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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaaaatctgcaatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgctataggttcaactatggctgacattctgaactgacattag

Basic information

species Zea mays
transcript GRMZM2G083716_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 11
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgt--aaaaacaaaatctgc--aatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgctataggttcaactatggctgacattctgaactgacattag-------------------------------------------------------------
 ||||||||||||||||||||||||||||||||||||||| || | || ||||||| ||| |||||||||||||| |  |||||||| || |||||||||||  | || ||  |||| |   || |  |  ||   ||  |      |  |  |  ||   | |||   | || |   |    ||    ||     | ||   |   | |                                                               
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGCAGAAGgtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttag

upper sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G18760.3 (Glycine max), 5'ss of exon 10
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaa----------------aacaaaatctgcaatccc--------gtaattcatttgaaagaggatggaggcaacagagcacaacc-ttgctat-aggttcaactatggctgacattctgaactgacattag-----------------------
    ||||||||||||||||||||||| || ||||||||| || | |||||| | || || || || ||||||||||  || || || || ||  | || || |                  | | ||| |    | ||        || ||   |||      || ||  || ||  |  |   ||  ||| | | |  |||||||          |  |||  | | | | |                       
----GAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAGTGAgtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcaggttggag

upper sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 10
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaa----------------aacaaaatctgcaatccc--------gtaattcatttgaaagaggatggaggcaacagagcacaacc-ttgctat-aggttcaactatggctgacattctgaactgacattag----------------
 || ||||||||||||||||||||||| || ||||||||| || | |||||| | || || || || ||||||||||  || || || || ||  | || || |                  | | ||| |    | ||        || ||   |||      || ||  || ||  |  |   ||  ||| | | |  |||||||          |  |||  | | | | |                
TGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcag

upper sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaa-aacaaaatctgcaatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgctataggttcaactatggctgacattctgaactgacattag
 ||||||||||||||||| |||||||| || ||||||||  | ||||||||| | || ||||| |||||||||||||| || || || || ||  | ||||| |    |||||||   |||   | ||||  |||| ||               |  ||     ||| ||  |  |||||||||  |  |  |   |            
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattt-tttgcaa---------------attgcttgctcttactgcattttcaactatttcccatctctag------------

upper sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 11
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaa--aacaaaatctgcaatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgctataggttcaactatggctgacattctgaactgacattag
 || ||||||||||||||||||||||| || ||||||||  | || |||||  | || || || ||||| || |  || || || || || ||  | ||||||||  ||  || ||| ||      ||| ||||      ||   |   |            ||| |||||   | |||  || | |                       
TGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAGAAAAGgtaaatcaatcaagtcttcagattt-taactcat------gaaccttcggttt-----ctctaactttgctgatgattcc-ctttag-----------------------

upper sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaaaatctgcaatcc---cgtaattcatttgaaa----gaggatggagg----caacagagcacaaccttgct--ataggttcaactatggctgacattctgaactgacattag-------------------------------------
 ||||||||||| |||||||| ||||| |||||||||||  || | |||||  | || || || ||||||||||| || || || || || ||| | ||||| | |       |||   ||     |  |||  |   | |    |||  | |       ||| ||     || | ||||  ||  ||||||     |   | ||  ||  | |    |||                                     
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttg-aatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag

upper sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 10
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaa-acaaaatctgcaatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgct-ataggttcaactatggc-tgacattctgaactgacattag----------------------
|||||||||||||||||| |||||||| ||||||||  | ||||| || ||||| ||||| || || ||||| || || || || |  || ||||| ||||| | | |   || ||  |  |   | |||   |||        |   || |   | | | ||   |||| | |  ||    | |  | |||  |  ||| || |   | |                      
CGTTGAGGAAGGTATTGTGGTTGGTGGCGGGTGCACATTGTTGCGTCTAGCAGCAAAAGTTGATGCTATCAAAGACACTCTTGATAGTGATGAGCAAAAGgtgatacatttaaact-tatacatatgattatattgtttttatcttttggaag--gggtataaaagtgcttacacttttgcttctaacctgatgtcttgatctaatgcttggtttactgggaatgattggcag

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|110524823|gb|EE029007.1|EE029007
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|78080917|gb|DV509329.1|DV509329
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|148983128|gb|EE029059.2|EE029059
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|149099157|gb|EE185182.2|EE185182
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|33094001|gb|CF053995.1|CF053995
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTGAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|5069818|gb|AI737783.1|AI737783
EST:     GACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: GACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|60342862|gb|DN209835.1|DN209835
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|60395675|gb|DN228545.1|DN228545
EST:     CAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|211360073|gb|FL471663.1|FL471663
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTGAGGAGGGCCCTGAGCTACCCACTTAATTTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|87156784|gb|DY401573.1|DY401573
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAAT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAAT
EST: gi|24934364|gb|CA452582.1|CA452582
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|6601638|gb|AW256034.1|AW256034
EST:     CCATCAAGGAT-C-CTGGAG-ACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTGAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32837828|gb|CD977506.1|CD977506
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTGAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|60355768|gb|DN222741.1|DN222741
EST:     CAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|5761879|gb|AI966852.1|AI966852
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCCCTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|211500916|gb|FL458285.1|FL458285
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|211268071|gb|FL357474.1|FL357474
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTGAGGAGGGCCCTGAGCTACCCACTTAATTTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|71764883|gb|DR962820.1|DR962820
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32914512|gb|CF019324.1|CF019324
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTGAGGAGGGCCCTGAGCTACCCTTTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|148961769|gb|EE012546.2|EE012546
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|120480889|gb|EH211078.1|EH211078
EST:     CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaa ... ctgacattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaaaacaaaatctgcaatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgctataggttcaactatggctgacattctgaactgacattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG