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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGGGCGAAGAGTGGCAAGATCGGAGTTGCTGGTGTCTGCAACGGTGGAGGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactcaaaacaccgaatatatctcaactcaaattgattcttttactagctggcagtaggagctaaccagtataaggtgctattatcaaactgtaatatggtcgcatattcagctaggcctaattaagttgtattttttccttttacaactgttgtgcaatttgactaactgctgcaccttgatattgcag

Basic information

species Zea mays
transcript GRMZM5G866758_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os09g07830.2 (Oryza sativa), 5'ss of exon 14
----TCAGGGCGAAGAGTGGCAAGATCGGAGTTGCTGGTGTCTGCAACGGTGGAGGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactcaaaacaccgaatatatctcaactcaaattgattcttttactagctggcagtaggagctaaccagtataaggtgctattatcaaactgtaatatggtcgcatattcagctaggcctaattaagttgtattttttccttttacaactgttgtgcaatttgactaactgctgcaccttgatattgcag
    | |||| |||  ||||||| ||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| ||||| |||||||||       ||||||||| | ||| ||| |   |   | || |||| |    | |   |||||           |   |    || | |  ||| |   |   ||   |||| |                                                                                             
GTTCTTAGGGAGAAAGGTGGCAAAATCGGAGTTGCTGGTGTTTGCAATGGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAG------CCTTgtaaggcgcaatacatct--ttcttttctactcgag--aaatagcttact-----------gagacctgtcatttttgggt-caggtgctaactggtaacag--------------------------------------------------------------------------------------------

upper sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os09g07830.3 (Oryza sativa), 5'ss of exon 13
----TCAGGGCGAAGAGTGGCAAGATCGGAGTTGCTGGTGTCTGCAACGGTGGAGGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactcaaaacaccgaatatatctcaactcaaattgattcttttactagctggcagtaggagctaaccagtataaggtgctattatcaaactgtaatatggtcgcatattcagctaggcctaattaagttgtattttttccttttacaactgttgtgcaatttgactaactgctgcaccttgatattgcag
    | |||| |||  ||||||| ||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| ||||| |||||||||       ||||||||| | ||| ||| |   |   | || |||| |          |  ||  |||  |   |    |     |  | ||||||||      ||| || | || |  |                                                                                       
GTTCTTAGGGAGAAAGGTGGCAAAATCGGAGTTGCTGGTGTTTGCAATGGCGGAGGCGGAGCATCTGCTCTCGTTCTCGAGCTTGCATAAGAAG------CCTTgtaaggcgcaatacatct--ttcttttctactcgagaaa------tagcttactgagacctgtcatt--tttgggtcaggtgctaactggtaacagtgacattgcag---------------------------------------------------------------------------------------

upper sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA07G39870.2 (Glycine max), 5'ss of exon 13
----TCAGGGCGAAGAGTGGCAAGATCGGAGTTGCTGGTGTCTGCAACGGTGGAGGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactcaaaacaccgaatatatctca-actcaaattgattcttttactagctggcagtaggagctaaccagtataaggtgctattatcaaactgtaatatggtcgcatattcagctaggcctaattaagttgtattttttccttttacaactgttgtgcaatttgactaactgctgcaccttgatattgcag
    | ||   |||||| || |||   || |||||||   |||||||||| ||||| |||||||| ||||||||||| ||||||   ||||   | |  |  |||| || |      ||   |  |||  | | | |  | || || ||  |         || || |||   |||||    |  | ||    |                                                                                                         
GTATTGAGACAGAAGAGAGGGAAGTATGGTGTTGCTGCCATCTGCAACGGGGGAGGAGGAGCATCTGCTCTTGTTCTTGAGCTCATgtaagcctttttaattttgtcagccattgttcagttataatagtttacagtgtagttaatcctgct-----tgaacaatatgag---accaggtccatattctcgggt---------------------------------------------------------------------------------------------------------

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|17931054|gb|BM268014.1|BM268014
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|30088105|gb|CB886310.1|CB886310
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|32919681|gb|CF024493.1|CF024493
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|33096645|gb|CF056639.1|CF056639
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|101395308|gb|EB819584.1|EB819584
EST:     GGCGGAGCATCAGCTCTTGTTTTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|71309358|gb|DR790968.1|DR790968
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|211193824|gb|FL472434.1|FL472434
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|78091101|gb|DV519475.1|DV519475
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|110525002|gb|EE029186.1|EE029186
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|93281704|gb|EB673968.1|EB673968
EST:     GGCGGAGCATCAGCTCTTGTTTTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|78087734|gb|DV516127.1|DV516127
EST:     GGCGGAGCATCAGCTCTTGTTTTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|76921549|gb|DV168617.1|DV168617
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|33095848|gb|CF055842.1|CF055842
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|71309359|gb|DR790969.1|DR790969
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|31909499|gb|CD650949.1|CD650949
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|211155574|gb|FL331213.1|FL331213
EST:     ATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: ATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|76284259|gb|DV023827.1|DV023827
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGCTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|193502028|gb|AM938160.1|AM938160
EST:     GGCGGAGAATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTGGCAAAAGCTCCCTGAGGTGATCTTGTTGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|193502203|gb|AM938237.1|AM938237
EST:     GGCGGAGAATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTGGCAAAAGCTCCCTGAGGTGATCTTGTTGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|30306466|gb|CD001139.1|CD001139
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|211522817|gb|FL338578.1|FL338578
EST:     ATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: ATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|149016999|gb|EE154316.2|EE154316
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|76936635|gb|DV174816.1|DV174816
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|211206261|gb|FL471226.1|FL471226
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|29544660|gb|CB605040.1|CB605040
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|32864390|gb|CF004072.1|CF004072
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|76017958|gb|DT945128.1|DT945128
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|32864696|gb|CF004378.1|CF004378
EST:     GGCGGAGCATCAGCTCTTGTTTTGGAGCTCGCATAAAAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
EST: gi|32862142|gb|CF001824.1|CF001824
EST:     GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTT                         GTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT
genomic: GGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactca ... gatattgcagGTAGTTAGCAAAAGCTCCCTGAGGTGATCTTGTAGTCTTATTTTCCGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGGGCGAAGAGTGGCAAGATCGGAGTTGCTGGTGTCTGCAACGGTGGAGGCGGAGCATCAGCTCTTGTTCTGGAGCTCGCATAAGAAATCTAGACCTTgtaagactcaaaacaccgaatatatctcaactcaaattgattcttttactagctggcagtaggagctaaccagtataaggtgctattatcaaactgtaatatggtcgcatattcagctaggcctaattaagttgtattttttccttttacaactgttgtgcaatttgactaactgctgcaccttgatattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA