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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaaacactttaccatgcacgatgaatgctgatttttgataattttttttaaaaataaatggttacctggtggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG

Basic information

species Zea mays
transcript GRMZM2G036534_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 3'ss of exon 2
-------gtcaaacactttaccatgcacgatgaatgctgatttttgataattttttttaaaaataaatggttacctggtggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG
       |      | | |  |||  ||    |||     ||| ||||    | | || |  | |||||||||  || |||||||||||||| ||||||||||| ||||| ||||||||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||||| ||||
gtacagtgcttgtaattgttgcatatacttaaaattggtgtttatgatggcgtctcttgatga-aaatggttaattgttggtttatgcagCTCGACATTTATTCTTTGTCGAGGAAATGGAAGGAGTTAGTCGATAAGGCTCGAGCGAAGCAGCTACAGCCCCATGAATACAATTCTG

upper sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 3
-----------------gtcaaacactttaccatgcacgatgaatgctgatttttgata----attttttttaaaaataaa-tggt-tacctggtggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG
                  | || ||  ||    | | |        |   ||| | |||    ||  || || |   |||| |||| ||  || ||  |  || || ||||  | |||||||||||||| || |||||||||||||||||||||||  |||| |||||||| || || ||||| |||||| |||
gttttccaatactctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG

upper sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G35960.2 (Glycine max), 3'ss of exon 3
-----------------gtcaaaca--ctttaccatgcacgatgaatgctgatttttgataa--------ttttttttaaaaataaatggttacctggtggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG
                  | || ||   | ||   | | |      ||||  | |   ||||        ||| || |||||    ||  |||  || ||  |  || || ||||  | |||||||||||||| || ||||||||||||||||| |||||  |||| |||||||| || || ||||| |||||| |||
gtttaccaatactctaatttaagcagcttctaatctccccacctcctgcttttctaatataagatggttctttattgtaaaatggtatatttatttgatgtatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG

upper sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcaaacactttaccatgcacgatgaatgctgatttttga---taattttttttaaaaataaat-------ggttacctggtggtttatg--cagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG
         |||    || | | |  ||      ||||||   || | | | || ||||    |       ||||      |  ||| |   ||| ||||||||||||| || || || |||||||| || |||||||||||||| ||||| |||||||||||||| || ||||||||| |||
----gttcttttcttttgtatgctttataagagattttgagtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG

upper sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 2
----gtcaaacactttaccatgcacgatgaatgctgatttttgataattttttttaaaaataaatggttacctggtggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG
    || || |  ||     |  ||  | |||  ||  |     ||    |||| || | | ||   |||  ||    ||  |  || | |||||||||||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||| || ||||| |||||  | |
gtttgttaatctgttcttgctaaac--ttaattttggctaccc-tatggcttttcaagagttaa--attaattgcaatttattatagGTGGACATTTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCCGAGCAAAGCAGCTGCAACCTCATGAATACAATACAG

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|6865176|gb|AW360526.1|AW360526
EST:     AGATGGTGGGTTGATTACACCGATTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: AGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|78106198|gb|DV524616.1|DV524616
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|23357491|gb|BU645140.1|BU645140
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|24768304|gb|CA403433.1|CA403433
EST:     TGGCCATAGATGGTGGGTTGATTACACCGATTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|211440164|gb|FL434174.1|FL434174
EST:     GTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: GTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|6022391|gb|AW067319.1|AW067319
EST:     TGGCCATAGATGGTGGGTTGATTACNCCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|71765103|gb|DR963040.1|DR963040
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|78088435|gb|DV516828.1|DV516828
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|149027250|gb|EE046447.2|EE046447
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|93013412|gb|EB638932.1|EB638932
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|71444183|gb|DR825233.1|DR825233
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|93284411|gb|EB676675.1|EB676675
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|74246257|gb|DT654171.1|DT654171
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|78074314|gb|DV502748.1|DV502748
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|71759734|gb|DR957671.1|DR957671
EST:     GCCCATAGATGGTGGGTTGATTACACCGGTT-TTCAAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: GGCCATAGATGGTGGGTTGATTACACCGGTTCTTC-AAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
EST: gi|74236968|gb|DT644882.1|DT644882
EST:     TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgatttttgataattttttttaaaaataaatggttacctggtggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG
     tttttgataatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaacactttaccatgcacgatgaatgctgatttttgataattttttttaaaaataaatggttacctggtggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG