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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG

Basic information

species Zea mays
transcript GRMZM5G816636_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||||    || | |||||| || ||| |||  |||   ||  ||||                               | | ||||  || |   |  |||||    | |||||||||||||  ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||| ||| || |||||||||||||
gtaatgatctttttcacattatattgacattagggtatgaattatggtg-----------------------------tatatgcat-aatttgtttctaccctatgtgcagGTAATTGACAGATCATTTGGTTTCGACACTGCAGTTGAGGAGGCCCAACGTGCAATAAATGCTGCTCATGTAGAAGCTGGAAGCGCCGAGAATGGTATAG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||||  | ||  |      |  | ||    |||      | || |  ||    |       |||       | ||  |  | |||     |||  || | |  |      |||| ||||| ||||| ||||| || ||||| || ||||||||||||||||| || |||||||| || ||||| ||||||| ||||| ||| ||||| ||||
gtaaggttttattttcttctacattgtggctttaaactcataatttaaaccccattagcatcattgattggtaaatttcttctgc--tgtctctttgatgcttaa----tagGTTATTGATAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTTGAAAATGGCATAG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 7
gtaa-tatgtttct-ccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcac--tgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|| |  ||| ||       |  |  |     ||    | |||   |         | || | | | |     |         |||   | || | ||  ||||   | ||  |||||| ||||| |||||||||||||| ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| | |||  ||||||||||||| |
gtgagcatgcttgaattggacatctgaagccttacaatagaagctactttgctgaaaatataaaaaggatttacttttaaactgtcacctaattaaccatgttgtacctgaatcagGTTATTGATAAGTCATTTGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcac-atgaaccttgtgtgcacgaactcactgttacccatgtttca---gGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                 |  | |  ||||     |       | |    | |   ||||  ||| | ||| |||| |    |||  |     | | ||||  |  ||  | |   ||| ||||| ||||| || || || |||||||| |||||||||||||||||||| |||||||| || ||||| || |||| ||||| ||| ||||| ||||
---------------gtacatcatggatag--cagctcttccatttattgct--tatttcccattagcaccatgagct---tgtaaaatggtttaatgttctctctggcttaatagGTTATTGATAAGTCCTTCGGCTTTGACACAGCTGTTGAGGAGGCTCAACGTGCTATAAATGCAGCACATGTTGAGGCTGAAAGTGGTGAAAATGGCATAG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 8
-----------------gtaatatgttt-ctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgt-ttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                 || |||| |||  | | |  |  |    || | |  |    |||||  |   |||  | | |  |    |   | |   |   | || |  |  | |||   |  | | || |||| |||||||| || |||||||| || || || |||||||||||||||||||| || ||||| |||||||| ||||||| ||||  |||||||||||| |
gtatgcttgttcacaatgtcatatttttgtttctccctggaactctaatcttatcattaaaatatatc-tgaagtgttagttctctatgaggaaacttcat-catgttcggattgtcttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 8
-----------------gtaatat-gtttctccacattttagtgatattttggtggaaaaa-atggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                 |||| || || | |    |  || || ||| |||  ||  |  | |    | | || |   ||  |||  |    |   |    |     |  ||| |  |     ||  | |||| |||||||||||| ||||||||||||| || ||||| ||||| ||||| ||||| ||| |||||||||||||||| | ||| ||||||||||| || |
gtaatgatgctttagttgtaaaattgtatatgtgaaaatt-gttatacttttatgctatcatactccaaaggaaaaaggatttgag-attaaagtgtcacctatttaatgtcatt-ctgtatttgaattagGTTATTGACAAGTCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCTGAGAATGGAATTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||||  | ||| |   | | |   |  |   ||       | |||  ||     |  ||  ||| || |  ||     | | | |         ||||  |     |   |||| ||||| ||||| ||||| || ||||| || ||||||||||||||||| || |||||||| || ||||| ||||||| |||||  || ||||| ||||
gtaagttttttttttccttctacattgtggctttaaactcataatttaaacc--ccattagcatcattaattggtaaatttcttc-------tgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||      || ||      |||   ||||  |||     |          |  ||     ||||| |   | ||     ||        |    |||  |     |   |||| ||||| ||||| || || || |||||||| |||||||||||||||||||| |||||||| || ||||| || |||| ||||| ||| ||||| ||||
gtacatctcttttctgtccattatcaatatcatggatagcagctcttgcattagcac----catgaacttgtaaa----atggtttaatgcatgttgtctctggcttaatagGTTATTGATAAGTCCTTCGGCTTTGACACAGCTGTTGAGGAGGCTCAACGTGCTATAAATGCAGCACATGTTGAGGCTGAAAGTGGTGAAAATGGCATAG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 7
gtaa-tatgtttct-ccacattttagtgatattttggtggaaaaaa--tggaagatgacatttgacatgatcacatgaaccttgt--gtgcacgaactcac--tgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||||  ||| ||       |  |  |     ||    | |||   |  | || ||  |  |   | |  |  | ||     |     ||   | || | ||  ||||   | ||  |||||| || || |||||||| ||||| ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| | |||  ||||||||||||| |
gtaagcatgcttgaattggacatccgaagccttacaatagaagctactttgatgagaatgta-aaaacaacgatatacttttaaacagtcacctaattaaccatgttgtacctgaatcagGTTATCGATAAGTCATTCGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATCG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
--------------------gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                      | | | | | |  | |||    |  | || ||       |   | |||   | |    |  |||    |  |   |    |     |  ||| |  |     || || |||| |||||||| ||| ||||||||||||| || ||||| ||||| ||||| ||||| ||| |||||||||||||||| | ||| || |||||||| || |
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagttta-aagtgtcacctatttaatgtcatt-ctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
-----------------gtaatatgtttc--tccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                 || |||| |||   ||| |  |  |    || | |  |    |||||  |   |||  | |    |    |     |   |   ||  || | |  ||  |     |  || |||| |||||||| || |||||||| || || || |||||||||||||||||||| || ||||| |||||||| ||||||| ||||  ||||||||| || |
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatt-tgaagtgttggttatctatgaagaaacttcatgttcggattgccttct---ttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaa--aatggaagatgacatt-tgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||||    |   |   |||| | ||  | |        ||    ||       |   ||| ||    | || || ||| ||    |  | ||      |  || |  || |  |||| ||||||||||| ||||| || || || || |||||||||||||||||||| || ||||| || ||||| |||||    ||||  || || || || |
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatga------tagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------gtaatatgtttctccacattt-tagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacga-----actcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                                        ||   || || | ||  |||| | |      | |      |||||       |  | | |    |  | ||     |  | | |    ||     ||   |   ||    || | ||||| ||||||||||| ||||| || ||||| || ||||||||||| |||||||| || ||||| || ||||| ||| ||| ||||   |||||| |||| |
gtacatctctttgtttccttaattgctgattataggaccggttggatattacacctgatttattgcatagatataaattcaaaaacaatttttttcctattttttattgaccaattctctttttagttgatttttacctccgactattgctggtacagGTTATTGACAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCCCAACGTGCTATTAATGCAGCACATGTTGAATCTGAAAGTATCGAGAATTGTATTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------gtaa-tatgtttct-----ccacattttagtgatattttggtggaaaaaatggaagatgacat--ttgaca------tgatcacatgaa--ccttgtgtgca-----cgaactcactgttaccca------tgtttcagGTAA-------TTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                                                  |||| || |||||      | |   ||| |  |  | |  | | ||| | |   |||||||||  || |        || |  | ||||  ||  ||||||      | ||  ||   ||  | |      | ||| ||||||       | || |||||||| || || || |||||||| || || ||||| |||||||| ||||| ||||||||||||||||  |||| | |||||||| | |
gtacgtcactgtcttttgatatacacttggtaggattacgtgcggtagaagtaactaagtttcaggaagctaatatttggatacgtgtgtgcgcaaagactaccagatgacatgattaattatgtattgttttcttgaagtccaagtgtgccaccgtctaatgcatatttgtcgaatgtggtatttgaggtaacagGTCATAGATAAGTCATTCGGATTTGATACAGCAGTGGAAGAAGCTCAGCGTGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTGTTCAGAATGGTCTTG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatatgtttct-------ccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaacc--ttg--tgtgcacgaactcactgttacccatgtttc--------------agGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||||| || | ||       | ||| || | |  | ||||  |  | |   | |        || |  |||||| | |  | ||  |||  | |  |   ||   ||  | |    ||| |              || ||||||| ||||| || || |||||||| || || || || || ||||| ||||| ||||| ||||||||||||||||  ||| || | |||||| | |
gtaatgtgctccttatagtacaacacttgaatttttttttactacacatgcttgcgtgct-tatgtcgcatgatgatagcatcccgttgcttatatattgacctcctagtccttgggttacttggagatgagagcagATAATTGATAAGTCCTTCGGGTTCGACACTGCCGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTACTCATAATGGTGTGG

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
-------------------gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacat-gatcacatgaaccttgtg-tgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                    |   |     |     | ||   || | |||   ||||   ||| |     |    |     | | | |    |  |  | | || | | |     || | | | | |  ||||| || ||||| ||||||||||| || || |||||||| || || || |||||||| |||||||| || ||||||||||  |||| | | ||||| || |
gtacgttttagacacggaaattcaacaacacgatggaattctctg-tttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 12

GAAGTTAGAAGACGCGGCCTCAAAGTTTCTGTTGCTGGCATTCCAAAGACTATTGATAATGACATCCCTgtaatatgtt ... catgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 8

GAAGTTAGAAGACGCGGCCTCAAAGTTTCTGTTGCTGGCATTCCAAAGACTATTGATAATGACATCCCTgtaatatgtt ... catgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
                               aactcac  putative branch site (score: 8)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG