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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttttggtctcatcttcagttgccaaaggggaaagatagttttgtctgaaatttgtatacttctattcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAATTTTCTGTATCTTATTTGGTATTGTTG

Basic information

species Oryza sativa
transcript LOC_Os12g39420.5
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g39420.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G041050_T03 (Zea mays), 3'ss of exon 13
gtaatcttttggtctcatcttcagttgccaaaggggaaa----gatagttttgtctgaaatttgta-tacttctattcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAATTTTCTGTATCTTATTTGGTATTGTTG----------------------
||||| | ||| | |  | ||  ||| || |  | |||      |   ||  |    || | ||   | | | | ||  ||||||||| ||||| || ||||||||||| || ||| |||| ||||| |||||||||| ||| ||||| || || ||||| |                      
gtaatttgttg-ttttttatttggttccctagagagaatttgcaactcttccgctcaaactgtgaggtccgtttttttttgcagGGAAATTTGGGGCCTTCTTTGCATCGATCCCACTGCCGATCTTTGCAGCAATTTACTGCATCTTGTTCGGCATTGTAGCTGCTGTGGGAGTCTCGTTCAT

upper sequence: LOC_Os12g39420.5 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv18s0001g11260.t01 (Vitis vinifera), 3'ss of exon 11
--------gtaatcttttggtctcatcttcagtt--gccaaagg-------ggaaagatagttttgtctgaaatttgtatacttctattcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAATTTTCTGTATCTTATTTGGTATTGTTG
         |  | ||||  |  |  | | | ||     |||         || |  ||   |   | |   |||    ||       || | |||||||||||||||| ||||||||||||||||| || ||||| || || || || | |||| |  ||||||| |||||||
gtctgttttttgttttttacttcccccattaattctattaaatcattgcctgggattatcactgaatgtttgattgagttatcctgcatctttcagGGAAGTTTGGTGCCTTCTTTGCATCTATTCCTTTACCAATATTTGCTGCCATATACTGTGTTCTATTTGGCATTGTTG
















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|29675659|gb|CB671934.1|CB671934
EST:     GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|218483052|gb|FG951433.1|FG951433
EST:     GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|218484784|gb|FG964505.1|FG964505
EST:     GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|218481129|gb|FG959236.1|FG959236
EST:     GAGAGTGATCCAGATATCACCTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|454451|gb|D28174.1|D28174
EST:     GAGAGTGATCCAGATATCAACTGGATTTATGATTTTNTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|86848319|gb|CI292148.1|CI292148
EST:     GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|29687155|gb|CB683430.1|CB683430
EST:     GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|7219928|gb|AU065533.2|AU065533
EST:     GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: GAGAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
EST: gi|218483040|gb|FG956505.1|FG956505
EST:     AGCAGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTG                         GGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA
genomic: AG-AGTGATCCAGATATCAACTGGATTTATGATTTTCTTCTCCATATTTGgtaatctttt ... attcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgccaaaggggaaagatagttttgtctgaaatttgtatacttctattcatgcagGGAAGTTTGGTGCTTTCTTTGCATCTATTCCATTGCCAATCTTCGCAGCAATTTTCTGTATCTTATTTGGTATTGTTG
                                        cttctattc  CT-rich tract
                             aaatttgtatactt  TA-rich tract