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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

Basic information

species Zea mays
transcript GRMZM2G010085_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcattt-tttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||||| ||||| |  |||   ||| | |||     | |||||  |  | ||||  ||| ||||||  | |        | |  ||  || |||||||||||||||||||||  ||||||||||  | |||||||| |||||||| |||||||| |||||||||||||| || |||||||| |||||||||||
gtatgtttttgctgcttgtattttatgtttaaga-aggcattcatgcagtagtaagatatggatttattt--------tgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||  | ||||    |     | |  |  |||    | | |  ||  |  |  |  ||     || |||||       ||    |  || |||||||||||||||||| ||  |||| |||||  | ||||||||||||||||| ||||| || ||||| ||||||||||| ||||| || |||||||| ||
gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaaca--tcaattaatgttcttctg-------tcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcatttt-ttactagtttgat---ctggattgttctg---acaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
     ||   | | | ||   ||| | || ||||| |  ||||| || |||| || ||    |  ||      |   ||||  |  |  | |||  |||||| ||||| |||||  | || ||||||||  | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
-----gtaagggtttctggattttatcttcgtttttattattttgttgctagatttatggattatataacatggtacacaatctatttgtgtatgcagCTGTTAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcatttt-ttactagtttgat---ctggattgttctg-acaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||| || |||    | ||   ||| | |||||||| |  ||||| || | || |||||    |  ||      | ||||  |  |  | |||  |||||| ||||| |||||  | || ||||||||  | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
gtaagggttt----tctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||| |  ||  ||   |  | |||||  ||  |||    |   ||   | | |||      || ||||      | ||    | | |  ||| || ||||| |||||  | || ||||||||  | ||||| |||||||||||||||||||| ||||| || ||||| || ||||| || |||||  | ||
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttt----tatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
|||||| ||  ||   |    |||||  ||  |||    |   ||   | | |||       | ||||     |  || | || |    ||| || ||||| |||||  | || ||||||||  | ||||| |||||||||||||||||||| ||||| || ||||| || |||||||| |||||  | ||
gtatggattcaatgaataatttttcttgtttctttgctgaaagttgtgtggattgtctaatgtggttccattga--tttttatgtgc--agCGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAGGATATTGATAGAAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
            ||  |||  | |  | |  ||    || || |  | | |||       ||  |   ||  |    ||| |  |||  ||||||||||||||||||  | || ||||||||  | | ||||||||| ||||| ||||||||||| || |||||||| || || ||||| |||||  | ||
-----------gtaagtgcgttatacagtgatt----gctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||| |   |||     ||    |  ||  ||| ||     || | |   |  |  ||   ||||  | |        |||    | |  |||||| |||||||||||  | || ||||||||| | | ||||||||||||||| || |||||||| || |||||||| || |||||||| |||||| | ||
gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttt--------tctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
gtatggttttgatat-ttgccatttctatttgttttaagcattttttactagtttgatctggattg------ttctgacaacattctcatttatta-agCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
||  |   ||  |   || | |  |   ||||   || |   |  | | |  |   |   | |         || ||      || |    | ||  |||||| || || ||||| || |||||||||||  ||||||||||||||||||||||||| || ||||| |||||||| || ||||| ||||| ||| | ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT

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|21891766|gb|BQ744979.1|BQ744979
EST:     AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGATCTTCTGCAAATGGTGCG
genomic: AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggtttt ... atttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCG
EST: gi|87155727|gb|DY400516.1|DY400516
EST:     AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
genomic: AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggtttt ... atttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
EST: gi|32930781|gb|CF035593.1|CF035593
EST:     AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
genomic: AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggtttt ... atttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
EST: gi|31351381|gb|CD435738.1|CD435738
EST:     AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
genomic: AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggtttt ... atttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
EST: gi|32930784|gb|CF035596.1|CF035596
EST:     AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
genomic: AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggtttt ... atttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
EST: gi|22546162|gb|BU098473.1|BU098473
EST:     AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA                         CTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG
genomic: AGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAAgtatggtttt ... atttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
                             ttctgac  putative branch site (score: 2)
                                        ttctcattt  putative PPT
                                       attctcatttattaa  TA-rich tract