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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatgcttgcatcattgataaccttaacgaatgaatgactctttattttgtggtagcaggaccaatgttttctgagtcgagtcatgcagttaccg...

Basic information

species Zea mays
transcript GRMZM2G147811_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147811_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 10
TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgt---tagtcatgcttgcatcattgataaccttaacgaatgaatgactctttattttgtggtagcaggaccaatgttttctgagtcgagtcatgcagttaccg---------------------------
||| ||||| |||||| ||||||| ||||||||||| |||| |||||||||||||||||||||| ||||||| || ||||| ||||| ||||||||||||||   |  ||||  |   |||  |  | ||||| | |   |||  | |||   |||  |  |  ||    |||   || || |||  |   || ||  |||                             
TTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAATAATGACATGCTTCGGCTTCATATGGAACTGAAGGGCCCCTTCCCCAAGAAAATGCTTCGAAAGgttcttcatcattttcaaatctcttcttaccttcaag---gaaacaatctacttttgatatttacatctgcaacagttgctaagtgaa--tatacaaatactttctaaggaattgttcccaattttgcag

upper sequence: GRMZM2G147811_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G24820.2 (Glycine max), 5'ss of exon 12
TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatgcttgcatcattgataaccttaacgaatgaatgactcttt---attttgtggtagcag-gaccaatgttttctgagt--cgagtcatgcagttaccg
 ||||  ||||| ||  | || || ||     ||||||||| |||||| |||||||| |||||| ||||||| || || || ||||||||||| || ||||| |       |||  |||||  |||  | |||  || | ||  || ||   ||||| |   |  || | |      | | |||||   |||| ||||| | |   
GTATATAGGGAAGGTTCTTTTCCCAGGGTTTACAAACAATGACATGCTACGGCTTCACATGGAACTGAAGGGCCCTTTTCCAAAGAAGATGCTGCGTAAGgtaaacatatattgtttcatt--taaattaaacatat-attgtttcatttaaattttttatcattagtgtctggcactgtttgagtgttgagt-atgca-taatt-

upper sequence: GRMZM2G147811_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G42220.1 (Glycine max), 5'ss of exon 15
TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatgcttgcatcattgataaccttaacga-atgaatgactctttattttgtg-gtagcaggaccaatgttttctgagtcgagtcatgcagttaccg
 ||||  ||||| ||  | || || ||||   ||||||||| |||||| |||||||| |||||| |||||||||| || || ||||||||||| || ||||| |       |||  |||||  |    ||      || | || ||    | | | || ||     |    |  | || | |  |  |  |     ||    
GTATATAGGGAAGGTTCTTTTCCCAGGTCTTACAAACAATGACATGCTACGGCTTCACATGGAACTGAAGGGTCCTTTTCCAAAGAAGATGCTGCGTAAGgtaaacatatattgtttcattttttttttttttatcattagtgtctggccactgtttgagtgttgagtatgaattattttaatacttgatacaagtttgt--

upper sequence: GRMZM2G147811_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT3G25840.1 (Arabidopsis thaliana), 5'ss of exon 10
TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttag--tcatgcttgcatcattgataaccttaacgaatgaatgactctttattttgtggtagcaggaccaatgttttctgagtcgagtcatgcagttaccg-------------------------------------------------------------------------
|||||  || |||||  | || |||||  |  |||||||||  ||| | || |||||||||||| |||| ||||| |||||||| ||||||||||| ||||||||  | |  || |  |   || |     |  |   ||| | |||  | |   |||  |   |     ||  ||   |  |   |  |||     |   |                                                                         
TTATAGTGGAAAAGTTCTTTTCCCTGGCGCCACAAACAATGATATGTTACGCCTTCATATGGAACTGAAAGGTCCCTTCCCTAAAAAGATGCTTCGCAAGgttagcattaaactagattgggtgttgtgaatgtcacctga-tcactgatcaaaatgtcttccaaatgataactttccttaggcaaatccatatgtatggtggagatatagttgtatgtttaagagaagcagtttttaatgcatgttctaatgtttctgttatttggtttaacag

upper sequence: GRMZM2G147811_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 5'ss of exon 10
TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttag--tcatgcttgcatcattgataaccttaacgaatgaatgactctttattttgtggtagcaggaccaatgttttctgagtcgagtcatgcagt-taccg
|||||| || |||||  | ||||| ||||| |||||||||| ||||||||||||||| ||||| ||||||||||| || || || ||||||||||||||||||||  |     |||  | ||| | |     |   || || |  |  ||| || | ||      |  |   | ||||   ||  |  | |       | |  
TTATACGGGAAAAGTTCTTTTTCCGGGTCCTTCAAACAATGACATGCTTCGGCTTCACATGGAGTTGAAGGGTCCTTTTCCAAAAAAGATGCTTCGAAAGgttagagtttaaattgt-ttatttagagatgcaggcaaagatt--ccttttcttctttgaagcttgcgctggttttttggtagcggtttaacttgacatgcta

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|32832656|gb|CD972334.1|CD972334
EST:     GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAG                         GGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC
genomic: GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatg ... tgttttgtagGGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC
EST: gi|32945651|gb|CF050470.1|CF050470
EST:     GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAG                         GGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC
genomic: GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatg ... tgttttgtagGGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC
EST: gi|160481281|gb|EY254203.1|EY254203
EST:     GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAG                         GGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC
genomic: GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatg ... tgttttgtagGGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC
EST: gi|32932428|gb|CF037240.1|CF037240
EST:     GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAG                         GGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC
genomic: GGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatg ... tgttttgtagGGTGCCTTTACTATGCAACACTTCGATCAAGATCTCAATTTTCATGCTACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATACCGGGAAAGTCTTATTTCCTGGTCCATCAAACAATGCCATGCTTCGGCTTCATATGGAATTGAAGGGTCCATTCCCTAAGAAGATGCTTCGAAAGgttagtcatgcttgcatcattgataaccttaacgaatgaatgactctttattttgtggtagcaggaccaatgttttctgagtcgagtcatgcagttaccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG