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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacattgcataagttatgcgtgtcacttagcactagttcttgtaatggctttgtcctttttaattctatataatctttacatctaatatttcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA

Basic information

species Oryza sativa
transcript LOC_Os08g41010.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G134770_T03 (Zea mays), 3'ss of exon 8
ccacattgcataagttatgcgtgtcactta-gcactagttcttgtaatggc-------tttgtccttt--ttaattctatataatctttacatctaatatt-tcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA
           |  ||  ||   | ||||| |  ||||||  | ||||||        ||| |  ||   | ||||||||  ||  ||     | ||| || |  ||  |||||||||||  ||||| || ||||||||||| ||| |||||||||||||||||||||| ||||| || ||||| || |||||    || |  || |||||
-----------atttttcgcacataacttatgggctagtttatctaatggtagaataatttattgttccatcaattctattcaaatttacaccccaatcttattttgatagAACCAAAGACACCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAACTATCCTTTCCGAACGAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

upper sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G107106_T06 (Zea mays), 3'ss of exon 7
-ccacattgcataagttatgcgtgtcacttagcactagttcttgtaatggctttgtcctttttaattctatataatctttacatctaatatttcat-ggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA
         ||||| ||||| |   |  |    | | ||   |||| |   ||  ||| |   |||||| |   | ||      | ||  | | || |  |||| ||||||||||||| || ||||||||||| ||| |||||||||||||||| ||||| ||||| |||||||| || |||||    || |  || |||||
attttcgcacataaattatgggctactttatctaatggtctatgtagtttattgttccatc--aattctgttcgaactcacaccccaacctctaattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAATTATCCTTTCCGAACAAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

upper sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G00920.1 (Glycine max), 3'ss of exon 8
------------ccacattgc-ataagttatgcgtgtcacttag----cactagttcttgtaatggctttgtcctttttaattctatataatctttacatctaatatttcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA
            |||   | |   | |  |    |||||| ||           | | ||  |           ||  ||||| | | |   |||||||| || | |||| |  |||| | ||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||| | || || || ||| | |  | ||| |  ||||| ||
gtaagtagcttcccaggctcccgcatgacaaatctgtcacataaatgatgtcgttacctgatacaaaacaacagttggtaattatgttt---ctttacatgta-tttttcctttcagAGCAAAAGATGCCTGAGGGAAGCTGGAAGTGCGAAAAGTGTAACAACATAAACTATCCTTTCAGAACCAAGTGCAACAGACAGAATTGTGGTGCTGACAA

upper sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G36990.2 (Glycine max), 3'ss of exon 8
--------------------ccacattgcataagttatg-cgtgtcacttagcactagttcttg---taatggctttgtcctttttaatt-ctatataatctttacatctaatatttcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA
                    || |||   |  |  | ||   |||| | ||   |  ||  ||    ||||      |      ||  |   ||| |  |||||   | || | || |||  |||| | ||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||| | || || || ||| | |  | ||| |  ||||| ||
gtaagtagcttcccaggctcccccatgataccatctgtgatctgtctcataattcatgtcttttacctaatacaaaagcaacagttggtaattatgtt-tctttgtttttatttttccatt-cagAGCAAAAGATGCCTGAGGGAAGCTGGAAGTGCGAAAAGTGTAACAACATAAACTATCCTTTCAGAACCAAGTGCAACAGACAGAATTGTGGTGCTGACAA

upper sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 8
ccacattgcataagttatgcgtgtcacttagcactagttcttgtaatggctttgtcctttttaattctatataatctttacatctaatatttcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA
                 || ||     ||     |  | ||  || ||||||||      |||| | |     ||  | ||||     ||||  |  |||||| ||||||||| || || ||||||||||| |||||||| |  |||||||||||||| ||| | || || || ||  | |  |  || | ||| || ||
----------------gtgagttcttttttaacttgctgctattattggctttgca----ttaactttg----atgctaacataattcatttatt--cagAACAAAAGATGCCTGATGGAAGTTGGAAGTGTGAGAAGTGTAGCAACATAAACTATCCCTTCAGAACCAAGTGCAATAGACAGAACTGTGGGGCCGATAA

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|29680937|gb|CB677212.1|CB677212
EST:     GGGTCCAAACCTGATGGTGCAAGAGGTCCAA                         AACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAA
genomic: GGGTCCAAACCTGATGGTGCAAGAGGTCCAAgtaagtttaa ... ttcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggctttgtcctttttaattctatataatctttacatctaatatttcatggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA
                                    atctaat  putative branch site (score: 3)
            tttttaattctatata  TA-rich tract