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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttctgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt...

Basic information

species Zea mays
transcript GRMZM2G064695_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatat-tagtggtgcatgcttgatgcttctgtta-gtcttcc--cgtaggaggcccttg-agtaaacccagatctattattcttgcctgtctt
||||||||||| || |||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||| |  |  |   ||  | |  |   |  | |     ||||  | ||| |||  |   |||  |  | | |    ||   ||| |  | ||   |        
GTTGACCTGAAGGTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgatgtcctgttgcag--------

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g40830.2 (Oryza sativa), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatat-tagtggtgcatgcttgatgcttctgtta-gtcttcc--cgtaggaggcccttg-agtaaacccagatctattattcttgcctgtctt
            || |||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||| |  |  |   ||  | |  |   |  | |     ||||  | ||| |||  |   |||  |  | | |    ||   ||| |  | ||   |        
------------GTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgatgtcctgttgcag--------

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttctgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt
||||  |||||||| || ||||| |||||  |||||||||||||||| || |||||||| || ||  | |||||||    ||||    ||| |  |  |  |||   |     |      |     ||| | |  ||| |         |||     ||  ||         
GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaa---tgttagatttattaatataatcttatagaaaacgaagcattaatgttagcaagtgcttaatatgtttttgatactcaatgattcaacag---

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttc-tgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt-----
|||   || ||||| || || ||||||||| | |||||||||||||| ||||||||||| || ||||| |||||||  ||      | |   |||       || ||      ||||         | |  |    |   |  | |    ||  | ||  ||     ||   |     
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag

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|18162086|gb|BM331925.1|BM331925
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|5714240|gb|AI944225.1|AI944225
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|113853280|gb|DW973854.1|DW973854
EST:     TTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAAAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|32846416|gb|CD986097.1|CD986097
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|148951068|gb|EC896727.2|EC896727
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|113791641|gb|DW913466.1|DW913466
EST:     GGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: GGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|60398611|gb|DN231427.1|DN231427
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|32940144|gb|CF044963.1|CF044963
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|166655145|gb|EG155168.1|EG155168
EST:     AGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: AGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|166652168|gb|EG083409.1|EG083409
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAAAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATG
EST: gi|211240437|gb|FL261944.1|FL261944
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAR
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|113831703|gb|DW948357.1|DW948357
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATC
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATC
EST: gi|166626099|gb|EG158853.1|EG158853
EST:     GTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: GTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttctgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt

- - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT