Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaaccataaacagaagctgacattttcttatctgctgtggtaattgaatatatgggatctgataacaaattttccag

Basic information

species Zea mays
transcript GRMZM2G102021_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102021_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g17280.1 (Oryza sativa), 5'ss of exon 2
TTCCTATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaaccataaacagaagctga------cattttcttat-----ctgctgtggta-attga--atatatgg----gatctgataacaaattttccag-------------------------------------------
| |||||||  ||||||||||||||| | ||||  ||||| |||||||||||||| ||||| |||||||||| ||||||||| ||||||| ||||||||||||||||||||||||    ||| |||      ||  || ||||        |||| ||  ||| |  || ||| |    ||| | || |   |  ||  ||                                           
TCCCTATAAGATCAGGAGCTTGGTGGCCGTATGCAATTCTTATCCTTACATCTGTTGCATTTCAAGAAGGCATTCGTCTTGTCTTTTGGAGGCTTTACAAgtaggtaaaccataattgaaagttgaacttcacacctttttatggcagtccctgtagtgtattcactatgtatagagatgatataattatggaacttgaagttgatttatgtctttatgatatgtgatggttactgtttttcag
















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|211287765|gb|FL258742.1|FL258742
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177671|gb|FL258730.1|FL258730
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|50328021|gb|CO523147.1|CO523147
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|33285553|gb|CF075348.1|CF075348
EST:     GAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: GAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287769|gb|FL258746.1|FL258746
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|26558953|gb|CA831188.1|CA831188
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177678|gb|FL258737.1|FL258737
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCCAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177677|gb|FL258736.1|FL258736
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177679|gb|FL258738.1|FL258738
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177680|gb|FL258739.1|FL258739
EST:     CTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTTGGATGCTTTACAA                         GAAAATGGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCAC
genomic: CTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTT-GGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGG-AAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCAC
EST: gi|211177673|gb|FL258732.1|FL258732
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177670|gb|FL258729.1|FL258729
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177676|gb|FL258735.1|FL258735
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177675|gb|FL258734.1|FL258734
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177668|gb|FL258727.1|FL258727
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287764|gb|FL258741.1|FL258741
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|22546043|gb|BU098364.1|BU098364
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287771|gb|FL258748.1|FL258748
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|149048871|gb|EE048372.2|EE048372
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|87155707|gb|DY400496.1|DY400496
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211105119|gb|FL057785.1|FL057785
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|91876597|gb|EB406554.1|EB406554
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177674|gb|FL258733.1|FL258733
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287768|gb|FL258745.1|FL258745
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|22818908|gb|BU498998.1|BU498998
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|37395770|gb|CF635168.1|CF635168
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|87156122|gb|DY400911.1|DY400911
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287767|gb|FL258744.1|FL258744
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|26559868|gb|CA832103.1|CA832103
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211287770|gb|FL258747.1|FL258747
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177672|gb|FL258731.1|FL258731
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|211177681|gb|FL258740.1|FL258740
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|40336955|gb|CK371025.1|CK371025
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAA                         GAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACG
EST: gi|148946112|gb|EC891406.2|EC891406
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTA                       
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTAC-A--Agtaggtaaac ... aattttcc
EST: gi|148946112|gb|EC891406.2|EC891406
EST:     TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAGTA                       
genomic: TCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTAC-A--Agtaggtaaac ... aattttcc

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 179

TTCCTATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACGTCTTAGATTGACTGACAAGATGCTGATTTCTTTAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 104

TTCCTATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACGTCTTAGATTGACTGACAAGATGCTGATTTCTTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

TTCCTATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACGTCTTAGATTGACTGACAAGATGCTGATTTCTTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

TTCCTATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaac ... aattttccagGAAAATGGAAGAGATGCTAGATGCTTTTGCTGATAGAATATCTAAGCCACGTCTTAGATTGACTGACAAGATGCTGATTTCTTTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTATAAAGTCAGGAGCTTGGTGGGCATATGTGATTCTGATCCTTACATCTGTCGCATTGCAAGAAGGCACTCGTCTTGTGTTTTGGATGCTTTACAAgtaggtaaaccataaacagaagctgacattttcttatctgctgtggtaattgaatatatgggatctgataacaaattttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG