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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGTTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGACCCTGTACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacgtctagcagaaccttattgcatatttgcttatgattgccatgcgtaggcaacatcatacatagaagtatgaaaaaatgagactgtatattc...

Basic information

species Zea mays
transcript GRMZM2G099452_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099452_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
CTTTGTTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGACCCTGTACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacgtctagcagaaccttattgcatat----ttgcttatgattgccatgcgtaggcaacatcatacatagaagtatgaaaaaatgagactgtatattc
 ||| |||||||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||| |||||||||||||||||||||| |||  ||||| ||      |  || ||  |   |   | |      |    |  |  | |   | ||  |   |  ||| ||            ||  |  |   |     
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctccgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcctctcaaccaatcacaac----

upper sequence: GRMZM2G099452_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G00580.1 (Glycine max), 5'ss of exon 7
CTTTGTTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGACCCTGTACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtatt---atacgtcta-gcagaaccttat-tgcatatttgcttatgattgccatgcgtaggcaacatcatacatagaagtatgaaaaaatgagactgtatattc
 |||||| ||  ||| || || | || |||||||||||||||||| || || || ||  |  | ||||| |||||||||||||||||||||||  |  ||||| |   | || |||   | |     ||| |||| |  |   | ||| |   ||||  |  |  |||  |   | |     | ||   ||   || ||  | | 
ATTTGTTCTTTGTGTTGAAAACAATTCCCCAGGAACAAAATTTGATCCAGTCCCTGTTGGTCTTCCTGGGATTCTCATCACAGATGTCAGCAATTCTAAGgtaatccgacacatctgtactggtgtatatatgcagaggtagat-tgagtttgatgctaaatc--cattttctcttggc-ccttaatttattccacagtcaagt-

upper sequence: GRMZM2G099452_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 5'ss of exon 8
CTTTGTTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGACCCTGTACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacgtctagcagaaccttattgcatatttgcttatgattgccatgcgtaggcaa-----catcatacatagaagtatgaaaaa-atgagactgtatattc
 |||||| |||||||||| |||  ||  ||||||||||| ||||| ||||| || ||||| || ||||| |||||||||||||| ||||||||| |     |  || |  |||     |  ||| ||   || |    |||  || |  |  ||||  |      ||   |   | | |  ||    || ||    || |   || 
GTTTGTTCTTGCTGTGGAAAATGTTTCTCCAGGAACAAAGTTTGATCCTGTTCCTGTCAGTATTCCTGGGATTCTCATCACAGAAGTCAGCAAATC---AATGgtaaatatctta---attcttcttctttaatgatatatatttccagtaggtagatagtggtccagtgtgactggcaccatctggaacatcccgctatcagttg

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|32835874|gb|CD975552.1|CD975552
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCATAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|61118150|gb|DN559111.1|DN559111
EST:     TCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAATAGATTGGGCTGGAAGG
genomic: TCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|86472826|gb|DY239196.1|DY239196
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGGTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|211288258|gb|FL396091.1|FL396091
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|31355042|gb|CD439399.1|CD439399
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|60358693|gb|DN225666.1|DN225666
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|60358392|gb|DN225365.1|DN225365
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|149033083|gb|EE154985.2|EE154985
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|31357749|gb|CD442106.1|CD442106
EST:     TACCAGTCAGCATCCCTGGAATGCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|61118149|gb|DN559110.1|DN559110
EST:     TCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|211319661|gb|FL415870.1|FL415870
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|31611998|gb|CD568620.1|CD568620
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|211102292|gb|FL386878.1|FL386878
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
EST: gi|19351725|gb|BM896257.1|BM896257
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACC
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACC
EST: gi|19351594|gb|BM896126.1|BM896126
EST:     TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAG                         GATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG
genomic: TACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacg ... gttcttgtagGATCTTATAGACTACTACAATTCTTCCACCGTAAGAGATTGGGCTGGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGTTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGACCCTGTACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacgtctagcagaaccttattgcatatttgcttatgattgccatgcgtaggcaacatcatacatagaagtatgaaaaaatgagactgtatattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG