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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcgaattacatctttgctacttcacctgtaaaatgtttatctctatcaatatctgttatccaagagttattttctcacagttatgtattatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT

Basic information

species Oryza sativa
transcript LOC_Os11g03380.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G179737_T02 (Zea mays), 3'ss of exon 8
---------------------------------actgcgaattacatctttgctacttcacctgtaaaa----tgtttatctctatca-atatctgt------tatccaagagttattttctcacagttatgtattatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT
                                  |     ||||| |  |   | |||   ||| ||||     ||     |  ||   ||   |||      |   ||   |     |      | |||  || |   ||||||| |||||||| || |||||| |||||||||||||||  || |||||||| || ||||| || || | ||| || ||||||| ||| || | | | |   
gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGATCTCTCC

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G179737_T03 (Zea mays), 3'ss of exon 7
---------------------------------actgcgaattacatctttgctacttcacctgtaaaa----tgtttatctctatca-atatctgt------tatccaagagttattttctcacagttatgtattatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT
                                  |     ||||| |  |   | |||   ||| ||||     ||     |  ||   ||   |||      |   ||   |     |      | |||  || |   ||||||| |||||||| || |||||| |||||||||||||||  || |||||||| || ||||| || || | ||| || ||||||| ||| || | |       
gtgagttgctgctgtgcttgtgctccgttccattcatttcattaccttatcagttcttattctgaaaaaaaaacgtgggcttgcattgcatccttgtgttgtattctcacacgcaccctgggtctacttaattactgcgtgcagGGGATAGTGCTTCTCATCATCCTGATATCAGGACTCATGTGCATGATGGGCATCGATACTCCCTCGAGGTTTGAAGCTCCCCAGGAGTCTTGA-------

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G017941_T01 (Zea mays), 3'ss of exon 8
--------------------------------------------------actgcgaattacatctttgctacttcacctgtaaaatgtttatctctatcaatat--ctgttatccaagagttattttctcacagttatgtattatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT
                                                  ||   |  || |||    |    |      | ||    | |  |  | ||| | |  ||  |||||  | ||| | |||||||  || | || ||| |||||||||||||||| || ||||||||||||||||| ||||  |||||||||||||| ||||| || || ||||| || ||||||| ||| || | | | |  |
gtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctgaacgtgggcttgcatgcaggggggtggggg-gaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcacgcttgtctactatgtgcagGGAATAGTGCTCCTTATCATCTTGATATCAGGGCTCATGTGTATGATGGGAATCGATACTCCCTCCAAGTTTGAAGCTCCCCAGGAGTCTTGATCTCCCT

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|29613045|gb|CB618058.1|CB618058
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|33689369|gb|CF317608.1|CF317608
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88239758|gb|CI238920.1|CI238920
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|218494343|gb|FG947228.1|FG947228
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29658171|gb|CB654446.1|CB654446
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGTTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86429763|gb|CI082186.1|CI082186
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29672707|gb|CB668982.1|CB668982
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|8856727|gb|AU094045.1|AU094045
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88455553|gb|CI521773.1|CI521773
EST:     TTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: TTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88488083|gb|CI425354.1|CI425354
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|33658023|gb|CF280637.1|CF280637
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29678425|gb|CB674700.1|CB674700
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88997202|gb|CI389868.1|CI389868
EST:     TAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: TAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86843126|gb|CI341311.1|CI341311
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86422104|gb|CI059677.1|CI059677
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88226799|gb|CI224784.1|CI224784
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|27545747|gb|CA763944.2|CA763944
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|87025284|gb|CI265849.1|CI265849
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|89184963|gb|CI049509.1|CI049509
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|33690613|gb|CF318852.1|CF318852
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88840637|gb|CI080091.1|CI080091
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATATATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29663529|gb|CB659804.1|CB659804
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|4715629|gb|AU056745.1|AU056745
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|14192245|gb|AU184456.1|AU184456
EST:     GTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|87016616|gb|CI275618.1|CI275618
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|29672708|gb|CB668983.1|CB668983
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|87025104|gb|CI263612.1|CI263612
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88222934|gb|CI220680.1|CI220680
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|33658125|gb|CF280739.1|CF280739
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTTTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86839088|gb|CI331404.1|CI331404
EST:     GGGAGTGCTTAGTAAAATCAACTCTCCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|88966191|gb|CI013067.1|CI013067
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|218480976|gb|FG957861.1|FG957861
EST:     GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTT                         GGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA
genomic: GTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGA

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 1 RNA-Seqlibrary.


Block sizes: 28 (upstream exon), 71 (downstream exon)
Score: 19

CAGGTACCTCGCAGAGAAGACCAATACTACTAAACCTGGCCGTGGAAAATGTGACGGGGAGTGCTTAGTAAAATCAACTCTGCTGGAAGGAAGCTTTGTTgtaagttgtc ... ttatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcaatatctgttatccaagagttattttctcacagttatgtattatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT
                             ttctcac  putative branch site (score: 19)
                                    agttatgtattatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcgaattacatctttgctacttcacctgtaaaatgtttatctctatcaatatctgttatccaagagttattttctcacagttatgtattatatgcagGGAATAGTGCTGCTGATCATCTTGATATCAGGACTCAAATGTATGATGGGAATTGATACCCCATCAAAGTTCGACGCTCCCCCGGAATCATAAGCCCATT

- - - - - - - - -tgctact
- - - - - - - - - - - - -cacctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtta