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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G070126_T02 (Zea mays), 3'ss of exon 8
gtatgtg--ctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC
|||||||  |||  |||| ||||         || | |    ||||  || ||| |||||  | ||| || | |   |       ||||| | | |||| ||||||||| || || ||||| || |||||||||||||| || ||||||||||| ||||| ||| | |||||||||||||| ||||||||||||||||| ||||
gtatgtgacctgtcttgaatgca---------cactattggccacactatcata-tgaaaagtagtcatcatattggt-------ttttggtgtgtgatgccagAAAGCAACTAAATGGTCAGAGAGAAGGGATGCTGTGGCAGAGCTAACCAAGCTTGCGTCAGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC

upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G068755_T02 (Zea mays), 3'ss of exon 8
gtatgtg--ctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC
||||| |  |||  |||| ||||        ||  | |   |||||  ||  || |||||  | ||  |  | | | |       ||||||| ||||||  |||||||| || || |||||||| |||||||||||||| || ||  ||||||| |||| |||  | |||||||||||||| ||||||||||||||||| ||||
gtatgggacctgtcttgaatgca-------cacgctattggtcacactatcgta-tgaaaagtagttattatattagt-------ttttgttgtctgatgtcagAAAGCAACAAAATGGTCTGAGAGAAGGGATGCTGTGGCAGAATTAACCAAGCTTGGTTCGGCAAAAAAAATTGCTCCTGGTGATTTTCATGAAATTTGCC

upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 8
gtatgtgctgatttgagtgcagcattgat-acattgtccatcacaac-attatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC
      | |  |||   |||  ||||  |   ||||| |     ||| | |  |     || ||  |    |  |  ||| ||| | ||||||    ||  |||||||||||||| ||||||||| | | ||| |||||||| |||||||| || ||||| ||||| |||| |||| |||| ||||||||   |||| | || |
------gttagttttc-tgccccatttctcggattgtactcagtaactaatgcacctttattttagctatatgagtttgaatctgtcttgttaat--at-tcagAAAGCTACCAAATGGTCTGAACGGAAGGAGGCTGTTGCTGAGCTAACAAAGCTTGCATCAACTAAAAGAATTTCTCCTGGTGATTTCTCTGAAGTTTGTC

upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 8
--------------gtatgtgctgatttgagtgcagca-ttgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttat-ctgatac-cagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC
                || |   |  |||    ||| | || || ||   |  ||   |    ||| |      ||    |||  ||   |  ||   ||||||  |  | |||  |||||||||||||| ||||||||| | | ||| |||||||| |||||||| || ||||| ||||| |||| |||| |||| ||||||||   |||| | || |
gtcagttttctgtcccatctctcggattgtactcagtaattaatgcacc-tatattttagttatatgggtttgaatctatctcagtttgttctttactttttgtcttattaatattcagAAAGCTACCAAATGGTCTGAACGGAAGGAGGCTGTTGCTGAGCTAACAAAGCTTGCATCAACTAAAAGAATTTCTCCTGGTGATTTCTCTGAAGTTTGTC

upper sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------------gtatgtgctgatttgagtgcagcattgatacattgtc--catcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgatacc-agAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC
                                       || ||||  ||    ||  |  ||   | | |||    ||    |  |   | | |  | || |      ||   |   | ||   | || | ||      ||||||||||||| ||||| ||||||| ||| |||||||| ||||| ||||| || |||||||| ||||  || || || ||||||||    ||||| ||  
gtcagtgctttctctctctctcatctcttattcagtgacatttgctacttattttgttgtgttttaatactgttgttattttgatctctcaatca--tgttattagaggttagtt--ctttaacattttgtttgtcctttagAAAGCTACCAAATGGTCAGAAAGAAAGGAGGCTGTTGCAGAGCTGACCAAGCTAGCTTCAACTAAAAGGATAGCACCTGGTGATTTCACAGAAATTTGTA

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|86490173|gb|CI132806.1|CI132806
EST:     CTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG                         AAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAA
genomic: CTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgtatgtgctg ... ctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAACTTGCTTCAACCAAAAAAATTGCTCCCGGTGATTTTCATGAAATCTGCC
                                           atctgat  putative branch site (score: 4)
                              attctattttgttat  TA-rich tract