                         SEQUENCE LISTING

<110>  UNIVERSITY OF PITTSBURGH - OF THE COMMONWEALTH SYSTEM OF 
       HIGHER EDUCATION
       Panousis, Constantinos
       Halvas, Elias
       Mellors, John
 
<120>  ALLELE SPECIFIC PCR ASSAY FOR DETECTION OF NUCLEOTIDE VARIANTS

<130>  8123-91977-02

<150>  US 61/892,993
<151>  2013-10-18

<160>  46    

<170>  PatentIn version 3.5

<210>  1
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  1
ctccartatt tgccataaaa cg                                                22


<210>  2
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  2
ctccartatt tgccataaaa ca                                                22


<210>  3
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  3
tattcctaat tgaacytccc a                                                 21


<210>  4
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (25)..(25)
<223>  Locked nucleic acid

<400>  4
gccataaaaa agaaggacca gtacg                                             25


<210>  5
<211>  25
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (25)..(25)
<223>  Locked nucleic acid

<400>  5
gccataaaaa agaaggacca gtaca                                             25


<210>  6
<211>  31
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (31)..(31)
<223>  Locked nucleic acid

<400>  6
ctaagtcaga tcctacatac aagtcatccc c                                      31


<210>  7
<211>  31
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (31)..(31)
<223>  Locked nucleic acid

<400>  7
ctaagtcaga tcctacatac aagtcatccc t                                      31


<210>  8
<211>  29
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  8
tagtataaac aatgagacac cagggatta                                         29


<210>  9
<211>  38
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (38)..(38)
<223>  Locked nucleic acid

<400>  9
ccctatttct aagtcagatc ctacatacaa agtcatgt                               38


<210>  10
<211>  38
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (38)..(38)
<223>  Locked nucleic acid

<400>  10
ccctatttct aagtcagatc ctacatacaa agtcatgc                               38


<210>  11
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (27)..(27)
<223>  Locked nucleic acid

<400>  11
cccacatcta gtactgtcac tgattga                                           27


<210>  12
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (27)..(27)
<223>  Locked nucleic acid

<400>  12
cccacatcta gtactgtcac tgattgt                                           27


<210>  13
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (27)..(27)
<223>  Locked nucleic acid

<400>  13
cccacatcta gtactgtcac tgattgc                                           27


<210>  14
<211>  29
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  14
aagtggagaa aattagtaga tttcaggga                                         29


<210>  15
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (27)..(27)
<223>  Locked nucleic acid

<400>  15
cccacatcta gtactgtcac tgattgg                                           27


<210>  16
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (27)..(27)
<223>  Locked nucleic acid

<400>  16
ctacatacaa gtcatccata tattgcc                                           27


<210>  17
<211>  27
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (27)..(27)
<223>  Locked nucleic acid

<400>  17
ctacatacaa gtcatccata tattgct                                           27


<210>  18
<211>  29
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  18
caccagggat tagatatcaa tataatgtg                                         29


<210>  19
<211>  28
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (28)..(28)
<223>  Locked nucleic acid

<400>  19
ctatgttgcc ctatttctaa gtcagagg                                          28


<210>  20
<211>  28
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (28)..(28)
<223>  Locked nucleic acid

<400>  20
ctatgttgcc ctatttctaa gtcagagc                                          28


<210>  21
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  21
aaacaatggc cattgacaga aga                                               23


<210>  22
<211>  24
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  22
gttcataccc catccaaaga aatg                                              24


<210>  23
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  23
ctccartatt tgccataaaa cg                                                22


<210>  24
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  24
ctccartatt tgccataaaa ag                                                22


<210>  25
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  25
ctccartatt tgccataaaa ca                                                22


<210>  26
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  26
ctccartatt tgccataaaa aa                                                22


<210>  27
<211>  31
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  27
ctaagtcaga tcctacatac aagtcatccc c                                      31


<210>  28
<211>  31
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  28
ctaagtcaga tcctacatac aagtcatccc t                                      31


<210>  29
<211>  37
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  29
ccctatttct aagtcagatc ctacatacaa gtcatgt                                37


<210>  30
<211>  37
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  30
ccctatttct aagtcagatc ctacatacaa gtcatgc                                37


<210>  31
<211>  34
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  31
ctatttctaa gtcagatcct acatacaagt catc                                   34


<210>  32
<211>  1680
<212>  DNA
<213>  human immunodeficiency virus

<400>  32
cccattagcc ctattgagac tgtaccagta aaattaaagc caggaatgga tggcccaaaa       60

gttaaacaat ggccattgac agaagaaaaa ataaaagcat tagtagaaat ttgtacagag      120

atggaaaagg aagggaaaat ttcaaaaatt gggcctgaaa atccatacaa tactccagta      180

tttgccataa agaaaaaaga cagtactaaa tggagaaaat tagtagattt cagagaactt      240

aataagagaa ctcaagactt ctgggaagtt caattaggaa taccacatcc cgcagggtta      300

aaaaagaaaa aatcagtaac agtactggat gtgggtgatg catatttttc agttccctta      360

gatgaagact tcaggaagta tactgcattt accataccta gtataaacaa tgagacacca      420

gggattagat atcagtacaa tgtgcttcca cagggatgga aaggatcacc agcaatattc      480

caaagtagca tgacaaaaat cttagagcct tttagaaaac aaaatccaga catagttatc      540

tatcaataca tggatgattt gtatgtagga tctgacttag aaatagggca gcatagaaca      600

aaaatagagg agctgagaca acatctgttg aggtggggac ttaccacacc agacaaaaaa      660

catcagaaag aacctccatt cctttggatg ggttatgaac tccatcctga taaatggaca      720

gtacagccta tagtgctgcc agaaaaagac agctggactg tcaatgacat acagaagtta      780

gtggggaaat tgaattgggc aagtcagatt tacccaggga ttaaagtaag gcaattatgt      840

aaactcctta gaggaaccaa agcactaaca gaagtaatac cactaacaga agaagcagag      900

ctagaactgg cagaaaacag agagattcta aaagaaccag tacatggagt gtattatgac      960

ccatcaaaag acttaatagc agaaatacag aagcaggggc aaggccaatg gacatatcaa     1020

atttatcaag agccatttaa aaatctgaaa acaggaaaat atgcaagaat gaggggtgcc     1080

cacactaatg atgtaaaaca attaacagag gcagtgcaaa aaataaccac agaaagcata     1140

gtaatatggg gaaagactcc taaatttaaa ctgcccatac aaaaggaaac atgggaaaca     1200

tggtggacag agtattggca agccacctgg attcctgagt gggagtttgt taatacccct     1260

cccttagtga aattatggta ccagttagag aaagaaccca tagtaggagc agaaaccttc     1320

tatgtagatg gggcagctaa cagggagact aaattaggaa aagcaggata tgttactaat     1380

agaggaagac aaaaagttgt caccctaact gacacaacaa atcagaagac tgagttacaa     1440

gcaatttatc tagctttgca ggattcggga ttagaagtaa acatagtaac agactcacaa     1500

tatgcattag gaatcattca agcacaacca gatcaaagtg aatcagagtt agtcaatcaa     1560

ataatagagc agttaataaa aaaggaaaag gtctatctgg catgggtacc agcacacaaa     1620

ggaattggag gaaatgaaca agtagataaa ttagtcagtg ctggaatcag gaaagtacta     1680


<210>  33
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  33
ctccartatt tgccataaaa cc                                                22


<210>  34
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  34
ctccartatt tgccataaaa ct                                                22


<210>  35
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  35
ctccartatt tgccataaaa a                                                 21


<210>  36
<211>  560
<212>  PRT
<213>  human immunodeficiency virus

<400>  36

Pro Ile Ser Pro Ile Glu Thr Val Pro Val Lys Leu Lys Pro Gly Met 
1               5                   10                  15      


Asp Gly Pro Lys Val Lys Gln Trp Pro Leu Thr Glu Glu Lys Ile Lys 
            20                  25                  30          


Ala Leu Val Glu Ile Cys Thr Glu Met Glu Lys Glu Gly Lys Ile Ser 
        35                  40                  45              


Lys Ile Gly Pro Glu Asn Pro Tyr Asn Thr Pro Val Phe Ala Ile Lys 
    50                  55                  60                  


Lys Lys Asp Ser Thr Lys Trp Arg Lys Leu Val Asp Phe Arg Glu Leu 
65                  70                  75                  80  


Asn Lys Arg Thr Gln Asp Phe Trp Glu Val Gln Leu Gly Ile Pro His 
                85                  90                  95      


Pro Ala Gly Leu Lys Lys Lys Lys Ser Val Thr Val Leu Asp Val Gly 
            100                 105                 110         


Asp Ala Tyr Phe Ser Val Pro Leu Asp Glu Asp Phe Arg Lys Tyr Thr 
        115                 120                 125             


Ala Phe Thr Ile Pro Ser Ile Asn Asn Glu Thr Pro Gly Ile Arg Tyr 
    130                 135                 140                 


Gln Tyr Asn Val Leu Pro Gln Gly Trp Lys Gly Ser Pro Ala Ile Phe 
145                 150                 155                 160 


Gln Ser Ser Met Thr Lys Ile Leu Glu Pro Phe Arg Lys Gln Asn Pro 
                165                 170                 175     


Asp Ile Val Ile Tyr Gln Tyr Met Asp Asp Leu Tyr Val Gly Ser Asp 
            180                 185                 190         


Leu Glu Ile Gly Gln His Arg Thr Lys Ile Glu Glu Leu Arg Gln His 
        195                 200                 205             


Leu Leu Arg Trp Gly Leu Thr Thr Pro Asp Lys Lys His Gln Lys Glu 
    210                 215                 220                 


Pro Pro Phe Leu Trp Met Gly Tyr Glu Leu His Pro Asp Lys Trp Thr 
225                 230                 235                 240 


Val Gln Pro Ile Val Leu Pro Glu Lys Asp Ser Trp Thr Val Asn Asp 
                245                 250                 255     


Ile Gln Lys Leu Val Gly Lys Leu Asn Trp Ala Ser Gln Ile Tyr Pro 
            260                 265                 270         


Gly Ile Lys Val Arg Gln Leu Cys Lys Leu Leu Arg Gly Thr Lys Ala 
        275                 280                 285             


Leu Thr Glu Val Ile Pro Leu Thr Glu Glu Ala Glu Leu Glu Leu Ala 
    290                 295                 300                 


Glu Asn Arg Glu Ile Leu Lys Glu Pro Val His Gly Val Tyr Tyr Asp 
305                 310                 315                 320 


Pro Ser Lys Asp Leu Ile Ala Glu Ile Gln Lys Gln Gly Gln Gly Gln 
                325                 330                 335     


Trp Thr Tyr Gln Ile Tyr Gln Glu Pro Phe Lys Asn Leu Lys Thr Gly 
            340                 345                 350         


Lys Tyr Ala Arg Met Arg Gly Ala His Thr Asn Asp Val Lys Gln Leu 
        355                 360                 365             


Thr Glu Ala Val Gln Lys Ile Thr Thr Glu Ser Ile Val Ile Trp Gly 
    370                 375                 380                 


Lys Thr Pro Lys Phe Lys Leu Pro Ile Gln Lys Glu Thr Trp Glu Thr 
385                 390                 395                 400 


Trp Trp Thr Glu Tyr Trp Gln Ala Thr Trp Ile Pro Glu Trp Glu Phe 
                405                 410                 415     


Val Asn Thr Pro Pro Leu Val Lys Leu Trp Tyr Gln Leu Glu Lys Glu 
            420                 425                 430         


Pro Ile Val Gly Ala Glu Thr Phe Tyr Val Asp Gly Ala Ala Asn Arg 
        435                 440                 445             


Glu Thr Lys Leu Gly Lys Ala Gly Tyr Val Thr Asn Arg Gly Arg Gln 
    450                 455                 460                 


Lys Val Val Thr Leu Thr Asp Thr Thr Asn Gln Lys Thr Glu Leu Gln 
465                 470                 475                 480 


Ala Ile Tyr Leu Ala Leu Gln Asp Ser Gly Leu Glu Val Asn Ile Val 
                485                 490                 495     


Thr Asp Ser Gln Tyr Ala Leu Gly Ile Ile Gln Ala Gln Pro Asp Gln 
            500                 505                 510         


Ser Glu Ser Glu Leu Val Asn Gln Ile Ile Glu Gln Leu Ile Lys Lys 
        515                 520                 525             


Glu Lys Val Tyr Leu Ala Trp Val Pro Ala His Lys Gly Ile Gly Gly 
    530                 535                 540                 


Asn Glu Gln Val Asp Lys Leu Val Ser Ala Gly Ile Arg Lys Val Leu 
545                 550                 555                 560 


<210>  37
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer

<400>  37
tattcctaat tgaacctccc a                                                 21


<210>  38
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Oligonucleotide primer

<400>  38
tattcctaat tgaacttccc a                                                 21


<210>  39
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  39
ctccaatatt tgccataaaa cg                                                22


<210>  40
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  locked nucleic acid

<400>  40
ctccagtatt tgccataaaa cg                                                22


<210>  41
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  Locked nucleic acid

<400>  41
ctccaatatt tgccataaaa ca                                                22


<210>  42
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  locked nucleic acid

<400>  42
ctccagtatt tgccataaaa ca                                                22


<210>  43
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  locked nucleic acid

<400>  43
ctccaatatt tgccataaaa cc                                                22


<210>  44
<211>  22
<212>  DNA
<213>  artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  locked nucleic acid

<400>  44
ctccaatatt tgccataaaa ct                                                22


<210>  45
<211>  22
<212>  DNA
<213>  artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  locked nucleic acid

<400>  45
ctccagtatt tgccataaaa cc                                                22


<210>  46
<211>  22
<212>  DNA
<213>  artificial sequence

<220>
<223>  oligonucleotide primer


<220>
<221>  modified_base
<222>  (22)..(22)
<223>  locked nucleic acid

<400>  46
ctccagtatt tgccataaaa ct                                                22


