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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtggcctttgaaagtgtgagacgaatacacactgcatgcatacttgaatgcgtcttttatctttttagtgagattaacttctctgcatatgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTTAAAGGACAGAATAGTTTCATGTGAAATGCATGGCCGTGGCATTGAATTG

Basic information

species Zea mays
transcript GRMZM2G170291_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170291_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g18200.1 (Oryza sativa), 3'ss of exon 7
-atgtggcctttgaaagtgtgagacgaatacacactgcatgcatacttgaat-gcgtcttttatctttttagtgagattaacttctctgcatatgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTTAAAGGACAGAATAGTTTCATGTGAAATGCATGGCCGTGGCATTGAATTG
  |     ||||   ||| | | |    ||   | ||     |   |||| |     |   |    |   |   ||| |||||  | |  | ||||||  ||||||||||| ||||||||| | || ||||| ||||||||||| ||| |  | ||||||  ||||||||||||||| || ||||| ||||| || ||  | 
cgttaaatcttttctagt-taatatct-tagctaatgggctaacttttgattcattacaactggaatcccatgaagactaactgatttaaaaatgcctacagGTACCGAGGGAAGAGAATGCGAATTGACTATTTCCTTGTTTCAGAAAAACTGAAGGACCAAATAGTTTCATGTGACATTCATGGTCGTGGAATAGAGCTA

upper sequence: GRMZM2G170291_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT3G48425.1 (Arabidopsis thaliana), 3'ss of exon 7
atgtggcctttgaaagtgtgagacgaatacacactgcatgcatacttgaatgcgtcttttatctttttagtgagat-taacttctctgcatatgcctc--tagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTTAAAGGACAGAATAGTTTCATGTGAAATGCATGGCCGTGGCATTGAATTG
  |||    | || | |         |     |  || || |  |  |||  |  |   | | | |  ||  | || |   || | ||  |  |   |  ||||||||| |||||||| |||||||||||||| || || || || |||||  | || ||| | |||||||| ||| | ||||| || ||||| || ||| | 
--gtgag--tggatactacacattttagttttatggcttggagtccagaac-ctccgcatgtttctaaagctatatattgattttttgttttggttgccatagGTACCGGGGAAAGAGGATGAGGATCGACTATTTTCTGGTCTCTGAACAACTCAAAGACCGTATAGTTTCTTGTAAGATGCACGGTCGTGGGATAGAACTT
















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|18167261|gb|BM337100.1|BM337100
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCGATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|5030707|gb|AI714901.1|AI714901
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|91873536|gb|EB403493.1|EB403493
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|76021195|gb|DT948365.1|DT948365
EST:     GAAAAGGACATAGACGGTGGCTTCTTTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|93284180|gb|EB676444.1|EB676444
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|91872354|gb|EB402311.1|EB402311
EST:     GAAAAGGACATAGACGGTGGCTTTTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTTGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|76010860|gb|DT938030.1|DT938030
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGCT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|76016190|gb|DT943360.1|DT943360
EST:     GAAAAGGACATAGACGGTGGCTTTTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|50332549|gb|CO527675.1|CO527675
EST:     GAAAAGGACATAGACGGTGGCTTTTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|76014034|gb|DT941204.1|DT941204
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|6465582|gb|AW191177.1|AW191177
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|78024045|gb|DV492432.1|DV492432
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|86472832|gb|DY239202.1|DY239202
EST:     GAAAAGGACATAGACGGTGGCTTTTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|211128671|gb|FL439959.1|FL439959
EST:     TCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: TCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|211321948|gb|FK966254.1|FK966254
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|89757610|gb|DY687139.1|DY687139
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|74236587|gb|DT644501.1|DT644501
EST:     GAAAAGGACATAGACGGTGGCTTTTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATGGATTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|149043280|gb|EE047341.2|EE047341
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|76018499|gb|DT945669.1|DT945669
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|78105399|gb|DV523817.1|DV523817
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|211321950|gb|FK966256.1|FK966256
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|60351954|gb|DN218927.1|DN218927
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|18661354|gb|BM501369.1|BM501369
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|60356095|gb|DN223068.1|DN223068
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
EST: gi|71771441|gb|DR969378.1|DR969378
EST:     GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAA                         GTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT
genomic: GAAAAGGACATAGACGGTGGCTTCTCTTGGTCCGGTCATCCAATTGGCAAgtaagaaaca ... atgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatgcgtcttttatctttttagtgagattaacttctctgcatatgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTTAAAGGACAGAATAGTTTCATGTGAAATGCATGGCCGTGGCATTGAATTG
                            gattaac  putative branch site (score: 2)
                                              tgcctct  putative PPT
         tcttttatcttttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtggcctttgaaagtgtgagacgaatacacactgcatgcatacttgaatgcgtcttttatctttttagtgagattaacttctctgcatatgcctctagGTACCGAGGAAAGAGAATGAGGATCGACTACTTCCTTGTTTCGGAACAGTTAAAGGACAGAATAGTTTCATGTGAAATGCATGGCCGTGGCATTGAATTG

- - - - - - - - - - - - - atacaca
- - - - - - - - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - -ttgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgca