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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGGCTGTGCTTCGCGCAGGACCGGTACATCTTCCACGTCCTCCGATCCGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactacccttcgttcctctcaattcgttcgttcgctcgctcgcttgctcgcatacataagatttttagctgctactgattgctagtactccagttggc...

Basic information

species Zea mays
transcript GRMZM2G149843_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g06540.1 (Oryza sativa), 5'ss of exon 1
TCCAGGCTGTGCTTCGCGCAGGACCGGTACATCTTCCACGTCCTCCGATC------------CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactacccttcgttcctctcaattcgttcgttcgctcgctcgcttgctcgcatacataagatttttagctgctactgattgctagtactcc-agttggc----
            |||||||||||||| |||||||||||||||||||| ||            || |||||  ||| ||||||||||||| |||||||||||||||||||||||||   || ||    | ||  | | |  ||  |   ||        || ||  ||  ||| |||    || ||     | |   |  |  ||  |||  |     
------------TTCGCGCAGGACCGCTACATCTTCCACGTCCTCCGCTCCCCTCCCCCCGCCGCCGCCGATGGCCTCACCTTCCTCTGCATGGCCAACGACACCTTCGGAAgtacaaactctcttatacttactagt-attactctactaatctatatgatc-tatggataggata---agatggattcgttcattcatcttcttagtatgttctt

upper sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G09680.1 (Glycine max), 5'ss of exon 1
------TCCAGGCTGTGCTTCGCGCAGGACCGGTACATCTTCCACGTCCTCCGATCCGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactacccttcgttcctctcaattcgttcgttcgc--tcgctcgcttgctcgcatacataagatttttagctgctactgattgctagtactccagttggc-
      |||||||| |||||| | ||||| || |||||||||||| | |||||||| || |      ||||||||| | ||||||||||||||||||||||||||||| | | |   |  ||| |||        || ||||   |||    |||  |  ||||  ||     |     |  ||||  | | ||  ||   || ||   
TCCGACTCCAGGCTCTGCTTCTCTCAGGATCGCTACATCTTCCACATACTCCGATCGGATG------GCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttcttcttcttcttcttctcctcctccttcgtaatcgtaatcttaatttcatatttatacaatccgatt--tacttttagttaagacgt-agatgcta

upper sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G18760.1 (Glycine max), 5'ss of exon 1
------TCCAGGCTGTGCTTCGCGCAGGACCGGTACATCTTCCACGTCCTCCGATCCGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactacccttcgttcctctcaattcgttcgttcgctcgctcgcttgctcgcatacataagatttttagctgctactgattgctagtactccagttggc----
      |||||||| |||||| | ||||| || |||||||||||| | ||||||||||| |      ||||||||| | ||||||||||||||||||||||||||||| | |   ||||||   | ||   |   ||||   ||   |  | |  |   |         | | |  | | ||   | ||   |  || | |  |      
TCCGACTCCAGGCTCTGCTTCTCTCAGGATCGCTACATCTTCCACATACTCCGATCCGATG------GCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagt--tcttcgtctttttcttcttaatcgtaatcttaatttcgttgttatacgatccgattctctttcagtta--aaatgtaggatctactgaagagtctt

upper sequence: GRMZM2G149843_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0080g00800.t01 (Vitis vinifera), 5'ss of exon 1
------TCCAGGCTGTGCTTCGCGCAGGACCGGTACATCTTCCACGTCCTCCGATCCGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactacccttcgttcctctcaattcgttcgttcgctcgctcgcttgctcgcatacataagatttttagctgctactgattg--ctagtactccagttggc-
      |||||||| || ||| ||||||| || ||||| || ||| | ||| || |||| |      |  || | ||||| || ||||||||||||||||||||||||   ||  | ||| | || ||  ||  ||  ||   |       ||  |   ||   |    | ||  | |  |  || |||  || |  |   || | |  
GCCGATTCCAGGCTCTGTTTCTCGCAGGATCGCTACATATTTCACATACTCAGAGCCGATG------GACTCGCGTTCCTTTGCATGGCCAACGACACCTTCGGAAgtctgtagtcatcgcttct-tcgttttattttttaatttttggttttattataatttttgttttgttcggttttt--tggttgatctggcccgggagctaggg

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|15198942|gb|BI423572.1|BI423572
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTC-NTACCTGGAGGACATCCAAATGAGG-TCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|91050464|gb|EB160882.1|EB160882
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211398006|gb|FL167601.1|FL167601
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211395387|gb|FL167591.1|FL167591
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211395384|gb|FL167588.1|FL167588
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|78077927|gb|DV506349.1|DV506349
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211395376|gb|FL167580.1|FL167580
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211397999|gb|FL167594.1|FL167594
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|60393990|gb|DN226860.1|DN226860
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|71298112|gb|DR785033.1|DR785033
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|148997924|gb|EE035912.2|EE035912
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211398010|gb|FL167605.1|FL167605
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|71448766|gb|DR829816.1|DR829816
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|89760100|gb|DY688661.1|DY688661
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCT
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCT
EST: gi|211395375|gb|FL167579.1|FL167579
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211395385|gb|FL167589.1|FL167589
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|60401449|gb|DN234256.1|DN234256
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211398003|gb|FL167598.1|FL167598
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|94479642|gb|EB708600.1|EB708600
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211022376|gb|FL167612.1|FL167612
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|93013841|gb|EB639361.1|EB639361
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211397998|gb|FL167593.1|FL167593
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|93282854|gb|EB675118.1|EB675118
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|211395377|gb|FL167581.1|FL167581
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
EST: gi|71424443|gb|DR806311.1|DR806311
EST:     CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAA                         GAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA
genomic: CGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactaccc ... cgtgatgcagGAAGGATCCCCTTTCTCTACCTGGAGGACATCCAAATGAGGTTCATGAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGGCTGTGCTTCGCGCAGGACCGGTACATCTTCCACGTCCTCCGATCCGACGCCGCCGGCATCACCTTCCTCTGTATGGCCAACGACACCTTCGGAAgtaactacccttcgttcctctcaattcgttcgttcgctcgctcgcttgctcgcatacataagatttttagctgctactgattgctagtactccagttggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcgctc