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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatatacaatatgatcattaccaaatttgttgcag

Basic information

species Zea mays
transcript GRMZM2G128688_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g54910.1 (Oryza sativa), 5'ss of exon 2
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtc------ctcatataattttctatgttttgaaccaa-----aatgtagattctgatgtgatatacaatatgatcattaccaaatttgttgcag
||||||||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||| || |||     ||      ||  ||||||||  ||   ||   | |||     ||||  |||| |  | || |||   | |||||| | ||||| | |||  |||
GTCACTTCTGTCTCTTGGAAGGAGAACGAACTCAACATGGTTGATACACCTGGTCACGCTGATTTTGGTGGCGAAgtacacactcagcactcttttataatttcatacagttaagaacaagaagaaatgatgatttttctatggtatctgacatgatcctcaccaattatgtgacag

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G14080.1 (Glycine max), 5'ss of exon 2
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatatacaatatgatcattaccaaattt-gttgcag-----------
||||| ||||| || |||||||| ||||| || |||||||||||||| || || |||||||||||||||||||||||  | | |  ||||  |||||  |    ||  |  ||  |  ||      || |  | | | ||| || |  |    ||  |  | |  |            
GTCACGTCTGTTTCGTGGAAGGAGAATGAGCTGAACATGGTTGATACTCCCGGACACGCTGATTTTGGTGGTGAGgtgag-gtttttcatcaaatttgttccaatt--agtcaggaactaataagagaagaaaaaaaaaatgtgtttttccataagctgagctaaaattagcttatgc

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G43820.2 (Glycine max), 5'ss of exon 2
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtg-atatacaatatgatcattaccaaatttgttgcag----------
||||| ||||| || |||||||| ||||| || |||||||||||||| || || ||||| |||||||||||||||||  | |||  ||||  || ||  |    || |     || | |   || | ||    | ||  ||    ||  |||     || |||   |          
GTCACGTCTGTTTCGTGGAAGGAGAATGAGCTGAACATGGTTGATACTCCCGGGCACGCCGATTTTGGTGGTGAGgt--gaggttttcatcgaaattgttccaattagtctggaactatttttttttatcaacaaatggaaataaattgttaatttgttagtttttgttagcagcag

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT2G31060.3 (Arabidopsis thaliana), 5'ss of exon 2
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgt----tttgaaccaaaatgtagattctgat-gtgatatacaatat--gatcattaccaaatttgttgcag--------------------------------------------------------------------------------------------------
|| || ||  | | ||||||||| || ||||| |||||||| || |||||||| ||||| ||||||||||||||||||||   | || || | | |||    ||    |||||  |  |   | | || |  | |  ||  | | ||   ||  |     |||||  ||  |                                                                                                   
GTGACATCAATATTTTGGAAGGACAACGAACTTAACATGGTAGACACACCTGGTCACGCAGATTTTGGTGGTGAGgtatg--atactgatcttacttttagcgtattatttgattctcatgctcgtttttagtagaaatgcatattagtggacaaaagataaattaattagaagttctcaatacctactcatggtctgttgacattaggatactccttactgtagaacataggtgctatctttgtgactattttgtgtatttgaattatag

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 5'ss of exon 2
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatatacaata-------tgatcattaccaaatttgttgcag-------
|| ||  |  | |  ||||||||||| ||||| || |||||||||||||| ||||| || || ||||||||||| ||||||  | ||  |   ||||  |     | | ||||| || | | |  || | | | | | ||         |||    |    ||| | | ||||       
GTTACGGCCATTTTGTGGAAGGAAAACGAACTAAATATGGTTGATACACCCGGCCATGCGGACTTTGGTGGTGAAgtatgt--ttctgctgagatttctt---catagtaccaatattttgttaatggtttaaaagataaagagttggttgaaggctgaggaatatttagcagttaaccc

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ08344 (Selaginella moellendorffii), 5'ss of exon 2
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatatacaatatgatcattaccaaatttgttgcag
   |||||| |    |||      | |   |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||      || |    |  |   ||||| |||      ||    || |||                                      
TATACTTCTATGATCTGGGGAACCAGTTCTCTCAACATTGTTGATACTCCTGGTCACGCAGATTTTGGTGGAGAGgtatgaaagtttcttc--gtcgttcctgtttagaaatttcttgcttcttttgacag-----------------------------------

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ15282 (Selaginella moellendorffii), 5'ss of exon 2
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatatacaatatgatcattaccaaatttgttgcag
   |||||| |    |||      | |   |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||      || |    |  |   ||||| |||      |     || |||                                      
TATACTTCTATGATCTGGGGAACCAGTTCTCTCAACATTGTTGATACTCCTGGTCACGCAGATTTTGGTGGAGAGgtatgaaagtttcttc--gtcgttcctgtttagaaatttccttcttcttttgacag-----------------------------------

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|149065568|gb|EE286688.2|EE286688
EST:     ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG                         GTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
genomic: ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtc ... tttgttgcagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
EST: gi|30705082|gb|CD058659.1|CD058659
EST:     ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG                         GTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
genomic: ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtc ... tttgttgcagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
EST: gi|149096163|gb|EE181859.2|EE181859
EST:     ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG                         GTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
genomic: ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtc ... tttgttgcagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
EST: gi|94477374|gb|EB706332.1|EB706332
EST:     ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG                         GTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
genomic: ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtc ... tttgttgcagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
EST: gi|71428852|gb|DR809902.1|DR809902
EST:     ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG                         GTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
genomic: ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtc ... tttgttgcagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
EST: gi|149075128|gb|EE163621.2|EE163621
EST:     ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG                         GTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT
genomic: ATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtc ... tttgttgcagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAGgtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatatacaatatgatcattaccaaatttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG