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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagcatccgtttaatatgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG

Basic information

species Zea mays
transcript GRMZM2G421857_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T04 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 8
gtaaaaaaaaagctaattctcttttgta-gaagatcaaatttcgtaaggattgaagcatccgtttaatatgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG
         || | | |||  | || || |||||| | || || | |||||| ||||||  ||||||| || |      | | |  | |||||||||||||||||||||||||||||||||      || |||||||| |||||||||||||| ||||| |||
-------gtaaacaagttccatcttttatgaagataacatgtc-tgaggattaaagcattagtttaatctgttg----tactgcactacagACATGGCCTGTGCGTTCACCAAGGCCTGTTATGGAAAAACTTGCTGCAGATACACCTCTTCTTACAGGACAG

upper sequence: GRMZM2G421857_T04 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 8
--------------------gtaaaaaaaaagctaattctcttttgtagaag-atcaaatttcgtaaggattga-----agcatccgtttaatatgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG
                     | |  |     ||     |  ||  | |||| ||     ||| | | ||||       |  |    ||   |  |  || || |     || ||||| |||||||| ||| |||| |||||||||||||| || ||||| || ||||| |||||||| || || |||
gtttctagccatttattttgttcatcatttcactgtagttgcttcattgaagtattggtattccttatgattatcctacattacaacttccttgcgtgtactttacccattttcagACTTGGCCTGTACGTACACCCAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAG

upper sequence: GRMZM2G421857_T04 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 8
---------------------gtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattga-----agcatccgtttaatatgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG
                       |  |   ||    | |  |||   || |  ||      || | | ||||       |  |    ||   | ||  || || |     || ||||| ||||| || ||| ||||||||||||||||||| || ||||| || ||||| |||||||| || || |||
gtttctagccatttatttcgttcaccacttaattgtagttacttcattaaagtattggtactccttatgattatcctacattacaacttccttgtgtgtactttacccattttcagACTTGGCCCGTACGTACACCAAGGCCTGTTGCATCAAAACTTGCAGCTGATACTCCTCTTCTTACTGGTCAG

upper sequence: GRMZM2G421857_T04 (Zea mays), 3'ss of exon 9
lower sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 9
--gtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagca-tccgtttaatatgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG
   |  |   |    ||||  || |   |  ||    ||||||        |||   || || ||| |||  | ||  || || |   | ||||  |||||||| ||| | || ||||| |||||||| ||||||||||| ||||| ||||| || || ||||||
gtttgcatgtatctttaatcttcctacttgcaaacgtaaattttaagctatttggttcactctgttaaattggtttggttgatatatgt-cagAGCTGGCCTGTACGTACGCCTAGGCCAGTTGCATCAAAGCTTGCTGCCGATACTCCTCTACTTACGGGGCAG

upper sequence: GRMZM2G421857_T04 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagcatccgtttaata-------tgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG
     |       |   | |   ||     | |  ||| |  | | ||    ||||||| | |||||        |  ||| || |  |   | ||||| |||||||| ||| |||| ||||||||||| || ||||||||||| ||||||||||| || || ||||||
--gttattggtattttctatgcattaccttaaagtaaaatctgcatggt---aagcatctgattaatgactcctttttttattttacctttcttcagACTTGGCCTGTCCGTACACCTAGGCCTGTTGCCTCAAAGCTTGCTGCTGATACACCTCTCCTTACTGGGCAG

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|149070206|gb|EE158608.2|EE158608
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211532178|gb|FL123452.1|FL123452
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAA-TTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAG-CCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211152796|gb|FL123506.1|FL123506
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGNCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGA
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGG-CCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGA
EST: gi|211529167|gb|FL123433.1|FL123433
EST:     TGCTAGAATTGGAATTTCAGGNCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCCTGTGCGT-CACCAAGGCCTGNTGCATCGAAGCTTGCTGCGGA
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCC-TGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGA
EST: gi|31355789|gb|CD440146.1|CD440146
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211535168|gb|FL123457.1|FL123457
EST:     TGCTAGNATTGGAATTTCAGGGCATAAAAAAGAA-TTTACCATGCTTCAG                         ACATGGCCTGTGCGTT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTT
EST: gi|148968185|gb|EE019478.2|EE019478
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211156004|gb|FL123539.1|FL123539
EST:     GCTAGAAATTGGAATT-CAGGGCATAAAAAAGAA-TTTACCATGCTTCAG                         ACATGGCCTGTGCCGT-CACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGA
genomic: GCTAGAA-TTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGC-GTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGA
EST: gi|148962822|gb|EE013742.2|EE013742
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|6012344|gb|AW061700.1|AW061700
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCCCCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|148966031|gb|EE016965.2|EE016965
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTC-CCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211154396|gb|FL123515.1|FL123515
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGA
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGG-CCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGA
EST: gi|211532167|gb|FL123441.1|FL123441
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|149098348|gb|EE184321.2|EE184321
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGG
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGG
EST: gi|148966043|gb|EE016977.2|EE016977
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGC
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGC
EST: gi|149095258|gb|EE180885.2|EE180885
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|6636981|gb|AW261253.1|AW261253
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211541200|gb|FL123497.1|FL123497
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211541195|gb|FL123492.1|FL123492
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACAAAGGCCTGTTGCATCGAAG
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttcgtaaggattgaagcatccgtttaatatgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG
                                  gcttaat  putative branch site (score: 4)
                                        ttcatttcctt  CT-rich tract
                          tttaatatgcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagcatccgtttaatatgcttaattcatttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC