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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgacttcttcttcattttacactttcccatcctttgtcaaagaaaaaaaaagctctcctgtttctggtgatgttttcatcacaatggcatgcataccggttagccatctcctttgtactgccaaataaggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG

Basic information

species Oryza sativa
transcript LOC_Os12g40830.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G398107_T01 (Zea mays), 3'ss of exon 3
gtga---atgacttcttcttcattttacactttcccatcctttgtcaaagaaaaaaaaagctctcctgtttctggtgatgttttcatcacaatggcatgcataccggttag-ccatctcctttgtactgccaaataaggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG
|| |   ||||  | |   | ||| || |  ||   ||  | |||     || | |    |   |  | | | | ||| |      |     |||  |     | |||||| |||     |||  ||| |  |                 | ||| ||||| ||| | ||||||||||  |||||||| || ||  | ||||||||||||| |||| | |||||||||||||||||||||||||||||||||||||| |||||||| |
gtaagttatgaactttatgtgattgta-atattttgattttatgtggtcaaatatatggaccgacacggtcc-gatgaaggcacggt----gtggtttaggaccgggttaggccactgtttttacacttcgga----------------ctgacacaaagtgacaagctgtttatggttctcagGTTACATAGGCCCGGTTTCCTTTTTAAATACTATGCTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGACCTTGTATACG

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 5
gtgaatgacttcttcttcattttacactttcccatcctttgtcaaagaaaaaaaaagctctcctgtttctggtgatgttttcatcacaatg-gcatgcataccggttagccatctcctttgtactgccaaata-aggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG
                                                                                  |   ||||    ||  |||    |           | | ||     | ||| |  | |          ||| ||||| ||||| ||||||||||  ||||||||||| || || ||||||||||||  |||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||
----------------------------------------------------------------------------------actgcaatatatatatatatatatatatatatatatatatatatatatatatatatatacacacacacacacaaagtgacatgctgtttatggttctcagGTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATG
















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|58661072|gb|CK049752.1|CK049752
EST:     TGAAGGGCTGGTGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
EST: gi|88448481|gb|CI693864.1|CI693864
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
EST: gi|88301040|gb|CI592220.1|CI592220
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAAC
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAAC
EST: gi|88443713|gb|CI591938.1|CI591938
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
EST: gi|88580749|gb|CI697698.1|CI697698
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTAC
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTAC
EST: gi|88335844|gb|CI645445.1|CI645445
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTCAACT
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACT
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAG                         GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA
genomic: TGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATTAACAGgtgaatgact ... tggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaataaggtttgtgtgttttaacaaaaagtaacatgatgtttatggtattcagGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG
                            aagtaac  putative branch site (score: 2)
                  ttttaacaaaaagtaa  TA-rich tract