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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtcccctagaaaacaattcttagattggatattttccccctcataatggccatgagtttatggtgcctcattaacaactcagcagcattgagg...

Basic information

species Zea mays
transcript GRMZM2G038791_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 5'ss of exon 6
GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtcccctagaaaacaattcttagattggatattttccccctcataatggccatgagtttatggtgcctcattaacaactcagcagcattgagg-----------------------------------------------------------------
|| ||||||||||||||||| || ||||||||||||||||||||||||||||||||||| || ||||| |||| ||| ||  ||    |||  |||| |     |||   | |       |   |    | | ||||  |      |||    || || |   | | |                                                                   
GTAATGAATCTTATTGGAGATGTTAGAGGAAAAGTGGCTGTTATGATGGATGATATGATTGATACAGCTGgtaagttctcatctg---aactgttctcattcatgattcatccaaggcagttgagaatttaatttta--gcattaaattgcacacacaactaaaattactctttgcctttctttgagatatttcgcttccaaatatcaatattctaatgaaaccaattaaattag

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G16400.3 (Glycine max), 5'ss of exon 6
GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtcccc--tagaaaac---aattcttagattggatattttccccc-tcataatggccatgagtttatggtgcctcattaacaactcagcagcattgagg
|||||||| || ||||| || || | ||||||||| ||||| ||| | ||||||||||||||||| || |||| |   ||  |  |    ||    || | | |     ||||||||   |  | ||  |   ||  ||| | || ||  |     | | ||    |  |      
GTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGgtatgccatcgtcattgtccaatttgaactttgaagagagatattttgttctgtgattttttgcac-agtgtttgctgggttgaagaaatctagttaagaa-----

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G06110.1 (Glycine max), 5'ss of exon 6
GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtcccctagaaaacaattcttagattggatattt-tccccctcataatggccatgagtttatggtgcctcattaacaactcagcagcattgagg--
|||||||| || ||||| || || | ||||||||| ||||| ||| ||||||||||||| ||||| || |||| |   ||  | |     |||||   |  ||| | ||   |     |   | ||    | | ||| | |  | |  |    |  |  || |  || | |  
GTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTGGATGATATGATTGACACTGCTGgtatgccatcttc-aatgcccaatttgaaatttgaagatagattttttttccagtgttttttattttgttgcacttggtgtttactt--gctgggttaaagaa

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 6
GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtcccctagaaaacaattcttagattggatattttccccctcataatggccatgagt-ttatggtgcctcattaacaactcagcagcattgagg
|| |||||| | ||||| || || |  || ||||||||||||||| ||||||| ||||| |||||||| |||  ||  |    | |||    ||| |   | |   | || | |   |   ||     || | | || |          |        || | |||  |  
GTCATGAATTTGATTGGTGATGTTAAGGGTAAAGTGGCTGTTATGGTGGATGACATGATTGACACAGCTGgtgagtcttatatttgaactgcattttgttacttttttttcttcttttgcaaacaaatattaatcttctaaaaagatgatcttggaaaagta-catcaaat

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S152_123V6.1 (Physcomitrella patens), 5'ss of exon 6
GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtcccct-------agaaaacaattcttagattg-----gatattttccccctcataatggccatgagtttatggtgcctc------attaacaactcagcagcattgagg-
|| |||||| | ||||||||||| | ||||||||||||||| ||| |||| || ||||| ||||| || |||| |   ||  ||       ||||   |||  ||  |||      | | ||   | | |  | | |   || | |  |  |    |       ||||| ||||   || | ||     
GTCATGAATTTGATTGGAGACGTCAAAGGAAAAGTGGCTGTCATGGTGGACGACATGATAGACACTGCCGgtatgaactcgtcttaccatgagaatctaatcatttaatttattctggttttgaacacttgctgaagtatatcaatcaaccgaattttcttgctattaataactttacatccttcgcag

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|211009691|gb|FL435043.1|FL435043
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|211126323|gb|FL371824.1|FL371824
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|60338563|gb|DN205536.1|DN205536
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|91052223|gb|EB162641.1|EB162641
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|19770111|gb|BQ034832.1|BQ034832
EST:     GGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: GGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|74243299|gb|DT651213.1|DT651213
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|78085035|gb|DV513428.1|DV513428
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|60350838|gb|DN217811.1|DN217811
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|71429935|gb|DR810985.1|DR810985
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|76011084|gb|DT938254.1|DT938254
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|93016209|gb|EB641729.1|EB641729
EST:     CGGGAGAGGAAAAGTGGCTGTTTTGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGGTACTGCACCCAGGAAGGCGCCCGAGAA
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCA-CCAGGAAGGCGCCCGAGAA
EST: gi|211276932|gb|FL386926.1|FL386926
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|86468618|gb|DY234988.1|DY234988
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|78544258|gb|DV621756.1|DV621756
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|211123271|gb|FL408205.1|FL408205
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|110204864|gb|EC886761.1|EC886761
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|60398185|gb|DN231001.1|DN231001
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|78125653|gb|DV544037.1|DV544037
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|78544420|gb|DV621918.1|DV621918
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|211292499|gb|FL395084.1|FL395084
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|19769635|gb|BQ034356.1|BQ034356
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
EST: gi|26457160|gb|CA828743.1|CA828743
EST:     CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG                         GTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG
genomic: CGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtc ... acccaaacagGTACCATTTCCAAAGGAGCTGAGCTACTGCACCAGGAAGGCGCCCGAGAAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAGgtacgttgtcccctagaaaacaattcttagattggatattttccccctcataatggccatgagtttatggtgcctcattaacaactcagcagcattgagg

- - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - GATGGA