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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaacatatacttccagtcacttttcttatagatacttgctttggtttcatattttttggcgtattacttgtgttgcag

Basic information

species Zea mays
transcript GRMZM2G052880_T01
intron # 5
splice site 5'
intron type U2

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|211376580|gb|FL160476.1|FL160476
EST:     ATTGTCATGGTCCTATCCGANATGGCAGGAAGAAGCCCTTTGTACNAGAA                         GGCAT-TGGTGGTTTTCAGTTCTCCC
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATG-TGTTTTTCAGTTCTCCC
EST: gi|211371250|gb|FL160440.1|FL160440
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTT
EST: gi|211373914|gb|FL160460.1|FL160460
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAG
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAG
EST: gi|211371256|gb|FL160446.1|FL160446
EST:     TTGTCATGTTCCTATCCGACATGTCAGGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGNGTTTTTCAGTTCTCCCCGTACATAAAGAATTAG
genomic: TTGTCATGTTCCTATCCGACATGTCAGG-AAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCC-GTACATAAAGAATTAG
EST: gi|211371258|gb|FL160448.1|FL160448
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211504197|gb|FL160497.1|FL160497
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACAT
EST: gi|211373918|gb|FL160464.1|FL160464
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGT
EST: gi|211373920|gb|FL160466.1|FL160466
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|50336915|gb|CO532041.1|CO532041
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211373917|gb|FL160463.1|FL160463
EST:     AATGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCA
EST: gi|211501864|gb|FL160492.1|FL160492
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211373908|gb|FL160454.1|FL160454
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAG
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAG
EST: gi|211376585|gb|FL160481.1|FL160481
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGGTGGTTTTTC
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATG-TG-TTTTTC
EST: gi|211501859|gb|FL160487.1|FL160487
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATA
EST: gi|211376576|gb|FL160472.1|FL160472
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGGTGTTTT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATG-TGTTTT
EST: gi|76280654|gb|DV020222.1|DV020222
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211501861|gb|FL160489.1|FL160489
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCC
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCC
EST: gi|211373910|gb|FL160456.1|FL160456
EST:     ATTGTCNTGTTCCTATCCGACATGTCAGGAANAAGCCCTTTGTACAAGAA                         A
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcag-
EST: gi|211373910|gb|FL160456.1|FL160456
EST:     ATTGTCNTGTTCCTATCCGACATGTCAGGAANAAGCCCTTTGTACAAGAA                         A
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcag-
EST: gi|211376571|gb|FL160467.1|FL160467
EST:     ATTGTCATGTTCCTATCCGACANGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAA
EST: gi|211501867|gb|FL160495.1|FL160495
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211501856|gb|FL160484.1|FL160484
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211376572|gb|FL160468.1|FL160468
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACA
EST: gi|211501854|gb|FL160482.1|FL160482
EST:     TGTCATGTTCCTATCCGACATGTCAGGAANAAGCCCCTTTTGTACAAGAA                         GGCATATGGTGTTTTT
genomic: TGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCC-TTT-GTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATG-TGTTTTT
EST: gi|211504199|gb|FL160499.1|FL160499
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGGATATGTGTTTTTCA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCA
EST: gi|211371253|gb|FL160443.1|FL160443
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211501857|gb|FL160485.1|FL160485
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGC
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGC
EST: gi|211371261|gb|FL160451.1|FL160451
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCG
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCG
EST: gi|211376578|gb|FL160474.1|FL160474
EST:     TTGTCATGTTCCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTC
genomic: TTGTCATGTTCC-TATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTC
EST: gi|211373907|gb|FL160453.1|FL160453
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211501860|gb|FL160488.1|FL160488
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGGTGTTTTTCAGTTCTCCCGTA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATG-TGTTTTTCAGTTCTCCCGTA
EST: gi|211373912|gb|FL160458.1|FL160458
EST:     TGTCATGTTCCTATCCCGACATGTCAGGAAGAAAGNCCTTTGTACAAGAA                         AGCATATGGNGTTTTTCAGTTCTCCCGTACATA
genomic: TGTCATGTTCCTATCC-GACATGTCAGGAAGAA-GCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGT-GTTTTTCAGTTCTCCCGTACATA
EST: gi|211501858|gb|FL160486.1|FL160486
EST:     TTGTCATGTTCCTATCCGACATGTCAGGGAAGAAGCCCTTTGTACAAGAA                         A
genomic: TTGTCATGTTCCTATCCGACATGTCAGG-AAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcag-
EST: gi|211501858|gb|FL160486.1|FL160486
EST:     TTGTCATGTTCCTATCCGACATGTCAGGGAAGAAGCCCTTTGTACAAGAA                         A
genomic: TTGTCATGTTCCTATCCGACATGTCAGG-AAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcag-
EST: gi|211376583|gb|FL160479.1|FL160479
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATAGGGGGTTTTTCAGTTCTCCCGTACATAAAGAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTG-TTTTTCAGTTCTCCCGTACATAAAGAAT
EST: gi|93015686|gb|EB641206.1|EB641206
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211371254|gb|FL160444.1|FL160444
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGGTGTTTTTCAG
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATG-TGTTTTTCAG
EST: gi|211376577|gb|FL160473.1|FL160473
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGGTGTTTTTCAGTTCTCCCGTACA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATG-TGTTTTTCAGTTCTCCCGTACA
EST: gi|211504198|gb|FL160498.1|FL160498
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATAGGGGGTTTTTCAGTTCTCCCGTACATAAA
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTG-TTTTTCAGTTCTCCCGTACATAAA
EST: gi|76294182|gb|DV033750.1|DV033750
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|74234513|gb|DT642427.1|DT642427
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211376573|gb|FL160469.1|FL160469
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
EST: gi|211376584|gb|FL160480.1|FL160480
EST:     ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAA                         GGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT
genomic: ATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAAT

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), 49 (downstream exon)
Score: 239

CATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAATAAAAAAGGATTCAAGTGTACTACCTCGTATTGCCGCACTTAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

CATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAATAAAAAAGGATTCAAGTGTACTACCTCGTATTGCCGCACTTAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

CATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAATAAAAAAGGATTCAAGTGTACTACCTCGTATTGCCGCACTTAGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

CATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaa ... tgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAATAAAAAAGGATTCAAGTGTACTACCTCGTATTGCCGCACTTAGTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGTCATGTTCCTATCCGACATGTCAGGAAGAAGCCCTTTGTACAAGAAgtatgtacaacatatacttccagtcacttttcttatagatacttgctttggtttcatattttttggcgtattacttgtgttgcag

- - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - -  AGAAGC