reference for the paper:
Association and linkage analyses of RGS4 polymorphisms in schizophrenia
Human Molecular Genetics, 2002, Vol. 11, No. 12 1373–1380- click here to download our RGS4 poster presented at the 2002 ASHG conference in Baltimore.
- Corrigendum: we recently discovered an unfortunate error in the snp7 data for the Bipolar sample reported on in the above paper. This error does not change the association reported in the schizophrenia sample. Click here to view the erratum to be published in Human Molecular Genetics, along with the relevant tables omitted from the published erratum.
05/06/03
untranslated region
GTACGCTCAAAGCCGAAGCCACAGCTCCTCCTGCCGCATTTCTTTCCTGCTTGCGAATTCCAAGCTGTTAA
ATAAG
mRNA sequence with amino acid labeled
| ATG | TGC | AAA | GGG | CTT | GCA | GGT | CTG | CCG | GCT | TCT | TGC | TTG | AGG | AG/T |
| M | C | K | G | L | A | G | L | P | A | S | C | L | R | S |
| GCA | AAA | GAT | ATG | AAA | CAT | CGG | CTA | GGT | TTC | CTG | CTG | CAA | AAA | TCT |
| A | K | D | M | K | H | R | L | G | F | L | L | Q | K | S |
| GAT | TCC | TGT | GAA | CAC | AAT | TCT | TCC | CAC | AAC | AAG | AAG | GAC | AAA | GTG |
| D | S | C | E | H | N | S | S | H | N | K | K | D | K | V |
| GTT | ATT | TGC | CAG | AG/A | GTG | AGC | CAA | GAG | GAA | GTC | AAG | AAA | TGG | GCT |
| V | I | C | Q | R | V | S | Q | E | E | V | K | K | W | A |
| GAA | TCA | CTG | GAA | AAC | CTG | ATT | AGT | CAT | GAA | TGT/ | GGG | CTG | GCA | GCT |
| E | S | L | E | N | L | I | S | H | E | C | G | L | A | A |
| TTC | AAA | GCT | TTC | TTG | AAG | TCT | GAA | TAT | AGT | GAG | GAG | AAT | ATT | GAC |
| F | K | A | F | L | K | S | E | Y | S | E | E | N | I | D |
| TTC | TGG | ATC | AGC | TGT | GAA | GAG | TAC | AAG | AAA | ATC | AAA | TCA | CCA | TCT |
| F | W | I | S | C | E | E | Y | K | K | I | K | S | P | S |
| AAA | CTA | AGT | CCC | AAG | GCC | AAA | AAG | ATC | TAT | AAT | GAA | TTC | ATC | TCA |
| K | L | S | P | K | A | K | K | I | Y | N | E | F | I | S |
| GTC | CAG | GCA | ACC | AAA | GAG | GT/G | AAC | CTG | GAT | TCT | TGC | ACC | AGG | GAA |
| V | Q | A | T | K | E | V | N | L | D | S | C | T | R | E |
| GAG | ACA | AGC | CGG | AAC | ATG | CTA | GAG | CCT | ACA | ATA | ACC | TGC | TTT | GAT |
| E | T | S | R | N | M | L | E | P | T | I | T | C | F | D |
| GAG | GCC | CAG | AAG | AAG | ATT | TTC | AAC | CTG | ATG | GAG | AAG | GAT | TCC | TAC |
| E | A | Q | K | K | I | F | N | L | M | E | K | D | S | Y |
| CGC | CGC | TTC | CTC | AAG | TCT | CGA | TTC | TAT | CTT | GAT | TTG | GTC | AAC | CCG |
| R | R | F | L | K | S | R | F | Y | L | D | L | V | N | P |
| TCC | AGC | TGT | GGG | GCA | GAA | AAG | CAG | AAA | GGA | GCC | AAG | AGT | TCA | GCA |
| S | S | C | G | A | E | K | Q | K | G | A | K | S | S | A |
| GAC | TGT | GCT | TCC | CTG | GTC | CCT | CAG | TGT | GCC | TAA | ||||
| D | C | A | S | L | V | P | Q | C | A | stop |
untranslated region
TTCTCACCTGAAGGCAGAGGGATGAAATGCCAAGACTCTATGCTCTGGAAAACCTGAGGCCAAATATTGAT
CTGTATTAAGCTCCAGTGCTTTATCCACATTGTAGCCTAATATTCATGCTGCCTGCCATGTGTGAGTCACT
TCTACGCATAAACTAGATATAGCTTTTGGTGTTTGAGTGTTCATCAGGGTGGGACCCCATTCCAGTCCAAT
TTTCCTAAGTTTCTTTGAGGGTTCCATGGGAGCAAATATCTAAATAATGGCCTGGTAGGTCTGGATTTTCA
AAGATTGTTGGCAGTTTCCTCCTCCCAACAGTTTTACCTCGGGATGGTTGGTTAGTGCATGTCACATGACA
TCCACATGCACATGTATTCTGTTGGCCAGCACGTTCTCCAGACTCTAGATGTTTAGATGAGGTTGAGCTAT
GATATGTGCTTGTGTGTATGTCTATGTGTATATATTATATATACATTAGACACACATATACATTATTTCTG
TATATAGATGTCTGTGTATACATATGTATGTGTGAGTGTATGTATACACACACACACACACACACACACAC
ACTTTTGCAAGAGTGATGGGAAAGACCCTAGGTGCTCATAACTAGAGTATGTGTATGTACTTACATGGGTG
TTTTGATCTCTGTTCTTTCATACTACATTTGAACAGGGCAAAATGAACTAACTGCCATGTAGGCTAAGAAA
GAAATGCTAACCTGTGGAAAGTTGGTTTTGTAAAATTCCATGGATCTTGCTGGAGAAGCATCCAAGGAACT
TCATGCTTGATTTGACCACTGACAGCCTCCACCTTGAGCACTATTCTAAGGAGCAAATACCTTAGCTCCCT
TGAGCTGGTTTTCTCTGATGGCACTTTTGAGCTCCTAAGCTGCCAGCCTTCCCTTCTTTTCCTGGGTGCTC
AGGGCATGCTTATTAGCAGCTGGGTTGGTATGGAGTTGGCAGACAGGATGTTCAACTTAATGAAGAAATAC
AGCTAAGGCCTTGCCAGCAACACCTGCCGTAAGTTACTGGCTGAGTGAGGGCATAGAAGTTAAAGGTTACT
GTTTTTATCCTCTATCCTTTTTTCCTTTCCTGATCAAGGTGCTCTTCTCATTTTTTCCTGAGAACCTTAGC
CATCAGATGAGGCTCCTTAGTTTATTGTGGTTGGTTGTTTTTTCTTTATAATGGCTCTGGGCTATATGCCT
ATATTTATAAACCAGCAGCAGGGGAAAGATTATATTTTATAAGAGGGAACAAATTTTCACAATTTGAAAAG
CCCACATAAGTTTTCTCTTTTAAGGTAGAATCTTGTTAATTTCATTCCAAACATCGGGGCTAACAGAGACT
GGAGGCATTTCTTTTTAGGCTCTGAGACTAAATGAGAGGAAAAGAAAAGAAAAAAAAAATGATTGTCTAAC
CAATTGTGAGAATTACTGTTTGAAACTTTTCAAGGCACATTGAAATACTTGAAAACTTCTCATTTATGTTA
TTTATGATGTTATTTTGTACGTGTTATTATTATTATATTGTTTTATAAATGGAGGTACAGGATATCACCTG
AATTATTAATGAATGCCCAGGAAGTAATTTTCTTCTCATTCTTCTAAAACTACTGCCTTTCAAAGTGCACA
CACACGCGTCCACATACACTGCATTCGTTGCTCCAGTATAAATTACATGCATGAGCACCTTTCTGGCTTTT
AAGCCAATATAATGGGCTGCAAAATGAAGACACCAGAGTGTATGCATACAAATCTCACTGTATTAAAGATG
CAGGTTTTCTAATTGTACCCTTCTTGTCTCTCTGGCAATCTTGCCCTTAATATCCCTGGAGTTCCTCATCA
GTGTCATTTTCTGTTATACACAGTTCCACAATTTTGTCTCTAGTTGACTTCAAATGTGTAACTTTATTGGT
CTTGCCCTATTATAATTGTCATGACTTTCAGATTGTATCTGAACTCACAGACTGCTGTCTTACTAATAGGT
CTGGAAGGTCACGCTGAATGAGAAGTAAATTATTTTATGTAATACATTTTTGAGTGTGTTTTTCAGTTGTA
TTTCCCTGTTATTTCATCACTATTTCCAATGGTGAGCTTGCCTGCTCATGCTCCCTGGACAGAATACTCCT
TCCTTTTGCATGCCTGTTTCTATCATGTGCTTGATAGGCCTCAAAGCTAATGCTTCCAGTGAAACACACGC
ATCTTAATAATAAGGGTAAATAAACGCTCCATATGAAAC
Assay information:
| SNP | type | annealing temp | PCR product(bp) | Assay method | Forward primer(5'-3') | Reverse primer(5'-3') | FP primer | ddNTP |
| 27859 | T/C | 500C | 386 (277+109) | SphI | aattgccccaatccttctct | gcatctggacaatgtcttgg | ||
| 90387 | G/A | 600C | 324 (262+62) | MboII | gctagttgtgtgatttgggaca | tgctctcacttagcctgctg | ||
| SNP1 | G/A | 500C | 310 (187+123) | BstNI | ggtgtcatggaaagtgcttg | ggcacagaacaggggaaata | ||
| SNP4 | T/G | 500C | 115 | SSCP/FP | cagaagcctccctccttctt | tatacagcatcctccagccc | 5' TCT TTG CTT TTT AGT CCT AAA A3' | A/C |
| SNP7 | G/A | 600C | 191(153+38) | DdeI | agaaagaaagcttgggaggc | gttcacatcctgctgtgtgg | ||
| SNP14 | Ins/Del | 600C | 150/157 | PAGE | ggaccaaaggagggagtagat | ttttctgcctgctctctctc | ||
| SNP18 | A/G | 600C | 138 | SSCP/FP | tggggcagagagataaggaa | aggtttggctccatcatcag | 5' CTC CAT CAT CAG AAA GGC ACT A 3' | C/T |
| SNP23 | C/A | 600C | 207 (155+52) | BamHI | ctcctctgcttccctgactg | taagcacacttaccccctgc | ||
| 118740 | C/G | 600C | 341 (215+75+51) | BstNI | tgcctttgagggtgttaaaaa | tgggtatcagatgggagattg | ||
| 130121 | G/C | 600C | 317 (205+112) | EcoRV | aggcacactgggaagttaca | tccttcctcactttatttctctgg | ||
| 187688 | C/G | 600C | 399 (273+126) | PvuII | ggcaggggacttgatcttct | cattgcatttgattgtttgga | ||
| 208899 | A/T | 600C | 345 (227+118) | ApoI | tggtttctcagtggagtgga | ttgaatgagatcactttgggataa | ||
| 217761 | C/T | 600C | 329 (258+71) | AvaI | tgccataacactgcatgagc | tgaccttgggttagagtgtgc | ||
| 322448 | A/T | 600C | 344 (247+97) | EcoRI | gcctttcaaaagtgaagagca | tttgccaacaaaaaccatca |
DNA sequence information for RGS4 SNPs
(bold face indicates the SNP and the Primers positions)
SNP 27859
ggattaatcatgacaaaagtaatctaaatctcgttaagactacttaatgatcaatctttc
cctctgttttccctgactatagggaagtg aattgccccaatccttctct atcacccccct
gcagccatgccaatgccttacctctgttatattcagccataggggaagcttattctcata
gaatcaggggttggcatg t/c agtcactagctattcttggtgagactagtgaagatgagtga
aggaaaatattgcataggtgaaatctcataggcacaaataggtgtttgtgagagtaacaa
taaaagaaagtcattcccatactctagtagatgactcattttctcctcattttttttttt
tcaaggcgttctctacaacggttaacctagtaccaaaaatccttctcttttttcttggac
aaatcctgttcaagttagcatggcatttactacgt ccaagacattgtccagatgc tgtgg
SNP 90387
ataatctcctttcaagtttttatcctgtcactt gctagttgtgtgatttgggaca aatca
tttaactccttgtaaagggagagaag g/a aaggctgtaaaaaaattaagtaataaaaagata
aactccttgtggtatattttgttattgttcaaaaatatttattgcccctcttaggatgtc
ttaggtcattcttgcattgctataaagaaatacccaagtctgggtaatttataaagaata
gaggttaaattggctcacagttctgcaggctgcacaggaagcatcccactggcgtctact
cacttctggtgaggactcagaaagcttttgcttatga cagcaggctaagtgagagca ggt
SNP 1
aggggaagaaaaccttgtttcccaagaaggaggagaaaacccaaaatagccttatcccaaagattaaatc
ttttttctgcaacatttagcccaggatagaaacagcagtttcataagagttcatttgcattgtgcaggtg
gaaagaaacagtat ggtgtcatggaaagtgcttg aactttacagagaggcagatctggattccaattcta
gatcctctaggaaatcttggtaaattagggtaaactttatgacctctagttttgtaacgtgccctg g/a act
tcaatttgccctcacattttaaaatctagattccttagcataacattctggtactttcataattcatccc
cattccaacttttcatctttcccttccactcttttcttcattatattctactatgtagtcatcccagacc
actgaatattcccacacatttatg tatttcccctgttctgtgcc atcaacctgaaatgtcttcacagtac
cctgcggtcaagctcttttttctcctgtcgccagtggtaatcaactgctacctcttatgcactctagaag
tatggtgtttgagccagacctctgtttcgctcctctttaaatccgatcatgttacatttgccaataacgt
SNP4
gagttgcgttctttagttctaccagatattaaatggggcactgatcctccacttgggcaggatgtaggcc
aaggctcagccccaggctgtgcttgcaccacttcagatgacaatttcctctcagttgt cagaagcctccc
tccttctt tattgtttactacaatggcctagacatcaatgagagttcagttattga g/t ttttaggactaaa
aagcaaagatatg gggctggaggatgctgtata ccaggaaggtaaacagggacttcccagtatgtcttac
ttttgggaaatgtgtccaattctttgcaccaagctttgtgggcacatgcaataaatcaggaactccaacc
SNP7
Aagaggtagttcaagtacttaagccgatcaggttagcattct agaaagaaagcttgggaggc agagtaaa
agaatagattggatatcagagaaactggcaaaaagtttgaaggctattttaagttccttaaattgtaaaa
tgctaacatctggaaggtattgttgacaataggctttagaagaactgtttcctactg g/a ggggcagacatt
cag ccacacagcaggatgtgaac tatgtgtggtctctaggtaaatttcaaatttttccaacctttgctca
gggagaacaaaagaaaacatttctcaaggattgacggtatcaaatgcagggaaataagtcattgtggcag
SNP18
tttaagatgagatcttctacaaaactattaactgatttgtaatgatcaatatttctcaaccaaactcata
tgagacacttcaagaactagaga tggggcagagagataaggaa gatctggctttaaaactcatatctcat
tgtaacattttcttataagaacatagagagtgaaagttactgcaccaccacacggaaagc g/a tagtgcctt
t ctgatgatggagccaaacct cattctggggtacctttcctgaaacaagttgtagcatacaatcagaaag
cccagagccaggcttctatgtactccagggatgctcaaatagcagtagtaatcacagatggagatattac
SNP23
Tcc ctcctctgcttccctgactg atgactgttcaggggatgcaacatcctttttgattataacaagatac
aatcctgaatgttagggtgattccaaggtgataatgtaaatatatcatgaagtccaaatagaaacgaatt
catatttctatgtgctggatc c/a acctgagatcctagagttattaatcaat gcagggggtaagtgtgctta
gcaagtattcttataataaaaccataaaaataaaaaacaaaatgacttcagaagttactggagtcaggaa
SNP118740
catggtatttttactacccattgccttctaggaaagggtataacaaataggaaatattaa
tatttttaa tgcctttgagggtgttaaaaa gcacaactctaaggactgtttgtaaattc c/g
aggtcaaatgttgtttctccttctctatttcctaccttggtgatggcctgatcttatatg
gagtcactccaactagaaaccacagaatcatccctagttcctacttctgactcactccat
acactcaaaagtcacctgactctgcagaatttctctagaaaaactctatgaaaacctatt
cctgcctctccacctgcatagatgtagcttcatccaggctcttatggtgcatggcctcgg
ttactgccttatcctttctactggcctct caatctcccatctgataccca ttaatgtact
SNP130121
ccaaatacttttt aggcacactgggaagttaca ttgtttcttgcaagtgacaggttgtcc
tttaattagttctttctctcaaaaagagactgctgactccaaactgggaagaaacccact
caccagcaaaatgctgctgaattcactctgatagttttctaatctctcatcagtagatga
caataatgaagccagtattgttaccacaagactcagatat g/c tctatcacccaagatgatt
tctctttaagacgcaataaaagggaacttttctccccatttattagcaactaagatgaaa
tgagag ccagagaaataaagtgaggaagga aagagaatttactacctttacaagctgaaa
SNP187688
tt ggcaggggacttgatcttct tgtaatcctcacaggcaatccagaactcaaggttttcc
tcactgaattcagacttcaggaaacttttgaaactggcaagtccatctggaaagaaaaaa
acagtca c/g ctggagaaatttattaatttacttaacaaatattgtatccatgagagaaagg
gaaagggcttagcaatactcttctatgcacaaagttttagctcattcatgtctagcttcc
tttactccttcattcaaatgcagaaggaatgagacagagatggaagatagacagcagaga
acacagagctcaagccctgctcatcatgcagagccgtatggaactctagaactagacaga
gagatttaccacattgtctt tccaaacaatcaaatgcaatg tctatttaagtgacaaacg
SNP208899
gtattccttaaattaacaatctttttctctgtgaagaatat tggtttctcagtggagtgg
a agtatataaacaatcccaaatcaagacatagatttgctctgtcttcaaggagtttacaa
acacatcaaagaagagaagatatatttagaccttttta a/t aattttttaaagtaataaagc
cacagtgaagaaaatgtaaagaaaagagaaaaatcaacccccaatcccaccactctaaca
gtctctggccatgtcttttaataacttatgctgatccctccttttcttgtggattcttaa
tgtatcagaacccagggtttggtccttggacttctcatcttttctatcgtttctatcttc
ac ttatcccaaagtgatctcattcaa tcttatggctttaaatgctatctgtatgctgatg
SNP 217761
atttccagtgttgtatgtaatacagggatatagaattcagattcaaagcctatgcttttt
tctcatga tgccataacactgcatgagc cttgagtttgaaattaatttggatttgaagta
ataaaaataaatttaggtcc c/t gagtgatttttctttttgcttctcttgctttacagtcaa
ttgatgagatctttggatggtttgcatcattttttaatcctatataaatatttgtttctt
tcatttgcctattttggctttctttagaaaatggtcttagtttattgaaattatcgccag
tgctttaaagagtatgacttccagtcaattcagttccacagttttattgagcaaatatca
tggattcaaaattagc gcacactctaacccaaggtca tatagagtggtataaaggacttt
SNP 322448
cagttatttgaggacaggtatttcatttta gcctttcaaaagtgaagagca gtattttaa
tctattttgctgtgttaagttctgttccagttgaagagcaagaagagttcaagcagcttt
cagatgg a/t attcaggagctacaacaatcactaaatcaggattttcatcaaaaaacggtat
ctgttgtgaggcaccttaaactttaaaaaataaaatttgtttgtagatgtggtgggacat
atagtggaggtaacagcacattgctttctctattaccaaagaaacagaatatatttctgt
gcccatttgtgccccttataatggatacatacttctctcaaccatctagaaccg tgatgg
tttttgttggcaaa gttttttgttgtcttattgaatagaattttttagggttttcctagg
| dbSNP (NCBI rs#) | snp no in the manuscript |
| 879719 | 27859 |
| 1507754 | 90387 |
| not listed | SNP1 |
| 951436 | SNP4 |
| 951439 | SNP7 |
| 2661319 | SNP18 |
| not listed | SNP23 |
| 1395967 | 118740 |
| 925128 | 130121 |
| 1354939 | 187688 |
| 976288 | 208899 |
| 1396549 | 217761 |
| 1509022 | 322448 |
PCR Conditions for RGS4 SNPs
10xPCR buffer 1.0ul
dNTP(5mM) 0.4ul
MgCl2(25mM) 0.6ul (for FP, use 1.2ul)
F-primer(20uM) 0.125ul (for FP, use 0.025ul)
R-primer(20uM) 0.125ul (for FP, use 0.025ul)
Taq Polymerase(5U/ul) 0.05ul
DNA(20ng/ul) 3.0ul
Sterile water ---
Total 10.0ul
PCR reaction conditions
Initial denaturation
95° C for 4min(if it is AmpliTaq Gold do it for 10min)
35 cycles of
94° C for 45sec
60° C for 45 sec(see table for change in temp)
72° C for 1min
followed by
final extension at 72° C for 7min.
SSCP :
MDE gel solution (2X concentration), 10% glycerol,
Run at 10W for 6hrs
3.2ml of water
7.0ml of glycerol
42ml of 1X TBE buffer
17.5ml of MDE2X gel solution
37.5ul of TEMED
375ul of 10% APS
FP method :
SAP treatment :
10X SAP buffer 1.0ul
Alkaline Phosphatase 2.0ul
Exonuclease I 0.1ul
Sterile water --
Total 10.0ul
37° C for 1hr 30min, followed by 95° C for 15min.
FP labeling :
10uM Detection primer 1.0ul
Thermoseq buffer 1.0ul
25uM ddNTP 0.05ul
Thermoseq (8u/ul) 0.1ul
Sterile water
Total 10ul
Reaction conditions
94° C for 1min
followed by
94° C for 10sec
55° C for 30sec (for SNP18 at 60° C)
for 35 cycles
4° C forever