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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctttcctcgacaaccaagagagagctctcgtgttctaaatggtttttcgttccttttctttcgctcgctcgctcgatcgatcgatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG

Basic information

species Selaginella moellendorffii
transcript EFJ35297
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35297 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: EDO98738 (Chlamydomonas reinhardtii), 3'ss of exon 4
gtttgttctttcctcgacaaccaagagagagctctcgtgttctaaatggtttttcgttccttttctttcgctcg--ctcgctcgatcgatcgatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG
| | | || || | || | | |||| || || | | ||||||| | | ||| | | | | || || | ||||||||||| || |||||||| ||||| || ||||| |||||||| || || || || || |||||||| ||||| |||||||||||| | | ||| |
gatcggtccttatcccgcagacctccgctcgctc-cgccccgccaacgcatgttcgttcgtaccccttcaaccaaaccaacgccgtccttccctgctgcagGTGCTGCTCTCGATCTGCTCCTTGCTCACGGACCCCAACCCCGATGACCCGCTTGTGCCGGAGATCGCGCACATCTACAAGACCGACCGCCGGCGGTACG

upper sequence: EFJ35297 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S69_142V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgttctttcctcgacaaccaagag--agagctctcgtgttctaaatggtttttcgttc---cttttctttcgctcgctcgctcgatcg---atcgatttac-cagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG
| | || | || | | | | | | | | | ||| | | | | | | | | | | | | | || ||||||||||| ||||||||||| ||||| || ||||||||||| || |||||||| || || || ||||| |||||||||||||| ||||| | ||||| |
--------tggtgtagaggaacaggggtatgggttgtgggaatgcatctgggaagttgggaaggcacgtgacgggatgggggacatggttgtgtgtgggttggtgcagGTGCTGCTGTCAATCTGCTCTTTGCTGACAGACCCAAACCCGGATGATCCCCTTGTACCGGAAATCGCTCACATGTACAAGACAGACAGACATAAGTACG

upper sequence: EFJ35297 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S69_31V6.1 (Physcomitrella patens), 3'ss of exon 3
---gtttgttctttcctcgacaaccaagaga--gagctctcgtgttctaaatggtttttcgttccttttctttcgctcgctcgctcgatcgatcgatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG
||| | | | || | || | || | | | || | | | | || | | | | | | | | ||||||||| | ||||||||||| ||||| || |||||||| || || |||||||| || || || ||||| |||||||||||||| ||||||| ||||| |
ggggttgaggttggcgtagaggaacacgggattgggttacgagaagctgggatggcacgtgacgggatggtgacgtgggtgtg-tgagtgggttggtg---cagGTGCTGTTGTCAATCTGCTCATTGCTGACAGACCCAAATCCGGATGATCCCCTTGTACCGGAAATCGCTCACATGTACAAGACAGACAGGCATAAGTACG

upper sequence: EFJ35297 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S34_302V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgttctttcctcgacaaccaagagagagctctcgtgttctaaatggtttttcgttccttttctttcgctcgctc---gctcgatcgatcgatttac--cagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG
|| | ||| | | ||| |||| | | ||| ||| | || | | | | | | | || | ||||||||||| |||||||||||| |||| || ||||| || || || || || || ||||| || || || |||||||| ||||| ||||||| |||||||
--ttaatatttttt--gtggcgaagcatgagcctatattgtgcgaatatatttgtaaactttgcaaggcaaatgacccgaacatgtttgtgtgacatggcgcagGTGCTGCTCTCAATCTGCTCGCTGCTTACGGACCCTAATCCAGATGACCCGCTGGTCCCAGAAATTGCTCACATGTATAAGACAGACAGGCAAAAGTATG

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|169025632|gb|FE436545.1|FE436545
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169078304|gb|FE490337.1|FE490337
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169105950|gb|FE504310.1|FE504310
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169038738|gb|FE446959.1|FE446959
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|70670995|gb|DN839572.1|DN839572
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|70670805|gb|DN839382.1|DN839382
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169105396|gb|FE506420.1|FE506420
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|70670872|gb|DN839449.1|DN839449
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169022096|gb|FE429105.1|FE429105
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169112483|gb|FE512760.1|FE512760
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169039764|gb|FE449426.1|FE449426
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169079016|gb|FE488579.1|FE488579
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|70670087|gb|DN838664.1|DN838664
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169086731|gb|FE494368.1|FE494368
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169020751|gb|FE430152.1|FE430152
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169079924|gb|FE487368.1|FE487368
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169095814|gb|FE498895.1|FE498895
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169020893|gb|FE429306.1|FE429306
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169046060|gb|FE453957.1|FE453957
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169026535|gb|FE434796.1|FE434796
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169032175|gb|FE439289.1|FE439289
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169082868|gb|FE491120.1|FE491120
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169032189|gb|FE439290.1|FE439290
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169046059|gb|FE453956.1|FE453956
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169061380|gb|FE470428.1|FE470428
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|70669831|gb|DN838408.1|DN838408
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAACCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169081704|gb|FE488162.1|FE488162
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169078305|gb|FE490338.1|FE490338
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|70669414|gb|DN837991.1|DN837991
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
EST: gi|169092996|gb|FE495290.1|FE495290
EST:     GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAG                         GTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC
genomic: GTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCC

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: 34 (upstream exon), 35 (downstream exon)
Score: 90

ATTCAGAACAAAGGTGTTTCATCCCAACATCAATAGCAATGGTAGCATCTGTCTCGACATTCTCAAGGAGCAGTGGAGCCCCGCCTTGACAATCTCCAAGgtttgttctt ... gatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggtttttcgttccttttctttcgctcgctcgctcgatcgatcgatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG
 ttctaaa  putative branch site (score: 90)
 ttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttctttcctcgacaaccaagagagagctctcgtgttctaaatggtttttcgttccttttctttcgctcgctcgctcgatcgatcgatttaccagGTGCTGCTATCAATCTGCTCGTTGCTAACCGACCCAAACCCCGACGATCCCCTCGTCCCCGAGATCGCCCACATGTACAAGACCGACAGGCCCAAGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC