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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtgcaaagatcattttccatcacttcagtgttccctgtataatattgctggctgcatcacatctcttattacttaattttcctcttcatctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT

Basic information

species Oryza sativa
transcript LOC_Os02g53060.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G152775_T01 (Zea mays), 3'ss of exon 5
------------------------------------------agagtgcaaagatcattttc-catcacttcag--tgttccctgtataatattgctggc----tgcatcacatctctta--ttacttaattttcctct-----tcatctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT-------------------------
| | | | ||| || || ||| || | || ||| ||||| | | || ||| | | || | |||| | ||| |||| | | ||||| |||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || ||
gtatgtctccaagttccttcttacttggatcttggcaatgagatattctctctagcatattagtatgactgaaggttattagttgtgtaataaaacgaatagagtacaacactagccccaattttcctaatatgtttctaatgttcatatatgcagAAATTTGTGGTGAAGGTAGTTTCCCTTGCTATGGCCCGTGATGGTGCTAGTGGAGGGGTTGTCCGTACAGTTACAGTAAGTTCTCTCTCTATTTTTTATG

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 6
------------------------------------------agagtgcaaagatcattttc-catcacttcag--tgttccctgtataatattgctggc----tgcatcacatctctta--ttacttaattttcctct-----tcatctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
| | | | ||| || || ||| || | || ||| ||||| | | || ||| | | || | |||| | ||| |||| | | ||||| |||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || ||
gtatgtctccaagttccttcttacttggatcttggcaatgagatattctctctagcatattagtatgactgaaggttattagttgtgtaataaaacgaatagagtacaacactagccccaattttcctaatatgtttctaatgttcatatatgcagAAATTTGTGGTGAAGGTAGTTTCCCTTGCTATGGCCCGTGATGGTGCTAGTGGAGGGGTTGTCCGTACAGTTACA

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 6
-agagtg--caaagatcattttccatcacttcagtgttccctgtataatattgctggctgcatcacatctcttattacttaattttcctcttcatctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
|| || ||| | ||| | | | || || | || ||| ||| | || || || | || | | |||| | ||||||| |||||||| |||||||||||||||||||| ||||||||||||||||| ||||||||||| ||||| || ||
tagtatgactgaaggttattaattgtgtaaagcgaatagactatagagtacaaa-acttgcctcaattttcctaata--tgtttctaatggtcatatatacagAAATTTGTGGTGAAGGTAGTTTCCCTTGCTATGGCCCGTGATGGTGCTAGCGGAGGGGTTGTCCGTACAGTTACA

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|88260289|gb|CI362582.1|CI362582
EST:     TGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: TGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|86496862|gb|CI139495.1|CI139495
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88482025|gb|CI419296.1|CI419296
EST:     CGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTNTGGTTAA-GTNAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAG
genomic: CGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGT-AGTTTCCCTTGCTATAGCCCGTGATGGTGCTAG
EST: gi|2797950|gb|AA751244.1|AA751244
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGT-CCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|8527814|gb|AU092629.1|AU092629
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTNCCCTTGCTATANCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88514156|gb|CI441662.1|CI441662
EST:     CGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: CGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|86535862|gb|CI176068.1|CI176068
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCTCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88271757|gb|CI387810.1|CI387810
EST:     GGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88961062|gb|CI096465.1|CI096465
EST:     GATTGCTNGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|218488196|gb|FG970072.1|FG970072
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|58692319|gb|CK081006.1|CK081006
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATA
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATA
EST: gi|25799545|gb|CA755506.1|CA755506
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAG
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAA-GGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAG
EST: gi|88517598|gb|CI445252.1|CI445252
EST:     TGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: TGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|87028372|gb|CI263714.1|CI263714
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88503321|gb|CI430827.1|CI430827
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|218498714|gb|FG963991.1|FG963991
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88974504|gb|CI022045.1|CI022045
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|86513098|gb|CI155731.1|CI155731
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|86533509|gb|CI173715.1|CI173715
EST:     TTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: TTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88551157|gb|CI481189.1|CI481189
EST:     GGAAGAAGCTGAG                         AAGTTTNTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|16754672|gb|BM039051.1|BM039051
EST:     GGGCATGTCCCAGGAAGAA-CTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCGTATAGCCCGTGATGGTGCTAG
genomic: GGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGC-TATAGCCCGTGATGGTGCTAG
EST: gi|88261543|gb|CI365119.1|CI365119
EST:     GATTGCTTGACCACGAATGTAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGGCTAG
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGT-GCTAG
EST: gi|88965355|gb|CI011606.1|CI011606
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88829940|gb|CI004978.1|CI004978
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88242742|gb|CI242591.1|CI242591
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|218504275|gb|FG947024.1|FG947024
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCCTAG
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGC-TAG
EST: gi|86491932|gb|CI134565.1|CI134565
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAAGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88846360|gb|CI373128.1|CI373128
EST:     CACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: CACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|66919202|gb|CX106050.1|CX106050
EST:     CACGAATGGAAGGAGGGCATGT-CCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCTGTGATGGTGCTAG
genomic: CACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCC-GTGATGGTGCTAG
EST: gi|86595130|gb|CI260369.1|CI260369
EST:     GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88261592|gb|CI365168.1|CI365168
EST:     GATTGCTTGACCACGAATGTAAGGAGGGCATGTCCCAGGAAGAAGCTGAG                         AAGTTTGT-GTTAAGGTAGTTTCCCTTGCTATAGCCCGTGAT-GTGCTAGT
genomic: GATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT
EST: gi|88997224|gb|CI389890.1|CI389890
EST:     GGAGGGCATGTCCCACGAAGAAGCTGAG                         AAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCCTGATGGTGCTAGT
genomic: GGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGT

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: 56 (upstream exon), 75 (downstream exon)
Score: 36

GTTCAGGCTCTAGTTACCTCTATGGATTGCTTGACCACGAATGGAAGGAGGGCATGTCCCAGGAAGAAGCTGAGgtacatcatc ... atctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgctggctgcatcacatctcttattacttaattttcctcttcatctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
                            acttaat  putative branch site (score: 36)
 cttaattttcctcttc  CT-rich tract
 tcttattacttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagtgcaaagatcattttccatcacttcagtgttccctgtataatattgctggctgcatcacatctcttattacttaattttcctcttcatctttacagAAGTTTGTGGTTAAGGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - -ccctgta
- - - - - - - - - - - - - - - - - - - - - - - - tgctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatca