XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T Gene Polymorphisms Associated with Male Infertility Risk: Evidences from Case-Control and In Silico Studies
Table 4
The prediction of the consequence of XRCC7 -6721G>T mutation via HSF 3 tool.
(a) HSF matrices
Sequence position
cDNA position
Splice site type
Motif
New splice site
Wild type
Mutant
If cryptic site use, exon length variation
Variation (%)
83
+83
Acceptor
TATGAAAAACAGCG
TATGAAAAACAGCT
75.52
76.12
NA
+0.79
94
+94
Acceptor
GCGGACTCTTAGGC
GCTGACTCTTAGGC
75.48
78.56
NA
+4.08
(b) Branch points
Sequence position
cDNA position
Branch point motif
CV for reference sequence (0–100)
CV for mutant sequence (0–100)
Variation
93
+93
AGCGGAC
71.15
86.24
+15.9
(c) ESE Finder matrices for SRp40, SC35, SF2/ASF, and SRp55 proteins
Sequence position
cDNA position
Linked SR protein
Reference motif (value 0–100)
Linked SR protein
Mutant motif (value 0–100)
Variation
92
+92
SF2/ASF (IgM-BRCA1)
CAGCGGA (90.08)
SF2/ASF (IgM-BRCA1)
CAGCTGA (77.77)
−13.66%
92
+92
SF2/ASF (IgM-BRCA1)
CAGCGGA (90.08)
SF2/ASF
CAGCTGA (78.10)
−13.29%
92
+92
SF2/ASF
CAGCGGA (89.23)
SF2/ASF (IgM-BRCA1)
CAGCTGA (77.77)
−12.84%
92
+92
SF2/ASF
CAGCGGA (89.23)
SF2/ASF
CAGCTGA (78.10)
−12.47%
93
+93
SRp55
AGCGGA (76.48)
Site broken −100
95
+95
SF2/ASF (IgM-BRCA1)
CGGACTC (74.23)
Site broken −100
96
+96
SC35
GGACTCTT (75.23)
Site broken −100
(d) ESE motifs from HSF
Sequence position
cDNA position
Linked ESE protein
Reference motif (value 0–100)
Linked ESE protein
Mutant motif (value 0–100)
Variation
94
+94
9G8
GCGGAC (77.99)
9G8
GCTGAC (78.59)
+0.77%
(e) Silencer motifs
Sequence position
cDNA position
Sironi motif reference
Reference silencer (value 0–100)
Sironi mutant motif
Mutant silencer (value 0–100)
Variation
89
+89
Motif 1: CTAGAGGT
AAACAGCT (66.19)
New site
91
+91
Motif 1: CTAGAGGT
ACAGCGGA (65.75)
Site broken 0.66
(f) hnRNP motifs
Sequence position
cDNA position
Linked hnRNP protein
Reference motif (value 0–100)
Linked hnRNP protein
Mutant motif (value 0–100)
Variation
92
+92
hnRNP A1
CAGCGG (66.67)
Site broken –100
(g) Interpreted data
Predicted signal
Prediction algorithm
cDNA position
Interpretation
ESS site broken
(1) Sironi et al., Motif 1
Alteration of an intronic ESS site Potential alteration of splicing
