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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG

Basic information

species Zea mays
transcript GRMZM2G059083_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059083_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtagagttaga-gtcagctcatccatccat-ctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtg----ttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
    |||  || | |  |  ||     ||   |   |||  |||      |    | |     | | || || | | || | | | ||| | |     ||| | |||| | ||| || || || || ||||| ||| | || || |||||||| |||||||| |||||||||||||||||||||
----gtatggtcatatattggcgtgctcacttagattagagagcagaatttagtggtatatagtcaaca-cttgtagtgattacttctgcttttctgtttccttagCTTGGAACAGGAACTGGAATAGCTCCATTCAGATCATTTTTGTGGAAAATGTTCTTTGAGGAGCACGAGGACTACAAG

upper sequence: GRMZM2G059083_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgat-gtgttcatc----agCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
               || || || | | ||  | |  | | | |||  ||  | |   |  | | |   |       | || |  |||  |   |||||    |||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| |||||||||||| |  | || |||||||||
---------------gtgagttc-tgcttcagtatcaccaaccatct-tctgttatgtcaatcagctgtttctttgagaaagtattgaaagcaatcatcttgcagCTTGCAACTGGTACTGGCATTGCTCCTTTTCGCTCATTCTTGTGGAAAATGTTCTTCGAGAAATATGAAGACTACAAG

upper sequence: GRMZM2G059083_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 3'ss of exon 5
--gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcat--cagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
   | | |     |  ||     |  |||         | | |  ||   |     |||    |||       | | || || | | |||| | |||||  ||||| ||||| || || || || ||||| |||||||| ||||||||||| |||||||| ||| |||| || |||||||||
gtattattcattctccagc--atttgtcctaatgctatggttgtaatggttttccaaaatgtattagtcgtatgtattgttacaacatgatttcttcattgcagCTTGCAACTGGAACTGGAATTGCTCCTTTCCGCTCATTCTTGTGGAAAATGTTCTTTGAGAAGCATGAAGACTACAAG

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|211014995|gb|FL081548.1|FL081548
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|78085945|gb|DV514338.1|DV514338
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13315987|gb|BG410434.1|BG410434
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13315986|gb|BG410433.1|BG410433
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|76015965|gb|DT943135.1|DT943135
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|6952551|gb|AW424619.1|AW424619
EST:     TGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGCTACCGGCATCGCTCCGTTCCGCTCCTTCTTGNGGAAGATG
genomic: TGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13382263|gb|BG458938.1|BG458938
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAG
EST: gi|13126400|gb|BG316970.1|BG316970
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
                                     tcctgat  putative branch site (score: 3)
                ttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA