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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgatgttatttccttatactaagccttattgatttggtgtcttctacttctgagctttaatctcaatccatgctattgctttcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG

Basic information

species Zea mays
transcript GRMZM2G421857_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 7
gttagttgatgtta------tttccttatactaagccttattgatttg-gtgtcttctacttctg---agctttaatctcaatccatgctattgctttcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG
|||||| |||| ||      |  | |||| | | | | ||||||| ||  ||  |||||  | ||   | | ||  | |  | || |||| ||||| |   |||||||| |||||||||||||||||||||||||| || |||||| ||||||||||||| |||
gttagtggatgctatcagtatcactttatcccatgtcctattgatctgcatgcattctaactttgcttaaccttg-tatggaaccctgcttttgctataa-atgcagGATACAGTGCTAGAATTGGAATTTCAGGGTATCAAAAAGGAATTTACCATGCTCCAG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 7
-------gttagttgatgttatttccttatactaagccttattgatttggtgtcttctacttctgagctttaatctcaatccatgctattgctttcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG
       || ||   ||  | | |  ||    ||   |||    ||||  ||| ||  | ||||    |      | | |  |  ||  |   |   |||||||||||||||||||||| | || ||||| ||  | |||||| |||||||||||||||||
gtcttttgtaaggcaataatgtctattttgttta--tcttgcctattta-tgt-ttagatttctacaatcagtcatgagttgactctcatatatgtatatgcagGACACAGTGCTAGAACTTGAGTTTCAAGGTGTCAAAAAGCAATTTACCATGCTTCAG
















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|148941860|gb|EC886839.2|EC886839
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAGAGAAAT
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAAT
EST: gi|149070206|gb|EE158608.2|EE158608
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211532178|gb|FL123452.1|FL123452
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAA-TTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211152796|gb|FL123506.1|FL123506
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211529167|gb|FL123433.1|FL123433
EST:     ATGGGGAAAAATA-GT-ACATTGCACCAGCTGGCCAGTANCA-CCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGNCATAAAAAAGAAATTTACCATG
genomic: ATGGGGAAAA-TAAGTTACATTGCACCAGCTGGCCAGTA-CAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|31355789|gb|CD440146.1|CD440146
EST:     CTATGGGGAAAATAAGTTATATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211535168|gb|FL123457.1|FL123457
EST:     TATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTANCA-CCTGCAG                         GACACAGTGCTAGNATTGGAATTTCAGGGCATAAAAAAGAA-TTTACCATG
genomic: TATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTA-CAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|148968185|gb|EE019478.2|EE019478
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211156004|gb|FL123539.1|FL123539
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAAATTGGAATT-CAGGGCATAAAAAAGAA-TTTACCAT
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAA-TTGGAATTTCAGGGCATAAAAAAGAAATTTACCAT
EST: gi|148962822|gb|EE013742.2|EE013742
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211535166|gb|FL123455.1|FL123455
EST:     TATGGGGAAAAATA-GTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAG
genomic: TATGGGGAAAA-TAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAG
EST: gi|148966031|gb|EE016965.2|EE016965
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|87152921|gb|DY397710.1|DY397710
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCAT
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCAT
EST: gi|211154396|gb|FL123515.1|FL123515
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|6012344|gb|AW061700.1|AW061700
EST:     CAGCTGGCCAGTACAACCTGCAG                         GACNCAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211532167|gb|FL123441.1|FL123441
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|149098348|gb|EE184321.2|EE184321
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|148966043|gb|EE016977.2|EE016977
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|18654718|gb|BM499523.1|BM499523
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAAATGGAATTTCAGGGCAT
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCAT
EST: gi|149095258|gb|EE180885.2|EE180885
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|6636981|gb|AW261253.1|AW261253
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
EST: gi|211541200|gb|FL123497.1|FL123497
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAAATTACCAAT
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCA-T
EST: gi|211541195|gb|FL123492.1|FL123492
EST:     CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAG                         GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG
genomic: CTATGGGGAAAATAAGTTACATTGCACCAGCTGGCCAGTACAACCTGCAGgttagttgat ... tcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcttctacttctgagctttaatctcaatccatgctattgctttcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG
                  ctttaat  putative branch site (score: 4)
                                       ttgctttctt  putative PPT
                   tttaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgatgttatttccttatactaagccttattgatttggtgtcttctacttctgagctttaatctcaatccatgctattgctttcttatgcagGACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA