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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcattaataccgctattgtataaatgcatttagtttgttattctatacaattttgcttttgatctgctatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG

Basic information

species Zea mays
transcript GRMZM2G008287_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008287_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g58060.2 (Oryza sativa), 3'ss of exon 5
tcttcattaataccgctattgtataaatgcatttagtttgttattctatacaattttgctttt--gatctgc---tatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
|||   | | ||  | |    |  ||||  |||||  ||  |||| | ||||  ||| |||||   ||||||   | ||| | |     |||| || || || ||||||||||  ||||||| ||||||||||| ||||||||||| |||||||| ||||||||||||||||||
tctgagtcattattgtt----tgaaaatatatttacattagtatttt-tacatctttactttttttatctgcatttttttaacttacactgaattgacagtgcagGATGTTGAAGTTGAGGATAAGGTTGATGTGATAATATCAGAGTGGATGGGTTATATGCTTCTCTATGAG

upper sequence: GRMZM2G008287_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G00220.1 (Glycine max), 3'ss of exon 5
tcttcattaataccgctattgtataaatgcatttagtttgttattctatac---aattttgcttt-tgatctgctatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
    | || | |    ||| || |       || |  ||  |||||  |||    |    ||| | | || |  ||||        |||   ||     || ||||||||||  || | ||| | || ||||||||||| || ||||||||||||||||||||||| ||||||
----ctttgaaatttttatagtttttcctttttcaactttatattcgttactaagaacaagctgtataattttatattcaccattggttatgctttttgtgcagGATGTTGAAATTAATGAAGAAGTGGATGTTATAATTTCCGAATGGATGGGCTATATGCTTCTGTATGAG

upper sequence: GRMZM2G008287_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 5
--tcttcattaataccgctattgtataaatgcattta-gtttgttattctatacaattttgcttttgatctgctatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
  |    |||  ||  | | ||   |       |||| ||| |||| |    |||| ||    | |  | |  ||||    |   |||   ||     || ||||||||||  |||| ||| |||| ||||||||||| |||||||||||||||||||||||||| ||||||
ctttgaaatttttatagtttttcctttttcaactttatgttcgttactaagaacaagttg---tatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG

upper sequence: GRMZM2G008287_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G23410.1 (Glycine max), 3'ss of exon 5
---tcttca-ttaataccgctattgtataaatgcatttagtttgttattctatacaattttgcttttgatctgctatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
   | |||| || |||  | | |   || |||   | || ||  |  |  ||      | |  | ||  ||   |||||  ||   |||    || |  || ||||||||||  | |  |||||||||||||||||||| |||||||||||||||||||||||||| | ||||
ttttgttcaatttatattgttttctgatcaatttgtatatttgatattattaactggctcttttgttcttcacatatttactta--gttatggtgcc--tgcagGATGTTGAAATCGGTGAAAAGGTTGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATGTGAG

upper sequence: GRMZM2G008287_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G10450.1 (Glycine max), 3'ss of exon 5
--tcttcattaatac-cgctattgtataaatgcatttagtttgttattctat--acaattttgcttttgatctgctatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
   |||    ||| | | ||    | ||  |  | || ||||  |  || ||    |  |||||| || ||   |   |   ||| | | |         || ||||||||||  |  ||||| | |||||||||||||| ||||||||||||||||||||||||||  || ||
agccttggacaatcctcacttcattgtatttatactttgttttctgatcaatttgtatatttgctgttaataatcggctgttttgttatggtgt-----ctgcagGATGTTGAAATCAAGGAACAAGTTGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTACATAAG

upper sequence: GRMZM2G008287_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0071g00750.t01 (Vitis vinifera), 3'ss of exon 5
tcttcattaataccgctattgtataaatgcatttagtttgttattctatacaattttgcttttgatctgctattt---cattgctgttgaact---ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
  |  |||  |    | |||| |  |    | |   |||    |   |   |    ||| || ||| |||   ||   || |  | ||||| |   |  | || ||||||||||  |||| |||  ||||||||||||||| ||||| |||||||| || ||||| || ||||||
--tgtattt-tgttcccattgcaccagcttactc--tttcacttggaagctagccatgcatt-gatgtgcatgttaaacactaatcttgaattcttgtaactgcagGATGTTGAAATTGATGAAGGGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTGCTGTATGAG

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|211226256|gb|FL422661.1|FL422661
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAA
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAA
EST: gi|50334394|gb|CO529520.1|CO529520
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|211212464|gb|FL408347.1|FL408347
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|22491240|gb|BU051163.1|BU051163
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|87151790|gb|DY396579.1|DY396579
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|91057010|gb|EB167428.1|EB167428
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|71770637|gb|DR968574.1|DR968574
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|211542749|gb|FL414688.1|FL414688
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTT
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTT
EST: gi|78081912|gb|DV510324.1|DV510324
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|71770385|gb|DR968322.1|DR968322
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|76286032|gb|DV025600.1|DV025600
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|74241224|gb|DT649138.1|DT649138
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|211307470|gb|FL415311.1|FL415311
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGANGTTATGATATCAGAATGGATG
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATG
EST: gi|101388230|gb|EB816129.1|EB816129
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|101395512|gb|EB819684.1|EB819684
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|211161432|gb|FL401324.1|FL401324
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGT
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGT
EST: gi|71447013|gb|DR828063.1|DR828063
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGC
EST: gi|78106122|gb|DV524540.1|DV524540
EST:     AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAG                         GATGTTGACCTTGAGGAAAAGGTTG
genomic: AAGCAAACAACCTAACTGATCAGATTGTGGTCATCCATGGACGTGTTGAGgtgaggttat ... ggcattgtagGATGTTGACCTTGAGGAAAAGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatacaattttgcttttgatctgctatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
              ttttgat  putative branch site (score: 4)
                         tatttcatt  TA-rich tract