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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttagtccagtttgtttcattttatctgtgcttttgtgggtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT

Basic information

species Zea mays
transcript GRMZM2G078826_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
cttagtccagtttgtttcattttatctgtgcttttgtgg----gtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
||||  | |||||   | |||  |  | | | |||||      || | |    |||     ||| |||    |   ||||  | ||| |||||  ||  |||||||| |||||||| ||||| |||||||||||  ||||||| || |||||| ||||||||||||| ||||||||||||||||||||||| || ||||| |||
ctta--caagttttggtaattgcacatttacatttgtacctatgtgcatcacgtgttgacgtttacattttaat--tgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT

upper sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
-----------cttagtccagtttgtttcattttatctgtg--cttttgtgggtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttct----------------ttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
            ||  |  |   |||||  |||  |||| |  |  |  ||||| ||||         | |     |   |  ||  |||   |  |||| || |                ||   |||||| ||  |||| ||||||||||| || || || ||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||  | || || || || 
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC

upper sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
-----------cttagtccagtttgtttcattttatctgtg-cttttgtg---ggtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttct----------------ttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
            ||  |  | | | |||  |||  |||| | |   ||||   ||| ||||         | |     |   |  ||  ||| | || |||| ||                  ||   |||||| ||  |||| ||||||||||| || || || ||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||  | || || || || 
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC

upper sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
--cttagtcca-gtttgttt-cattttatctgtgcttttgtgggtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
  |  |||    || | | |   | || ||  | ||||  |  |   |||    |  | || ||   | |  | | |  |  | |   || | | ||  |||||||| || ||||||||||| ||||| ||||| || || || || || ||||||||||| ||||| || ||||| ||||||||||| ||||| || ||||| 
gtcaaagtgtgtgtatatatgtctcttctccatcctttctttaga--tttcaaaggtaaaaattaggttataatgctagaatgacc--tgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC

upper sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S42_89V6.1 (Physcomitrella patens), 3'ss of exon 8
---cttagtccagtttgtttcattttatctgtgcttttgtgggtcc--tttttttgtcagaatt-tgcatcaacacgg---tgaagcgccttttgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
    ||| | |  |   ||  |||||||   |  || ||     ||  ||| |   | |   |  |  ||||   | |   |       | | || | |   ||  ||| || ||  | || ||||| ||||| || || |||||||||||||||||| |||||||  |||||||  | |||||||| || ||  ||||||||||||| 
gtgtttacttc--tcccttaaattttattgctcattatgcttaccccatttgtccattatggtcattaatcactcctgacttatgattgcgtgtggtattgctat-cagAGTTGTCGTGAATTATGATTTCCCTACGGGAGTTGAAGACTACGTTCACCGGATTGGACGGACAGGTCGAGCTGGTGCAACCGGGCTTGCATATACATTC

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|31360358|gb|CD444715.1|CD444715
EST:     TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAG                         GGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
genomic: TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAGgttagactaa ... ctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
EST: gi|87156102|gb|DY400891.1|DY400891
EST:     TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAG                         GGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
genomic: TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAGgttagactaa ... ctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
EST: gi|32844392|gb|CD984073.1|CD984073
EST:     TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAG                         GGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
genomic: TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAGgttagactaa ... ctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
EST: gi|26558556|gb|CA830791.1|CA830791
EST:     TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAG                         GGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
genomic: TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAGgttagactaa ... ctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
EST: gi|22472442|gb|BU036922.1|BU036922
EST:     TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAG                         GGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG
genomic: TTAGTGGCAACTGATGTTGCTGCGCGAGGTTTGGACATCAAAGATATCAGgttagactaa ... ctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtcagaatttgcatcaacacggtgaagcgccttttgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
                                cgccttttgttttctt  CT-rich tract
                                    ttttgttttcttta  TA-rich tract