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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCTATGAGCCAGACTCGCCTTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactccttatgtgtaattacatattgatcagggtccagtatattggccaactatcatgatcaaatggtttataaaagcattgcaacaaggtctaca...

Basic information

species Zea mays
transcript GRMZM2G166903_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166903_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 5'ss of exon 5
TGTCTATGAGCCAGACTCGCCTTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactccttatgtgtaattacatattgatcagggtccagtatattggccaactatcatgatc----aaatggtttataaaagcattgcaa-caaggtctaca
||| |||||||||||   |||||  || |||||||| | ||| || |||||||||||||| ||||||||||||||||| |||||||||||||| |||||||||| |||   |||||   |     |     |     | ||  ||| || |  | |||  |  |     || || || ||  || || ||||  | |    ||| 
TGTTTATGAGCCAGAAAAGCCTTATACACCTGAACCTGAGACTCAGCGCCTTTCTACCTTATATAATGCTGATGTTGGACTTTACATGCTAGCCAACAAGgtaatact---tatgttggaagcattgccactttaatttca--ataatgcctgaatattgtacttctgtaattgattaattgaaccactgcattccacacatact

upper sequence: GRMZM2G166903_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 5'ss of exon 4
TGTCTATGAGCCAGACTCGCCTTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactccttatgtgtaattacatattgatcagg--gtccagtatattggccaactatcatgatca-aatggtttataaaagca--ttgcaacaaggtctaca--
||| ||||| ||  |    |||  ||| |||||||| | ||| || |||||||| ||||||||||||||||||||||||||||||||||| || || ||||| | ||||      || | | ||| || | ||| |   ||| |    ||    || | |  || |     || ||||||     |  ||   | |||   ||    
TGTTTATGAACCCAATAAACCTACAACGCCTGAACCTGAGACTCAGCGCCTTTCCACCTTGTATAATGCTGATGTTGGTCTTTACATGCTGGCCAATAAGgttatactca----atgcattcacacatcggtcatgtcatcctgctcttta---aattttggtggttttgttgctttatatggttaatttattataagaaatatcac

upper sequence: GRMZM2G166903_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G40980.1 (Glycine max), 5'ss of exon 4
TGTCTATGAGC-CAGACTCGCC---TTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactccttatgtg-taattacatattgatcagggtccagtatattgg--ccaactat-catgatcaaatggtttataaaagcattgcaacaaggtctaca
    | ||||| ||||   |     ||  |  ||    || |  |   | || || || ||  ||||||| ||||||||||||||||||||||| || |||||||||  |     ||  |  | | |  ||| |  |     |  |    | | |   ||   |  |||||    |||    ||       || |||     |     
----TTTGAGCTCAGAGGTGTTGAGTTCCAGACCCATTCCTGAAATGGAGCGACTATCAACACTGTATAACGCTGATGTTGGTCTTTACATGCTTGCTAACAAGgtactataatatagataatgactggatagtactttccttttaagtaactagagtcagtgaggcatgactgcatgagagatgtcgtttttacaaatcaatg----

upper sequence: GRMZM2G166903_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G43630.1 (Glycine max), 5'ss of exon 4
TGTCTATGAGCC-AGACTCGCCTTTAACTCCTGAACCA-----GCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactccttatgtg-taattacatattgatcagggtccagtatattggccaactatcatgat-caaatggtttataaaagcattgcaacaaggtctaca
    | |||||| |||   |  ||||  ||| || |||     |  |   | || || || ||  ||||||||||||||||||||||||||||||| || |||||||||  |     ||  |  | | |  ||| |  |     || |    ||| |  | | |    ||   ||  | | |||       ||   |  |  | | | 
----TTTGAGCCCAGAGATG--TTTAGTTCCAGACCCATTCCTGAAATGGAGCGACTATCAACACTGTATAATGCTGATGTTGGTCTTTACATGCTTGCTAACAAGgtactatgatatagataatgagtgaatagtactttccttctaagtaattag--agccagtgagacataagagatatattccccattttagattaattatgct

upper sequence: GRMZM2G166903_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G37000.1 (Glycine max), 5'ss of exon 4
--TGTCTATGAGCCAGACTCGCCTTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgta--agactccttatgtgtaattacatattgatcagggtcca-gtatattggccaactatcatgatcaaatggtttataaaagcattgcaacaaggtctaca
  ||||    |   |   | |  |   |  || |  || |  |   | || ||||| ||  | |||||||| || ||||||||||||||||| || |||||||||   || |  |  |   |||    || ||        |  | |||  | ||   | ||  |   | | |   | |         || |  |    | ||  
TTTGTCCCCAAA--AATGTTGGATACTAGACCAGTTCCTGAAATGGAGCGACTTTCCACACTTTATAATGCAGACGTTGGTCTTTACATGCTGGCTAACAAGgtactggaatattggtaaataagaggatgtttccttacttttatgtaattaggggcaatacaacagtgataca-tctccctttttgtttcttccctttgta--

upper sequence: GRMZM2G166903_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G30700.1 (Glycine max), 5'ss of exon 6
--TGTCTATGAGCCAGACTCGCCTTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgta--agactccttatgtgtaattacata-ttgatcagg-gtccagtatattggccaactatcatgatcaaatggtttataaaagcattgcaacaaggtctaca
  ||||    || ||   | |    ||   || |  || |  |   | || ||||| ||  | |||||||| || ||||||||||||||||| || |||||||||   || |     |   |||    ||  ||  | |    | ||  |||  || ||| ||  |   | | |   | |         || |  |    | ||  
TTTGTCC-CCAGACATGTTGGATACTAGA-CCAGTTCCTGAAATGGAGCGACTTTCCACACTTTATAATGCAGACGTTGGTCTTTACATGCTGGCTAACAAGgtactggaatataggtaaataagaggatggttccttacttatacataataaggggcaa-tacaacagtgataca-tctccctttttgttacttccctttgta--

upper sequence: GRMZM2G166903_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 5'ss of exon 4
TGTCTATGAGCC--AGACTCGCCTTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactccttatgtgtaattacatattgatcagggtccagtatattggccaactatcatgatcaaatggtttataaaagcattgcaacaaggtctaca--
  | ||| | |   |||   |  |   |  || |  ||    |   |||| || || ||  | || |||||||||||||||||||||||||| || |||||||||  |  ||  |  | | |  | | | |  |     |  |||  ||      |  ||  | | |   |      | | |  |||  ||  | ||||     
--TTTATCACCTGAAGAGCGGAATGCTAGACCAGTTCCGAAAATGGAACGGCTGTCCACTCTATACAATGCTGATGTTGGTCTTTACATGCTTGCTAACAAGgtactaaacccaaacttttaacagaaagtattagctatttagtg-atgatgtgaacattgtaaacgtttttcagctcatattatt-taatgatgtctttttg

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|89760628|gb|DY688960.1|DY688960
EST:     TTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAACAAACAAG                         TGGATGGTTGATGAAA
genomic: TTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactcc ... tgtcatatagTGGATGGTTGATGAAA
EST: gi|50326138|gb|CO521264.1|CO521264
EST:     TTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAG                         TGGATGGTTGATGAAAAGGAATTAAGAATCATCCATTACACACTGGGTCCC
genomic: TTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactcc ... tgtcatatagTGGATGGTTGATGAAAAGGAATTAAGAATCATCCATTACACACTGGGTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCTATGAGCCAGACTCGCCTTTAACTCCTGAACCAGCGACACAACGCCTTTCTACCTTGTATAATGCTGATGTTGGTCTTTACATGCTAGCAAACAAGgtaagactccttatgtgtaattacatattgatcagggtccagtatattggccaactatcatgatcaaatggtttataaaagcattgcaacaaggtctaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT