Supplementary Table 1 – The list of total 73 RNA helicases encoded by the rice genome.
Chr / Locus Identifier / Putative Function1 / LOC_Os01g02884 / ATP-dependent RNA helicase DHX36, putative, expressed
1 / LOC_Os01g07080 / ATP-dependent rRNA helicase spb4, putative, expressed
1 / LOC_Os01g07740 / ATP-dependent RNA helicase-like protein DB10, putative, expressed
1 / LOC_Os01g08930 / ATP-dependent RNA helicase rhlE, putative, expressed
1 / LOC_Os01g10050 / ATP-dependent RNA helicase dbp2, putative, expressed
1 / LOC_Os01g11370 / ATP-dependent RNA helicase DHX35, putative, expressed
1 / LOC_Os01g36860 / ATP-dependent RNA helicase-like protein DB10, putative, expressed
1 / LOC_Os01g36890 / spliceosome RNA helicase BAT1, putative, expressed
1 / LOC_Os01g36920 / spliceosome RNA helicase BAT1, putative, expressed
1 / LOC_Os01g43120 / ATP-dependent RNA helicase has1, putative, expressed
1 / LOC_Os01g43130 / ATP-dependent RNA helicase HAS1, putative, expressed
1 / LOC_Os01g56190 / RNA helicase A, putative, expressed
1 / LOC_Os01g68320 / ATP-dependent RNA helicase dbp2, putative, expressed
1 / LOC_Os01g73900 / DEAD-box ATP-dependent RNA helicase, putative, expressed
2 / LOC_Os02g01740 / U5 small nuclear ribonucleoprotein 200 kDa helicase, putative, expressed
2 / LOC_Os02g01880 / U5 small nuclear ribonucleoprotein 200 kDa helicase, putative, expressed
2 / LOC_Os02g05660 / ATP-dependent RNA helicase DDX41, putative, expressed
2 / LOC_Os02g10770 / pre-mRNA-processing ATP-dependent RNA helicase PRP5, putative, expressed
2 / LOC_Os02g19860 / pre-mRNA-splicing factor ATP-dependent RNA helicase, putative, expressed
2 / LOC_Os02g42860 / ATP-dependent RNA helicase dhh1, putative, expressed
2 / LOC_Os02g55260 / ATP-dependent RNA helicase DDX51, putative, expressed
2 / LOC_Os02g57980 / ATP-dependent RNA helicase dbp4, putative, expressed
3 / LOC_Os03g01830 / DEAD/DEAH box helicase, putative, expressed
3 / LOC_Os03g06220 / ATP-dependent RNA helicase DBP5, putative, expressed
3 / LOC_Os03g06440 / RNA helicase SDE3, putative, expressed
3 / LOC_Os03g12000 / DEAD-box ATP-dependent RNA helicase, putative, expressed
3 / LOC_Os03g17432 / pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16, putative
3 / LOC_Os03g19530 / pre-mRNA-processing ATP-dependent RNA helicase prp-5, putative, expressed
3 / LOC_Os03g19960 / pre-mRNA-splicing factor ATP-dependent RNA helicase, putative, expressed
3 / LOC_Os03g46610 / ATP-dependent RNA helicase DDX47, putative, expressed
3 / LOC_Os03g50090 / ATP-dependent RNA helicase DDX23, putative, expressed
3 / LOC_Os03g51900 / ATP-dependent RNA helicase DDX56, putative, expressed
3 / LOC_Os03g53220 / U5 small nuclear ribonucleoprotein 200 kDa helicase, putative, expressed
3 / LOC_Os03g53500 / ATP-dependent RNA helicase SUV3, mitochondrial precursor, putative, expressed
3 / LOC_Os03g53760 / ATP-dependent RNA helicase DHX36, putative, expressed
3 / LOC_Os03g58810 / ATP-dependent RNA helicase has1, putative, expressed
3 / LOC_Os03g59050 / ATP-dependent RNA helicase ded1, putative, expressed
3 / LOC_Os03g61220 / nucleolar RNA helicase 2, putative, expressed
4 / LOC_Os04g38630 / ATP-dependent RNA helicase SUV3, mitochondrial precursor, putative, expressed
4 / LOC_Os04g40970 / DEAD-box ATP-dependent RNA helicase, putative, expressed
4 / LOC_Os04g43140 / ATP-dependent RNA helicase MAK5, putative, expressed
4 / LOC_Os04g45040 / ATP-dependent RNA helicase dhh1, putative, expressed
4 / LOC_Os04g45980 / ATP-dependent RNA helicase A, putative, expressed
5 / LOC_Os05g01990 / DEAD-box ATP-dependent RNA helicase, putative, expressed
5 / LOC_Os05g32370 / pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16, putative, expressed
6 / LOC_Os06g09280 / ATP-dependent RNA helicase DHX8, putative, expressed
6 / LOC_Os06g23530 / pre-mRNA-splicing factor ATP-dependent RNA helicase, putative, expressed
6 / LOC_Os06g34420 / ATP-dependent RNA helicase DDX18, putative
6 / LOC_Os06g40020 / ATP-dependent RNA helicase ded-1, putative, expressed
6 / LOC_Os06g48210 / ATP-dependent RNA helicase DDX41, putative, expressed
7 / LOC_Os07g05050 / nucleolar RNA helicase 2, putative, expressed
7 / LOC_Os07g10250 / ATP-dependent RNA helicase DED1, putative, expressed
7 / LOC_Os07g20580 / ATP-dependent RNA helicase DBP3, putative, expressed
7 / LOC_Os07g32430 / pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16, putative, expressed
7 / LOC_Os07g33340 / ATP-dependent RNA helicase dbp4, putative, expressed
7 / LOC_Os07g43980 / ATP-dependent RNA helicase DDX49, putative, expressed
7 / LOC_Os07g45360 / ATP-dependent RNA helicase DDX52, putative, expressed
7 / LOC_Os07g46580 / ATP-dependent RNA helicase DDX47, putative
8 / LOC_Os08g05810 / ATP-dependent RNA helicase DDX46, putative
8 / LOC_Os08g06344 / pre-mRNA-processing ATP-dependent RNA helicase prp5, putative, expressed
8 / LOC_Os08g24760 / pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16, putative, expressed
8 / LOC_Os08g32090 / ATP-dependent RNA helicase DDX54, putative, expressed
9 / LOC_Os09g21520 / DEAD-box ATP-dependent RNA helicase, putative, expressed
9 / LOC_Os09g34910 / nucleolar RNA helicase 2, putative, expressed
10 / LOC_Os10g02930 / helicase SEN1, putative, expressed
10 / LOC_Os10g35990 / ATP-dependent RNA helicase dhh1, putative, expressed
11 / LOC_Os11g09060 / ATP-dependent RNA helicase, putative
11 / LOC_Os11g20554 / pre-mRNA-splicing factor ATP-dependent RNA helicase F56D2.6, putative, expressed
11 / LOC_Os11g32880 / DEAD-box ATP-dependent RNA helicase, putative, expressed
11 / LOC_Os11g38670 / ATP-dependent RNA helicase ded-1, putative, expressed
12 / LOC_Os12g05230 / ATP-dependent RNA helicase, putative, expressed
12 / LOC_Os12g29660 / ATP-dependent RNA helicase DRS1, putative, expressed
12 / LOC_Os12g41715 / DEAD-box ATP-dependent RNA helicase, putative, expressed
(Chr – chromosome)
Supplementary Table 2 – The list of total 31 DNA helicases encoded by the rice genome.
Chr / Locus Identifier / Putative Function1 / LOC_Os01g19430 / Werner syndrome ATP-dependent helicase, putative, expressed
1 / LOC_Os01g36390 / DNA replication licensing factor mcm4, putative, expressed
1 / LOC_Os01g45190 / eukaryotic initiation factor 4A-3, putative, expressed
1 / LOC_Os01g49680 / DNA repair helicase XPB2, putative, expressed
1 / LOC_Os01g53580 / Werner syndrome ATP-dependent helicase, putative
2 / LOC_Os02g05330 / eukaryotic initiation factor 4A, putative, expressed
2 / LOC_Os02g48100 / ATP-dependent DNA helicase recG, putative, expressed
2 / LOC_Os02g54020 / ATP binding protein, putative, expressed[RecQl3 (RecQ-like 3) (AT4G35740)]*
2 / LOC_Os02g55410 / DNA replication licensing factor MCM5, putative, expressed
3 / LOC_Os03g36930 / eukaryotic initiation factor 4A-3, putative, expressed
4 / LOC_Os04g03990 / Werner syndrome ATP-dependent helicase, putative, expressed
4 / LOC_Os04g14810 / Werner syndrome ATP-dependent helicase, putative, expressed
4 / LOC_Os04g35420 / ATSGS1, putative, expressed [AtRECQ4B (AT1G60930)]*
4 / LOC_Os04g52960 / nucleolin, putative, expressed
5 / LOC_Os05g05260 / DNA repair helicase UVH6, putative, expressed
5 / LOC_Os05g05810 / DNA helicase RecQsim, putative, expressed[RecQSIM (AT5G27680)]*
5 / LOC_Os05g08100 / DNA replication licensing factor MCM3, putative, expressed
5 / LOC_Os05g14590 / DNA replication licensing factor MCM6, putative, expressed
5 / LOC_Os05g38850 / DNA replication licensing factor MCM8, putative, expressed
5 / LOC_Os05g39850 / DNA replication licensing factor MCM3, putative, expressed
6 / LOC_Os06g11500 / minichromosome maintenance protein MCM, putative, expressed
6 / LOC_Os06g33520 / ATP-binding DEAD/DEAH box helicase, putative, expressed
6 / LOC_Os06g48750 / eukaryotic initiation factor 4A, putative, expressed
7 / LOC_Os07g08729 / ATP-dependent DNA helicase 2 subunit 1, putative, expressed [Ku 80 & Ku 70 (AT1G16970)]*
7 / LOC_Os07g46590 / SNF2 family N-terminal domain containing protein
7 / LOC_Os07g48360 / superfamily II DNA helicase, putative, expressed
9 / LOC_Os09g36820 / MCM10 minichromosome maintenance deficient 10, putative, expressed
11 / LOC_Os11g44910 / bloom syndrome protein, putative, expressed = [RECQI1 (AT3G05740)]*
11 / LOC_Os11g48090 / ATP-dependent DNA helicase Q1, putative, expressed [RECQL2 (AT1G31360)] [RECQ4A similar to RECQ2 (AT1G31360)]*
11 / LOC_Os11g29380 / DNA replication licensing factor Mcm2, putative, expressed
12 / LOC_Os12g37400 / PROLIFERA protein, putative, expressed
(Chr – chromosome)
*Homologs of RecQ and Ku70-80 helicases in Arabidopsis are indicated. The accession numbers are indicated in parenthesis.
Supplementary Table 3 – The list of total 11 helicases (included as a separate category) that neither belong to RNA or DNA helicases encoded by the rice genome.
Chr / Locus Identifier / Putative Function1 / LOC_Os01g40980 / regulator of telomere elongation helicase 1, putative, expressed
2 / LOC_Os02g02150 / ATP-dependent helicase yprA, putative, expressed
2 / LOC_Os02g12840 / helicase conserved C-terminal domain containing protein, expressed (CTD1)
2 / LOC_Os02g43460 / helicase conserved C-terminal domain containing protein (CTD2)
3 / LOC_Os03g53760 / helicase associated domain family protein, expressed (HADfp)
4 / LOC_Os04g59624 / helicase conserved C-terminal domain containing protein, expressed (CTD3)
5 / LOC_Os05g32610 / helicase conserved C-terminal domain containing protein, expressed (CTD4)
6 / LOC_Os06g33520 / ATP binding protein, putative, expressed [Stress response suppressor 2 = (AT5G08620)]*
7 / LOC_Os07g48270 / ATP-dependent helicase C582.10c in chromosome II, putative, expressed
7 / LOC_Os07g49210 / helicase conserved C-terminal domain containing protein, expressed (CTD5)
11 / LOC_Os11g07500 / helicase C6F12.16c, putative, expressed
(Chr = chromosome)
*Homolog of Stress Response Suppressor-2 (SRS2) helicase in Arabidopsis is indicated. The accession number is given in parenthesis.
Supplementary Table 4: The list of 113 members of helicase gene family in Arabidopsis.
S. No. / Locus ID / Name1 / AT1G03750 / Chromatin remodeling 9
2 / AT1G05460 / Similarity to RNA helicases (silencing defective=SDE3)
3 / AT1G05490 / Chromatin remodeling 31
4 / AT1G06670 / Nuclear DEIH-box helicase (NIH)
5 / AT1G08600 / ATRX/CHR20
6 / AT1G08840 / EMBRYO DEFECTIVE 2411
7 / AT1G10930 / DNA helicase (AtRECQ4A)
8 / AT1G11100 / SNF2 domain-containing protein
9 / AT1G16280 / DEAD/DEAH box helicase(RH36)
10 / AT1G20920 / DEAD box RNA helicase (RH42)
11 / AT1G20960 / EMB1507; ATP-dependent helicase
12 / AT1G27880 / ATP-dependent DNA helicase, similar to RecQl3 (Recq-like 3)
13 / AT1G31360 / RECQL2
14 / AT1G31970 / STRS1 (STRESS RESPONSE SUPPRESSOR 1)(RH5)
15 / AT1G32490 / DEAH RNA helicases
16 / AT1G35530 / DEAD/DEAH box helicase
17 / AT1G48310 / SNF2 domain-containing protein
18 / AT1G48650 / Helicase domain-containing protein
19 / AT1G51380 / eukaryotic translation initiation factor 4A (RH2)
20 / AT1G55150 / DEAD box RNA helicase, putative (RH20)
21 / AT1G59760 / ATP-dependent RNA helicase, similar to HEN2
22 / AT1G59990 / DEAD/DEAH box helicase, putative (RH22)
23 / AT1G60930 / AtRECQ4B
24 / AT1G61140 / EDA16 (embryo sac development arrest 16)
25 / AT1G63250 / DEAD box RNA helicase (RH48)
26 / AT1G71280 / DEAD/DEAH box helicase (RH55)
27 / AT1G72730 / eukaryotic translation initiation factor 4A
28 / AT1G77050 / DEAD/DEAH box helicase (RH29)
29 / AT2G01130 / Helicase domain-containing protein
30 / AT2G01440 / ATP-dependent helicase
31 / AT2G02090 / Chromatin remodeling 19
32 / AT2G06990 / DExH-box RNA helicase
33 / AT2G07750 / DEAD box RNA helicase (RH33)
34 / AT2G13370 / Chromatin remodeling 5
35 / AT2G33730 / DEAD box RNA helicase (RH21)
36 / AT2G35920 / Helicase domain-containing protein
37 / AT2G40700 / DEAD/DEAH box helicase, putative (RH17)
38 / AT2G42270 / U5 small nuclear ribonucleoprotein helicase
39 / AT2G45810 / DEAD/DEAH box helicase (RH6)
40 / AT2G47250 / RNA helicase
41 / AT3G01540 / RNA HELICASE DRH1
42 / AT3G02060 / DEAD/DEAH box helicase
43 / AT3G05740 / RECQI1
44 / AT3G06480 / DEAD box RNA helicase (RH40)
45 / AT3G06980 / DEAD/DEAH box helicase (RH50)
46 / AT3G09620 / DEAD/DEAH box helicase (RH45)
47 / AT3G09720 / DEAD/DEAH box helicase (RH57)
48 / AT3G16600 / SNF2 domain-containing protein
49 / AT3G18600 / DEAD/DEAH box helicase (RH51)
50 / AT3G22310 / PMH1 (RH9)
51 / AT3G46960 / ATP-dependent helicase HEN2 (HUA ENHANCER 2)
52 / AT3G54280 / ATP binding / DNA binding / helicase
53 / AT3G58510 / DEAD box RNA helicase (RH11)
54 / AT3G61240 / DEAD/DEAH box helicase (RH12)
55 / AT3G62310 / RNA helicase
56 / AT4G01020 / Helicase domain-containing protein
57 / AT4G09730 / DEAD/DEAH box helicase (RH39)
58 / AT4G15850 / Plant DEAD box-like RNA helicase
59 / AT4G16630 / DEAD/DEAH box helicase, putative (RH28)
60 / AT4G16680 / RNA helicase, similar to MEE29
61 / AT4G18465 / RNA helicase (EMBRYO DEFECTIVE 2733)
62 / AT4G34910 / DEAD/DEAH box helicase, putative (RH16)
63 / AT5G07810 / SNF2 domain-containing protein
64 / AT5G08610 / DEAD box RNA helicase (RH26)
65 / AT5G08620 / STRS2 (STRESS RESPONSE SUPPRESSOR 2) (RH25)
66 / AT5G10370 / Helicase domain-containing protein
67 / AT5G11170 / DEAD/DEAH box helicase, putative (RH15)
68 / AT5G11200 / DEAD/DEAH box helicase (RH56)
69 / AT5G14610 / ATP-dependent helicase (RH46)
70 / AT5G19210 / DEAD/DEAH box helicase (RH58)
71 / AT5G20420 / CHR42 (chromatin remodeling 42)
72 / AT5G27680 / DNA helicase (RECQSIM)
73 / AT5G54910 / DEAD/DEAH box helicase (RH32)
74 / AT5G60990 / DEAD/DEAH box helicase (RH10)
75 / AT5G62190 / DEAD/DEAH box RNA helicase PRH75
76 / AT5G63120 / ethylene-responsive DEAD box RNA helicase (RH30)
77 / AT5G63630 / DEAD box RNA helicase (RH31)
78 / AT5G63950 / Chromatin remodeling 24
79 / AT5G65900 / DEAD/DEAH box helicase (RH27)
80 / AT1G16970 / Ku80 and ku70 heterodimer
81 / AT1G48050 / Ku80 and ku70 heterodimer
82 / AT1G48920 / Nucleolin genes
83 / AT3G53110 / DEAD-Box RNA Helicase (LOS4)
84 / AT4G35740 / RecQl3 (Recq-like 3)
85 / AT2G16440 / MCM family protein
86 / AT2G14050 / MCM9
87 / AT2G07690 / minichromosome maintenance family protein
88 / AT3G09660 / MCM8
89 / AT4G02060 / MCM7
90 / AT5G46280 / MCM3
91 / AT2G20980 / MCM10
92 / AT4G00660 / RH8
93 / AT3G16840 / RH13
94 / AT5G05450 / RH18
95 / AT2G47330 / RH24
96 / AT5G51280 / RH35
97 / AT2G42520 / RH37
98 / AT4G33370 / RH43
99 / AT1G12770 / RH47
100 / AT1G20750 / helicase-related
101 / AT1G79890 / helicase-related
102 / AT1G79950 / helicase-related
103 / AT2G03270 / DNA-binding protein
104 / AT2G30800 / RNA or DNA helicase (ATVT1)
105 / AT3G27730 / DNA helicase (MER3)
106 / AT3G51690 / DNA helicase homolog PIF1
107 / AT4G25120 / UvrD/REP helicase family protein
108 / AT5G05130 / SNF2 domain-containing protein
109 / AT5G22330 / DNA helicase (ATTIP49A)
110 / AT5G41360 / XPB2
111 / AT5G41370 / XPB1
112 / AT5G67630 / DNA helicase
113 / AT3G13920 / Eukaryotic translation initiation fator 4A1 (RH4)
1