Basic Information

Type: gene

Biological Identity

Species

rosa_multiflora

Chromosome

Rmu_sc0000976.1

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Reverse (-)

132755 .. 136821

Gene Structure 4067 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

N/A

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1095 bp

atgaagatactaaaggctgatgtcggagcacttgacaattttgaagtgctcgaattcctaaaatctaaaggggcctcaaagaatgatctatcacgggtggcaagagttacacaatcagagtataaggtttttgattatttggttgatactcctactggtactcacacaagagagagtgttgaagagttcaaggagaagtgtagacaatatgaccttgggaatgataagatcctcaatattattaacactaggccagcttcagtggttgaaatatatgcgatcgtggaggataatgctgatgagctagtagagctggttgcagaggtcttgactcctccaactgtaccatcccctaaacctgaagccgatactaatgagattgatgcagagaccatgaacgtggaacaaattgaacaaaatgatggcaataaagaaaaacctgaatttggggaagcaccaatggagactatttgggtagagcaccggcggcatccaggaggccatcgaagacgtttgtgtggtcgtcattgtcagcgccggtcgagcttgggcaagctgcagcaaaatcttggcaaaagtcgacccgcaccggcgaggcggttggacgcggtcgagctcacctgcgagttgcagcggaacctgggcgagaggtcgaacctcgccggagttggagatcagggagctaatcgacggctgccagaggtggctagagagagagagagacgcttgccggaggtggagaatggatcgatgcctgccgcagaacccaagtctttgaggaggaggccaacaagaaggtcctgcatgcagtgcgagaatgtcctggtgacaaacagtgagcttcatattcttaaaggccctcgctttctaaatgacatcatcatcgaattctacttcctccatatttctaatgccctccttcaatcccatgagtcgttccgagatgacatccttttggtttcgcatgccctctcattctttctgcagcaggattttggggatgactcccgtgtcaaagactttgcggagtccaacaaagtagatagcaagcaggttgtaatgggagttgagggtggatttccgcccttttcctag

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005886 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0007568 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009360 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030424 GO:0030425 GO:0030880 GO:0031974 GO:0031981 GO:0032502 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0036477 GO:0042575 GO:0042995 GO:0043005 GO:0043025 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044297 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044463 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0071944 GO:0090304 GO:0097447 GO:0097458 GO:0097659 GO:0097747 GO:0120025 GO:0120038 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RNA_pol_Rpb4

Protein Analysis

364

Amino Acids

41.22

Weight (kDa)

5.73

Isoelectric Point (pI)

63.5

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	11 - 100	4.4e-09	RNA polymerase Rpb4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0001390)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950
fragaria_vesca	FvH4_4g01070 FvH4_4g01070 FvH4_5g27570
malus_domestica	MD13G1198900.v1.1
prunus_persica	Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1
pyrus_communis	pycom13g17270
rosa_chinensis	RchiOBHm_Chr4g0387641 RchiOBHm_Chr6g0280701
rosa_laevigata	RLG00000010104 RLG00000013035
rosa_multiflora	Rmu_sc0000976.1_g000021 Rmu_sc0003953.1_g000006
rosa_roxburghii	Rroxscaffold_7G00187720
rosa_rugosa	Rorug03G0311800 Rorug03G0311900 Rorug03G0312000 Rorug03G0312100 Rorug06G0133900 Rorug06G0133900 Rorug06G0133900 Rorug06G0134000
rosa_samantha	Rh4AG017400 Rh4BG012200 Rh4CG018600 Rh4DG013200 Rh6AG246600 Rh6BG248900 Rh6CG250000 Rh6DG241500
rosa_wichuraiana	Rw4G001120 Rw6G021350

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	629
AasI	GACNNNNNNGTC	1 cut(s)	1010
Acc36I	ACCTGC	2 cut(s)	629, 1042
AccI	GTMKAC	2 cut(s)	202, 580
AccII	CGCG	1 cut(s)	608
AciI	CCGC	8 cut(s)	487, 585, 598, 608, 634, 759, 1025, 1082
AclWI	GGATC	2 cut(s)	223, 754
AcsI	RAATTY	3 cut(s)	53, 443, 887
AcuI	CTGAAG	2 cut(s)	243, 381
AfaI	GTAC	2 cut(s)	160, 345
AfiI	CCNNNNNNNGG	1 cut(s)	446
AgsI	TTSAA	6 cut(s)	44, 182, 190, 269, 413, 923
AjnI	CCWGG	3 cut(s)	493, 639, 822
AluBI	AGCT	8 cut(s)	257, 304, 313, 546, 556, 616, 683, 841
AluI	AGCT	8 cut(s)	257, 304, 313, 546, 556, 616, 683, 841
Alw21I	GWGCWC	4 cut(s)	31, 51, 483, 618
Alw26I	GTCTC	3 cut(s)	383, 458, 715
AlwI	GGATC	2 cut(s)	223, 754
AoxI	GGCC	5 cut(s)	72, 251, 499, 785, 856
ApeKI	GCWGC	5 cut(s)	556, 559, 631, 694, 985
ApoI	RAATTY	3 cut(s)	53, 443, 887
AspLEI	GCGC	1 cut(s)	537
AspS9I	GGNCC	3 cut(s)	72, 798, 857
AsuHPI	GGTGA	2 cut(s)	610, 838
AvaII	GGWCC	1 cut(s)	798
BanII	GRGCYC	1 cut(s)	618
BbsI	GAAGAC	1 cut(s)	514
Bbv12I	GWGCWC	4 cut(s)	31, 51, 483, 618
BbvI	GCAGC	5 cut(s)	543, 571, 643, 681, 997
BccI	CCATC	3 cut(s)	355, 416, 510
BceAI	ACGGC	1 cut(s)	707
BciT130I	CCWGG	3 cut(s)	495, 641, 824
BcoDI	GTCTC	3 cut(s)	383, 458, 715
BfaI	CTAG	4 cut(s)	249, 305, 708, 1093
BfmI	CTRYAG	2 cut(s)	557, 983
BfoI	RGCGCY	1 cut(s)	538
BfuAI	ACCTGC	2 cut(s)	629, 1042
BisI	GCNGC	7 cut(s)	488, 557, 560, 632, 695, 759, 986
BlsI	GCNGC	7 cut(s)	489, 558, 561, 633, 696, 760, 987
Bme1390I	CCNGG	3 cut(s)	495, 641, 824
Bme18I	GGWCC	1 cut(s)	798
BmgT120I	GGNCC	3 cut(s)	72, 798, 857
BmiI	GGNNCC	2 cut(s)	73, 638
BmrFI	CCNGG	3 cut(s)	495, 641, 824
BmsI	GCATC	3 cut(s)	373, 499, 741
BpiI	GAAGAC	1 cut(s)	514
Bsa29I	ATCGAT	1 cut(s)	749
BsaI	GGTCTC	1 cut(s)	383
BsaJI	CCNNGG	2 cut(s)	214, 640
Bsc4I	CCNNNNNNNGG	1 cut(s)	446
Bse118I	RCCGGY	3 cut(s)	483, 537, 589
Bse1I	ACTGG	1 cut(s)	160
BseBI	CCWGG	3 cut(s)	495, 641, 824
BseCI	ATCGAT	1 cut(s)	749
BseDI	CCNNGG	2 cut(s)	214, 640
BseGI	GGATG	4 cut(s)	347, 490, 948, 1006
BseLI	CCNNNNNNNGG	1 cut(s)	446
BseNI	ACTGG	1 cut(s)	160
BseRI	GAGGAG	3 cut(s)	324, 793, 796
BseXI	GCAGC	5 cut(s)	543, 571, 643, 681, 997
Bsh1236I	CGCG	1 cut(s)	608
Bsh1285I	CGRYCG	3 cut(s)	282, 542, 612
BshFI	GGCC	5 cut(s)	74, 253, 501, 787, 858
BshVI	ATCGAT	1 cut(s)	749
BsiEI	CGRYCG	3 cut(s)	282, 542, 612
BsiHKAI	GWGCWC	4 cut(s)	31, 51, 483, 618
BsiSI	CCGG	5 cut(s)	484, 538, 590, 663, 731
BslI	CCNNNNNNNGG	1 cut(s)	446
BsmAI	GTCTC	3 cut(s)	383, 458, 715
BsmBI	CGTCTC	1 cut(s)	715
BsnI	GGCC	5 cut(s)	74, 253, 501, 787, 858
Bso31I	GGTCTC	1 cut(s)	383
Bsp1286I	GDGCHC	4 cut(s)	31, 51, 483, 618
Bsp143I	GATC	5 cut(s)	85, 228, 279, 673, 746
BspACI	CCGC	8 cut(s)	487, 585, 598, 608, 634, 759, 1025, 1082
BspANI	GGCC	5 cut(s)	74, 253, 501, 787, 858
BspDI	ATCGAT	1 cut(s)	749
BspFNI	CGCG	1 cut(s)	608
BspLI	GGNNCC	2 cut(s)	73, 638
BspMAI	CTGCAG	2 cut(s)	561, 987
BspMI	ACCTGC	2 cut(s)	629, 1042
BspPI	GGATC	2 cut(s)	223, 754
BspTNI	GGTCTC	1 cut(s)	383
BsrFI	RCCGGY	3 cut(s)	483, 537, 589
BsrI	ACTGG	1 cut(s)	160
BssAI	RCCGGY	3 cut(s)	483, 537, 589
BssECI	CCNNGG	2 cut(s)	214, 640
BssMI	GATC	5 cut(s)	85, 228, 279, 673, 746
BssT1I	CCWWGG	1 cut(s)	214
Bst2UI	CCWGG	3 cut(s)	495, 641, 824
Bst4CI	ACNGT	2 cut(s)	343, 836
Bst6I	CTCTTC	1 cut(s)	177
BstAPI	GCANNNNNTGC	1 cut(s)	810
BstC8I	GCNNGC	7 cut(s)	255, 554, 728, 756, 806, 966, 1049
BstF5I	GGATG	4 cut(s)	347, 490, 948, 1006
BstFNI	CGCG	1 cut(s)	608
BstH2I	RGCGCY	1 cut(s)	538
BstHHI	GCGC	1 cut(s)	537
BstKTI	GATC	5 cut(s)	88, 231, 282, 676, 749
BstMAI	GTCTC	3 cut(s)	383, 458, 715
BstMBI	GATC	5 cut(s)	85, 228, 279, 673, 746
BstMCI	CGRYCG	3 cut(s)	282, 542, 612
BstMWI	GCNNNNNNNGC	4 cut(s)	310, 487, 543, 810
BstNI	CCWGG	3 cut(s)	495, 641, 824
BstNSI	RCATGY	2 cut(s)	808, 968
BstSCI	CCNGG	3 cut(s)	493, 639, 822
BstSFI	CTRYAG	2 cut(s)	557, 983
BstUI	CGCG	1 cut(s)	608
BstV1I	GCAGC	5 cut(s)	543, 571, 643, 681, 997
BstV2I	GAAGAC	1 cut(s)	514
BstX2I	RGATCY	1 cut(s)	228
BstXI	CCANNNNNNTGG	1 cut(s)	400
BstYI	RGATCY	1 cut(s)	228
Bsu15I	ATCGAT	1 cut(s)	749
BsuRI	GGCC	5 cut(s)	74, 253, 501, 787, 858
BsuTUI	ATCGAT	1 cut(s)	749
BtsCI	GGATG	4 cut(s)	347, 490, 948, 1006
BtsI	GCAGTG	1 cut(s)	815
BtsIMutI	CAGTG	3 cut(s)	267, 815, 841
BveI	ACCTGC	2 cut(s)	629, 1042
Cac8I	GCNNGC	7 cut(s)	255, 554, 728, 756, 806, 966, 1049
CfoI	GCGC	1 cut(s)	537
Cfr10I	RCCGGY	3 cut(s)	483, 537, 589
Cfr13I	GGNCC	3 cut(s)	72, 798, 857
ClaI	ATCGAT	1 cut(s)	749
CseI	GACGC	2 cut(s)	614, 732
Csp6I	GTAC	2 cut(s)	159, 344
CviAII	CATG	4 cut(s)	394, 805, 929, 965
CviQI	GTAC	2 cut(s)	159, 344
DpnI	GATC	5 cut(s)	87, 230, 281, 675, 748
DpnII	GATC	5 cut(s)	85, 228, 279, 673, 746
DrdI	GACNNNNNNGTC	1 cut(s)	1010
DseDI	GACNNNNNNGTC	1 cut(s)	1010
Eam1104I	CTCTTC	1 cut(s)	177
EarI	CTCTTC	1 cut(s)	177
EciI	GGCGGA	1 cut(s)	1071
Ecl136II	GAGCTC	1 cut(s)	616
Eco130I	CCWWGG	1 cut(s)	214
Eco24I	GRGCYC	1 cut(s)	618
Eco31I	GGTCTC	1 cut(s)	383
Eco47I	GGWCC	1 cut(s)	798
Eco53kI	GAGCTC	1 cut(s)	616
Eco57I	CTGAAG	2 cut(s)	243, 381
EcoICRI	GAGCTC	1 cut(s)	616
EcoO109I	RGGNCCY	3 cut(s)	72, 798, 857
EcoRI	GAATTC	2 cut(s)	53, 887
EcoRII	CCWGG	3 cut(s)	493, 639, 822
EcoT14I	CCWWGG	1 cut(s)	214
EcoT38I	GRGCYC	1 cut(s)	618
ErhI	CCWWGG	1 cut(s)	214
Esp3I	CGTCTC	1 cut(s)	715
FaeI	CATG	4 cut(s)	397, 808, 932, 968
FatI	CATG	4 cut(s)	393, 804, 928, 964
FauI	CCCGC	1 cut(s)	592
FblI	GTMKAC	2 cut(s)	202, 580
Fnu4HI	GCNGC	7 cut(s)	488, 557, 560, 632, 695, 759, 986
FokI	GGATG	4 cut(s)	334, 477, 935, 1013
FriOI	GRGCYC	1 cut(s)	618
Fsp4HI	GCNGC	7 cut(s)	488, 557, 560, 632, 695, 759, 986
FspBI	CTAG	4 cut(s)	249, 305, 708, 1093
GlaI	GCGC	1 cut(s)	536
GluI	GCNGC	7 cut(s)	488, 557, 560, 632, 695, 759, 986
HaeII	RGCGCY	1 cut(s)	538
HaeIII	GGCC	5 cut(s)	74, 253, 501, 787, 858
HapII	CCGG	5 cut(s)	484, 538, 590, 663, 731
HgaI	GACGC	2 cut(s)	614, 732
HhaI	GCGC	1 cut(s)	537
Hin1II	CATG	4 cut(s)	397, 808, 932, 968
Hin6I	GCGC	1 cut(s)	535
HinP1I	GCGC	1 cut(s)	535
HincII	GTYRAC	1 cut(s)	581
HindII	GTYRAC	1 cut(s)	581
HinfI	GANTC	4 cut(s)	331, 932, 1004, 1028
HpaII	CCGG	5 cut(s)	484, 538, 590, 663, 731
HphI	GGTGA	2 cut(s)	610, 838
Hpy166II	GTNNAC	2 cut(s)	203, 581
Hpy188I	TCNGA	3 cut(s)	26, 118, 941
Hpy188III	TCNNGA	1 cut(s)	328
Hpy8I	GTNNAC	2 cut(s)	203, 581
Hpy99I	CGWCG	1 cut(s)	693
HpyAV	CCTTC	2 cut(s)	789, 929
HpyCH4III	ACNGT	2 cut(s)	343, 836
HpyCH4IV	ACGT	2 cut(s)	399, 511
HpyCH4V	TGCA	7 cut(s)	320, 386, 559, 631, 804, 808, 985
HpyF10VI	GCNNNNNNNGC	4 cut(s)	310, 487, 543, 810
HpySE526I	ACGT	2 cut(s)	399, 511
Hsp92II	CATG	4 cut(s)	397, 808, 932, 968
HspAI	GCGC	1 cut(s)	535
Kzo9I	GATC	5 cut(s)	85, 228, 279, 673, 746
LmnI	GCTCC	2 cut(s)	26, 680
Lsp1109I	GCAGC	5 cut(s)	543, 571, 643, 681, 997
LweI	GCATC	3 cut(s)	373, 499, 741
MaeI	CTAG	4 cut(s)	249, 305, 708, 1093
MaeII	ACGT	2 cut(s)	399, 511
MaeIII	GTNAC	2 cut(s)	106, 826
MalI	GATC	5 cut(s)	87, 230, 281, 675, 748
MboI	GATC	5 cut(s)	85, 228, 279, 673, 746
MboII	GAAGA	3 cut(s)	16, 194, 519
MflI	RGATCY	1 cut(s)	228
MhlI	GDGCHC	4 cut(s)	31, 51, 483, 618
MluCI	AATT	5 cut(s)	37, 53, 408, 443, 887
MlyI	GAGTC	4 cut(s)	325, 941, 998, 1037
MmeI	TCCRAC	5 cut(s)	4, 362, 582, 649, 1056
MseI	TTAA	2 cut(s)	243, 852
MslI	CAYNNNNRTG	1 cut(s)	398
MspA1I	CMGCKG	1 cut(s)	634
MspI	CCGG	5 cut(s)	484, 538, 590, 663, 731
MspR9I	CCNGG	3 cut(s)	495, 641, 824
MvaI	CCWGG	3 cut(s)	495, 641, 824
MvnI	CGCG	1 cut(s)	608
MwoI	GCNNNNNNNGC	4 cut(s)	310, 487, 543, 810
NdeII	GATC	5 cut(s)	85, 228, 279, 673, 746
NlaIII	CATG	4 cut(s)	397, 808, 932, 968
NlaIV	GGNNCC	2 cut(s)	73, 638
NmuCI	GTSAC	1 cut(s)	826
NspI	RCATGY	2 cut(s)	808, 968
PaeI	GCATGC	2 cut(s)	808, 968
PaqCI	CACCTGC	1 cut(s)	629
PflFI	GACNNNGTC	1 cut(s)	608
PfoI	TCCNGGA	1 cut(s)	493
PkrI	GCNGC	7 cut(s)	489, 558, 561, 633, 696, 760, 987
Ple19I	CGATCG	1 cut(s)	282
PleI	GAGTC	4 cut(s)	325, 940, 998, 1036
PpsI	GAGTC	4 cut(s)	325, 940, 998, 1036
PpuMI	RGGWCCY	1 cut(s)	798
Psp124BI	GAGCTC	1 cut(s)	618
Psp5II	RGGWCCY	1 cut(s)	798
Psp6I	CCWGG	3 cut(s)	493, 639, 822
PspGI	CCWGG	3 cut(s)	493, 639, 822
PspN4I	GGNNCC	2 cut(s)	73, 638
PspPI	GGNCC	3 cut(s)	72, 798, 857
PspPPI	RGGWCCY	1 cut(s)	798
PstI	CTGCAG	2 cut(s)	561, 987
PsuI	RGATCY	1 cut(s)	228
PsyI	GACNNNGTC	1 cut(s)	608
PvuI	CGATCG	1 cut(s)	282
RsaI	GTAC	2 cut(s)	160, 345
RsaNI	GTAC	2 cut(s)	159, 344
RseI	CAYNNNNRTG	1 cut(s)	398
SacI	GAGCTC	1 cut(s)	618
SalI	GTCGAC	1 cut(s)	579
SaqAI	TTAA	2 cut(s)	243, 852
SatI	GCNGC	7 cut(s)	488, 557, 560, 632, 695, 759, 986
Sau3AI	GATC	5 cut(s)	85, 228, 279, 673, 746
Sau96I	GGNCC	3 cut(s)	72, 798, 857
SchI	GAGTC	4 cut(s)	325, 941, 998, 1037
ScrFI	CCNGG	3 cut(s)	495, 641, 824
SduI	GDGCHC	4 cut(s)	31, 51, 483, 618
SfaNI	GCATC	3 cut(s)	373, 499, 741
SfcI	CTRYAG	2 cut(s)	557, 983
SgrAI	CRCCGGYG	2 cut(s)	483, 589
SinI	GGWCC	1 cut(s)	798
SmiMI	CAYNNNNRTG	1 cut(s)	398
SphI	GCATGC	2 cut(s)	808, 968
Sse9I	AATT	5 cut(s)	37, 53, 408, 443, 887
SsiI	CCGC	8 cut(s)	487, 585, 598, 608, 634, 759, 1025, 1082
SspI	AATATT	1 cut(s)	238
SspMI	CTAG	4 cut(s)	249, 305, 708, 1093
SstI	GAGCTC	1 cut(s)	618
StyD4I	CCNGG	3 cut(s)	493, 639, 822
StyI	CCWWGG	1 cut(s)	214
TaaI	ACNGT	2 cut(s)	343, 836
TaiI	ACGT	2 cut(s)	402, 514
TaqI	TCGA	9 cut(s)	51, 505, 542, 580, 612, 653, 688, 749, 885
TasI	AATT	5 cut(s)	37, 53, 408, 443, 887
TauI	GCSGC	2 cut(s)	490, 761
Tru1I	TTAA	2 cut(s)	243, 852
Tru9I	TTAA	2 cut(s)	243, 852
TscAI	CASTG	3 cut(s)	267, 815, 841
TseFI	GTSAC	1 cut(s)	826
TseI	GCWGC	5 cut(s)	556, 559, 631, 694, 985
Tsp45I	GTSAC	1 cut(s)	826
TspDTI	ATGAA	3 cut(s)	17, 410, 833
TspRI	CASTG	3 cut(s)	267, 815, 841
Tth111I	GACNNNGTC	1 cut(s)	608
VpaK11BI	GGWCC	1 cut(s)	798
XapI	RAATTY	3 cut(s)	53, 443, 887
XceI	RCATGY	2 cut(s)	808, 968
XmiI	GTMKAC	2 cut(s)	202, 580
XspI	CTAG	4 cut(s)	249, 305, 708, 1093

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.