST: gi|24208295|gb|AU225322.1|AU225322
EST:     TCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG
genomic: TCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTGgtaggttctc ... actaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG
EST: gi|88256807|gb|CI354588.1|CI354588
EST:     TACTTTCATCGTGACCTGAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG
genomic: TACTTTCATCGTGACCTGAAACCTGgtaggttctc ... actaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG
EST: gi|33797218|gb|CF324473.1|CF324473
EST:     TCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG
genomic: TCTTGCATACATGCACCAGAGGGGTTACTTTCATCGTGACCTGAAACCTGgtaggttctc ... actaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtgggattgtattgtgcttatagctatggcactaatcactgtactaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCG
                                            tactaat  putative branch site (score: 1)
        attgtatt  TA-rich tract