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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaaccttgtgaagtatgctgaaatagtatcattggaacaaggaacattttattcttattaatgttttgtttgttgcttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC

Basic information

species Arabidopsis thaliana
transcript AT3G11940.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G078985_T01 (Zea mays), 3'ss of exon 2
----gtacta-accttgtgaagtatgctgaaatagtatcattggaacaaggaacattttat----tcttattaatgttttgtt----tgttgcttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC
    || |||     ||| || |||     || | |||   |   ||| |     | ||      ||  | |  |||| |||     | |||  |  || ||||| |||||||| ||||| ||| | ||||| || ||||||||||| || || || ||||| |||||||| || || ||| | || |||||||| |||| |
ttatgtgctatgagatgtcaactataactcaa-actattgattacacatgttggctcttgagatgtcaaactggtgttctgtgctgatattgtctttgc-agTGGACCACGTGAGGATGCCACCCGTATTGGTTCAGCTGGTGTTGTGAGAAGGCAGGCTGTGGATATCTCACCCCTGAGAAGGGTGAACCAGGCCATCTAC

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G37610.1 (Glycine max), 3'ss of exon 3
-----------gtactaaccttgtgaagtatgctgaaatagtatcattggaacaagg-aacattttattcttattaatgttttgtttgttgcttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC
            ||    | || | | | ||     | ||   | | |  || | |  |  | ||||| |||| | || |  ||||  ||  || |  ||||||||||||||||||||| || |||||||| || ||||| |||||||||||||| ||||| |||||||| || || || |||||||||||||||||||  
aatactattttttatgttcatttttatgaattgaacattaaatttactttaaaatgtcagtaatttat-cttactgatttgatgttgttttgtttattcagTGGTCCACGTGAAGATGCAACAAGAATTGGTTCAGCTGGAGTTGTTAGGAGACAGGCTGTGGATATCTCACCCCTTAGGCGTGTTAACCAGGCTATCTAT

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G32850.1 (Glycine max), 3'ss of exon 3
------gtactaaccttgtgaa-gtatgc-tgaaatagtatcattggaacaaggaacattttattcttattaatgttttgtttgttgcttg---agccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC
      || ||     ||      ||||  |  || | ||   ||     || |      | |||  | ||| ||||||| ||||   |||   |  ||||||||| ||||||||||| || |||||||| |||||||| ||||| ||||| || ||||| ||||| || || ||  | ||||| || |||||||| |  
tttgcagttcttgatgtgcatctatatgaattgaacactaaatttactttaaagtgtcagtaatttatcttactgttttgattgtgttttgtttattcagTGGTCCTCGTGAAGATGCAACAAGAATTGGTTCTGCTGGAGTTGTAAGGAGGCAGGCTGTGGATATTTCACCCCTTCGGCGTGTGAATCAGGCTATATAT

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ17708 (Selaginella moellendorffii), 3'ss of exon 3
gtactaaccttgtgaagtatgctgaaatagtatcattggaacaaggaacattttattcttattaatgttttgt--ttgttgcttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC
                             |||    |  |          ||  |   | ||| || ||| ||  ||  ||||||   ||||||||| ||||||||||||||  |||| || || |||||||| || ||| | || |||||||||||||| |||||  | || || || || || || | |
-----------------------------gtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgcttg---cagTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCGTCAGGCTGTTGATATCTCGCCTCTGCGTCGCGTGAATCAAGCCATTTAC

upper sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16239 (Selaginella moellendorffii), 3'ss of exon 3
gtactaaccttgtgaagtatgctgaaatagtatcattggaacaaggaacattttattcttattaatgttttgt--ttgttgcttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC
                             |||    |  |          ||  |   | ||| || ||| ||  ||  ||||||   ||||||||| ||||||||||||||  |||| || || |||||||| || ||| | || |||||||||||||| |||||  | || || || || || || | |
-----------------------------gtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgcttg---cagTGGTCCTCGTGAAGATGCTACACGAATCGGTTCCGCTGGTGTGGTGAGGCGTCAGGCTGTTGATATCTCGCCTCTGCGGCGCGTGAATCAAGCCATTTAC

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|301502573|gb|HO208113.1|HO208113
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|86084216|gb|DR379975.1|DR379975
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|124798485|gb|EH888164.1|EH888164
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TAGGTCCACGTGAAGATGCTACCAGAAT
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagT-GGTCCACGTGAAGATGCTACCAGAAT
EST: gi|124967156|gb|EL041210.1|EL041210
EST:     TCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|125171600|gb|EL194376.1|EL194376
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGA
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGA
EST: gi|124944262|gb|EL020378.1|EL020378
EST:     TCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCCACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|124985489|gb|EL058076.1|EL058076
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTG
EST: gi|164222946|gb|ES058717.1|ES058717
EST:     CTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGATCCACGTGAAGATGCTACCAGAATTGGATCTGC
genomic: CTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGC
EST: gi|164210972|gb|ES183291.1|ES183291
EST:     TCATCATTGACGCCATTGTCAACAG                         TCGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGA
genomic: TCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagT-GGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGA
EST: gi|164206188|gb|ES180935.1|ES180935
EST:     TCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGG
genomic: TCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGG
EST: gi|124951991|gb|EL027305.1|EL027305
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCT
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCT
EST: gi|86081585|gb|DR377342.1|DR377342
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|164170825|gb|ES200425.1|ES200425
EST:     GGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: GGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|125175164|gb|EL195401.1|EL195401
EST:     GACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: GACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|163975221|gb|ES011379.1|ES011379
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGT
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGT
EST: gi|86078785|gb|DR374542.1|DR374542
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|116479315|gb|EG521907.1|EG521907
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|164059083|gb|ES084320.1|ES084320
EST:     CCATTGTCAACAG                         TGGTCCACGTGAAGATGC-ACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: CCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|164144719|gb|ES061988.1|ES061988
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATC
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATC
EST: gi|309381104|gb|HO850325.1|HO850325
EST:     AGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: AGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|124807531|gb|EH893935.1|EH893935
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAG
EST: gi|125257319|gb|EL271404.1|EL271404
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGA
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGA
EST: gi|125199969|gb|EL214923.1|EL214923
EST:     CTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGG
genomic: CTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGG
EST: gi|124795714|gb|EH885393.1|EH885393
EST:     GACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: GACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|116465715|gb|EG508307.1|EG508307
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|125279476|gb|EL293561.1|EL293561
EST:     TCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|125099445|gb|EL155252.1|EL155252
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGC
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGC
EST: gi|125276356|gb|EL290441.1|EL290441
EST:     ATTGACGCCATTGTCGACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: ATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|164215093|gb|EL970217.1|EL970217
EST:     GAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: GAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|116480566|gb|EG523158.1|EG523158
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|164222535|gb|ES214630.1|ES214630
EST:     GAACCC-ATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: GAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|86074460|gb|DR370217.1|DR370217
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|125287681|gb|EL301766.1|EL301766
EST:     AACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
genomic: AACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAG
EST: gi|124956908|gb|EL031787.1|EL031787
EST:     TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAG                         TGGTCCACGTGAAG
genomic: TTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgtactaacct ... cttgagccagTGGTCCACGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggaacaaggaacattttattcttattaatgttttgtttgttgcttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC
                         tattaat  putative branch site (score: 2)
            aacattttattcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaaccttgtgaagtatgctgaaatagtatcattggaacaaggaacattttattcttattaatgttttgtttgttgcttgagccagTGGTCCACGTGAAGATGCTACCAGAATTGGATCTGCTGGTGTTGTTAGGAGACAAGCTGTTGATATCTCTCCTCTAAGACGTGTTAACCAGGCTATCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC