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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

Basic information

species Physcomitrella patens
transcript PP1S198_157V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os12g06660.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------gtcatgg--gccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggca-caaaacc-----taaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                                             |||      | |        | |        |  |  | |      |  || || | |  || ||| | |     ||||   ||| || |           || ||||| || ||||| || || ||||| || || || ||||| |||||||||||||| || ||  ||||||| || |||||||| || ||||| ||||||||||
gtcatcatcatcatcaactcaatccaattaaccacctctcacaaatcacaacaacaacaacaaaccataccttatgttcttgcgttcaaaaaattcagtaaacaacaacaacagcaacgataaaccattgataataataatccaaaattcagGCCGGGTTCGCGGGCGACGACGCGCCGCGGGCGGTGTTCCCGAGCATCGTGGGTCGCCCCCGGCACACGGGGGTGATGGTGGGGATGGGGCAGAAGGACG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                |   |  | ||  ||  ||||||| || |  ||| |||   |        ||||| |       |  |  |  |  |   ||||||||| |||||||| || ||||||||  | ||||| || || ||||||||||| || ||| | ||||||||||| |||||||| ||||| ||||||||||
----------------gtgagccaccggtttggtcacatc-tgtt--ctcggtggctgctg-gggccctaaca-------acagcaccaacctcg-gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 1
gtcatgggccaagctgggtcgttatcgtc--ttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
    |  ||||  | || | | |  | ||  ||||| | |  |     |    |    | ||      ||||| |       |     |  |  |   ||||||||| |||||||| || ||||||||  | ||||| || || ||||||||||| || ||| | ||||||||||| |||||||| ||||| ||||||||||
---gtaagcca--ccggtttggtcacatctgttcttgagaatgcaaggttctcggtggctgctggggccctaaca-------acaacaccaacctcg-gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM5G859691_T01 (Zea mays), 3'ss of exon 7
gtcatgggccaagctgggtcgttatcgtc--ttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
    |  ||||  | || | | |  | ||  ||||| | |  |     |    |    | ||      ||||| |       |  |  |  |  |   ||||||||| |||||||| || ||||||||  | | ||| || || ||||||||||| || ||| | ||||||||||| |||||||| ||||| ||||||||||
---gtaagcca--ccggtttggtcacatctgttcttgagaatgcaaggttctcggtggctgctggggccctaaca-------acagcaccaacctcg-gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGTCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G478779_T01 (Zea mays), 3'ss of exon 5
----------------gtcatgggccaagctgg-gtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                  |     |  | ||||  | || |  ||   |  |   |   |  |  |||||  ||||       |        |    |  |  |  |  |   ||||||||| |||||||| || ||||||||  | ||||| || || ||||||||||| || ||| | ||||||||||| |||||||| |               
tatccagcccctcgtctgcgacaacggaactggcatggtcaaggtgagccaccggtttggtcacatctgttctcggtg-gctgctggggccctaacaacagCACCAACCTCG-GCAGGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGA---------------

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacct--aaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                        |   || |  |  ||  | || || |||   |   |||  |  ||  | |||      |     |  | ||   ||||||||| ||||| || || ||||||||  | ||||| || || |||||||| || || ||| | ||||| ||||||||||| || ||||| |||||||| |
-----------------------gtaagctaccgccgat--ttgt-tccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 2
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                          |||  |  |    | ||  |  |     | |   ||    || || |||    || | |  |  | |  |  |||||||||| ||||| ||||| || ||  | || || || || ||||| || || || ||  | ||||||||||| ||||| || ||||||||||||||||
--------------------------gtcagcccccgtccctg--actttgacaacctttactt--ccaaatatgccactaat-tatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G067985_T06 (Zea mays), 3'ss of exon 2
-gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatct--ctgtgatcggcacaaaacctaaa-atgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
 ||| || | |||   |    |  || |||    |||   |   ||  ||  || |||    |   |   | ||| |||    || | |  |  | |  |  |||||||||| ||||| ||||| || ||  | || || || || ||||| || || || ||  | ||||||||||| ||||| || ||||||||||||||||
tgtc-tgcgacaa-tggcactggaatggtcaaggtca-gcccccgtccctgactttgacaacctttacttccaaatatgccactaat-tatgtctgtcttttagGCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGACG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
------------------------------gtcatgggccaagctgg--gtcgttatcgtcttcttcacatcgtggtatctctgtg-atcggcacaa--------aacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                               |  | |   || ||    ||| |  || | ||  |   || |   ||||  | |  ||       |        ||  | |||  ||   ||||     | | | || |||||||||| ||||||||||| ||||| || || |||||||| ||||| || || || ||  | ||||||||||||||||| || ||||| || || || |
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaaaatta--attgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G10170.1 (Glycine max), 3'ss of exon 2
-----------------------------------------gtcatgggccaagctgggtcgttatcgtcttctt---cacatcgtggtatctctgtgat-cggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                                             |        |    |  |||| |  ||  |    | ||| |  ||  |   || | |  |    ||  | |||  ||   ||||    || | | || ||||||| || ||||||||||| ||||| || || |||||||| ||||| || || || ||  | ||||||||||||||||| || ||||| || || || |
gtacatgagggatcttttgtttgtgtattaaatttgttgataatgtaactttgacatactttttattggttttatgggaatatcattttacattaatgttacttctgtgaatttgaaaaatta--attgcaatgaatctttgtagGCTGGATTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
-gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
 ||  ||      | |   |  | ||  |    ||     ||||| ||            |  |     | |    ||   ||| ||   | ||| |||||||||| || ||||||||||| || ||  | |||||||| || ||||| ||||| || ||  | ||||||||||||||||| || ||||| || ||||| |
agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattt-tgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G00850.1 (Glycine max), 3'ss of exon 1
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
     |  |  |       | || |||| |  | |   ||| || |  | | |   ||  |      |      |||   ||||    |  | | | ||||| || || || |||||||| ||||| || || |||||||| ||||| || || || ||  | ||||||||||||||||| |||||||| ||||| || |
-----gtacagaatgcacactttttcgtttgatgcttctcgagggaattgttttg-cgttaacttttccccttcgttctaattgcaatgtgtcttttcagGCAGGATTTGCAGGAGATGATGCCCCACGTGCTGTGTTTCCTAGCATTGTTGGTCGTCCTCGTCACACTGGTGTGATGGTTGGTATGGGCCAGAAAGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
-----gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
       ||    | ||    |   |  |  || |     |  | ||  | |   | |    |        | |    ||||| | |||||   | ||| |||||||||| || ||||||||||| || ||  | || ||||| || ||||| ||||| || ||  | ||||||||||||||||| || ||||| || |||||||
tggagaacaacacctaaaacagaatggaactgtatct---aagttgtcctttggtttttgatgatttttctctttcggtgttgat-ttgtgttcaattt-tgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 2
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
    || |  |  |||  |  |||   |  | |     ||      ||| |||  |        ||    |  || |  |  | |  | || |||  ||||||||||| ||||| ||||| |||||  | || ||||| || || || || || || || |||||||||||||| ||||| |||||||| ||||| || |
---gtgagttagactgtttatttag-atactgtatggttctaaccttctttgttgtacatgtgtaagactac-tgatcatgatttttgtatatta-acagGCTGGTTTTGCTGGTGATGATGCCCCGAGAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACACTGGTGTCATGGTTGGTATGGGTCAGAAAGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 3
--gtcatgggccaagctgggtcgttat-cgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
   |  ||   |   || | | | ||| |   ||  |    | ||    |     | |   || |||     | ||  ||   ||  |  |  || |||||||||||| || || || ||||| || ||| | || |||||||| || || ||||| ||||| |||||||||||||| ||||| || ||||| || || || |
gtctgttgtttctttcttgcttgatatgcagatttgttgtgttgtttgctgctcctcaaatgctcaatttgaataagctttccatgttatgctttatatgcagGCTGGATTTGCGGGTGATGATGCTCCCAGGGCAGTGTTTCCTAGTATTGTGGGTCGGCCAAGGCACACTGGTGTCATGGTTGGGATGGGTCAAAAAGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtcatgggccaagctgggtcgtta---tcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggt-attgtg-cggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
    |      | || || ||||      | | |   | |  ||  | | | |  || |||   |||| |  |   ||  | |   |||| ||   | |  ||||||||| || ||||| ||||| ||||| ||||| ||||| ||   ||||||||| |||||  | ||||| |||||||||||||| ||||| ||||||    
----tccatttaacttgggcgttgggcctggcgtgggccccgcgctgcagcgcgttgttcga-gcaaacctgatgctggcgatcgctgtgtcgccgtgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaa--aatgttggtattgtgcggat-tttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                                                |  |     ||| |     ||     || ||| |   | | |  | ||  |||||||||| || || ||||| || || ||| | ||||||||||| ||||| ||||| ||||| | |||||| || || ||||| || ||||| |||||||| |
-----------------------------------------------gtgcgctcctggcgcggtttcttgtggattttgatccggggggtgtgttcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

upper sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaa--aatgttggtattgtgcggat-tttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                                                |  |     ||| | |   ||     || ||| |   | | |  | ||| |||||||||| || || ||||| || || ||| | ||||||||||| ||||| ||||| ||||| | |||||| || || ||||| || ||||| |||||||| |
-----------------------------------------------gtgcgctcctggcgcgatttcttgtggattttgatccggggggtgtgtttttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

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|100365992|gb|BY967241.1|BY967241
EST:     ATACTAAGAGTATTTCTTCTCCATG                         GCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTG
genomic: ATACTAAGAGTATTTCTTCTCCATGgctggagagg ... ttttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
                    acctaaa  putative branch site (score: 3)
                       taaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

- - - - - - - - - - - - - - - -cttcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cggcaca