Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr4

Orthogroup ID

OG0003823

Physical Location & Seq

Genomic Coordinates Forward (+)

52723872 .. 52731584

Gene Structure 7713 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000019491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1077 bp

ATGATACTCGCAGTGTTATTCGCCAACTCTGAAGGGAACATCCTAGTTGAACGTTTCAATGGAGTTCCTGCTGAGGAACGGCTGCATTGGCGATCTTTCTTAGTCAAACTAGGAGCTGATAATCTTAGGGGCGTGAAGAATGAAGAACTCCTTGTTGCCTGCCACAAGTCAGTTTACATTGTTTACACTGTGCTTGGGGATGTCAGCATCTATGTTGTGGGGAAGGACGAATATGATGAACTAGCCTTGTCAGAGGTGATCTTCGTTATAACATCCGCTGTGAAGGACGTATGTGGGAAGCCTCCCACTGAGCGCCTTTTCCTGGACAAAAACAAGGCGGTTCTTGTGGATGATCTATGCAGAATTTGCTACAAGTTGATCAGAGACACCAACAACAAAGGAATGAGCAGATCACAAGGGCCTTCAGCCCTTAAACGGAAGCGCTTGGATTCGCAATCTGGATCTTTGACAGAGCATGAAAGCAAACTCTATGATGCCATCCGCAGCAAGACAGATATGGGTATGTCTGTACAAGACTTGAGGCGAGAAACAGGACTCCAGAACAATTTATTTACCAAGGCCATCAAAACACTTCAAGCCAAACAACTGATAAAAGAGGTTAAAAATTTTGAAAACAAGACGAGGAAACATTACATGGCTACAGAGTTTGAGCCCTCGAAGGAGATAACTGGTGGTACTTGGTATGATAATGGACGGTTAGATACCGAGTTTATAAAGGTTGTAAAAAGAGAGTTGGTGAAGGTCATTGATGATCAGGAGAATGCTACCTTGGAGAAAATTTCTCACACAATTAGAGTGAAGAACTTTCTAACTGTTAACTTATCCGATCAGGAAGTGAAGCAGATTCTGGATGCTTTGGTTTTGGACAATGAGCTCCTGAAGGTGGTGAGCACTGGGAAAGATTGTTATAAGTGCTGCAAGAGAAGAGGGGAACCAAACTTAGCGGCCATGGCTTCCATTCCATGCGGAGTCTGTCCGCGTATTAATCAATGTACCCCAGATGGCATTATTTCCCCAACCACCTGTGAATACTATAAAAAATGGTTGGAGTTCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002682 GO:0002684 GO:0003674 GO:0003676 GO:0003677 GO:0003690 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0008150 GO:0030880 GO:0031347 GO:0031349 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0045088 GO:0045089 GO:0048518 GO:0048583 GO:0048584 GO:0050776 GO:0050778 GO:0050789 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0080134 GO:0097159 GO:1901363 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rpc34

Protein Analysis

359

Amino Acids

40.58

Weight (kDa)

8.5

Isoelectric Point (pI)

44.5

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc34	PF05158	152 - 268	3.2e-29	RNA polymerase Rpc34 subunit
RNA_pol_Rpc34	PF05158	261 - 357	8.2e-10	RNA polymerase Rpc34 subunit

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0003823)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G23710
fragaria_vesca	FvH4_6g29950 FvH4_6g29950 FvH4_6g41460
malus_domestica	MD08G1239800.v1.1 MD15G1431400.v1.1
prunus_persica	Prupe.1G576300_v2.0.a1 Prupe.5G067300_v2.0.a1
pyrus_communis	pycom08g20810 pycom15g38120
rosa_chinensis	RchiOBHm_Chr2g0135951 RchiOBHm_Chr6g0271261 RchiOBHm_Chr6g0271271
rosa_laevigata	RLG00000019491 RLG00000020962
rosa_multiflora	Rmu_sc0004866.1_g000010 Rmu_ssc0000343.1_g000019
rosa_roxburghii	Rroxscaffold_2G00108750 Rroxscaffold_7G00200610
rosa_rugosa	Rorug02G0327000 Rorug02G0457600 Rorug06G0035800 Rorug06G0036000
rosa_samantha	Rh2BG385300 Rh2CG364400 Rh2DG401600 Rh6AG179300 Rh6BG182300 Rh6CG179200 Rh6DG170900
rosa_wichuraiana	Rw2G030860 Rw2G031070 Rw2G043270 Rw6G015420

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	3 cut(s)	269, 734, 930
AccII	CGCG	1 cut(s)	1000
AciI	CCGC	6 cut(s)	276, 338, 502, 965, 987, 998
AclI	AACGTT	1 cut(s)	52
AclWI	GGATC	1 cut(s)	469
AcoI	YGGCCR	1 cut(s)	966
AcsI	RAATTY	3 cut(s)	363, 625, 798
AcuI	CTGAAG	3 cut(s)	51, 408, 920
AfaI	GTAC	3 cut(s)	531, 697, 1015
AfeI	AGCGCT	1 cut(s)	443
AfiI	CCNNNNNNNGG	3 cut(s)	322, 435, 904
AgsI	TTSAA	4 cut(s)	50, 58, 596, 632
AjnI	CCWGG	1 cut(s)	321
AjuI	GAANNNNNNNTTGG	2 cut(s)	773, 805
AluBI	AGCT	2 cut(s)	116, 895
AluI	AGCT	2 cut(s)	116, 895
Alw21I	GWGCWC	2 cut(s)	897, 914
Alw26I	GTCTC	1 cut(s)	378
AlwI	GGATC	1 cut(s)	469
AlwNI	CAGNNNCTG	1 cut(s)	868
Aor51HI	AGCGCT	1 cut(s)	443
AoxI	GGCC	3 cut(s)	419, 579, 966
ApeKI	GCWGC	3 cut(s)	82, 504, 936
ApoI	RAATTY	3 cut(s)	363, 625, 798
AseI	ATTAAT	1 cut(s)	1005
AspLEI	GCGC	2 cut(s)	315, 444
AspS9I	GGNCC	1 cut(s)	419
AsuHPI	GGTGA	3 cut(s)	268, 769, 919
BanII	GRGCYC	2 cut(s)	675, 897
Bbv12I	GWGCWC	2 cut(s)	897, 914
BbvCI	CCTCAGC	1 cut(s)	72
BbvI	GCAGC	3 cut(s)	69, 516, 923
BccI	CCATC	3 cut(s)	506, 590, 1016
BceAI	ACGGC	1 cut(s)	95
BciT130I	CCWGG	1 cut(s)	323
BclI	TGATCA	2 cut(s)	378, 772
BcoDI	GTCTC	1 cut(s)	378
BfaI	CTAG	3 cut(s)	44, 110, 242
BfmI	CTRYAG	1 cut(s)	660
BfoI	RGCGCY	2 cut(s)	316, 445
BisI	GCNGC	4 cut(s)	83, 505, 937, 966
BlsI	GCNGC	4 cut(s)	84, 506, 938, 967
Bme1390I	CCNGG	1 cut(s)	323
BmgT120I	GGNCC	1 cut(s)	419
BmiI	GGNNCC	1 cut(s)	954
BmrFI	CCNGG	1 cut(s)	323
BmrI	ACTGGG	1 cut(s)	924
BmsI	GCATC	3 cut(s)	216, 484, 862
BmuI	ACTGGG	1 cut(s)	924
BpmI	CTGGAG	1 cut(s)	542
Bpu10I	CCTNAGC	1 cut(s)	72
BpuEI	CTTGAG	1 cut(s)	559
BsaJI	CCNNGG	3 cut(s)	576, 789, 969
Bsc4I	CCNNNNNNNGG	3 cut(s)	322, 435, 904
Bse1I	ACTGG	2 cut(s)	694, 919
BseBI	CCWGG	1 cut(s)	323
BseDI	CCNNGG	3 cut(s)	576, 789, 969
BseGI	GGATG	6 cut(s)	39, 205, 272, 355, 498, 877
BseLI	CCNNNNNNNGG	3 cut(s)	322, 435, 904
BseMII	CTCAG	2 cut(s)	63, 300
BseNI	ACTGG	2 cut(s)	694, 919
BseXI	GCAGC	3 cut(s)	69, 516, 923
Bsh1236I	CGCG	1 cut(s)	1000
BshFI	GGCC	3 cut(s)	421, 581, 968
BsiHKAI	GWGCWC	2 cut(s)	897, 914
BslI	CCNNNNNNNGG	3 cut(s)	322, 435, 904
BsmAI	GTCTC	1 cut(s)	378
BsmI	GAATGC	1 cut(s)	787
BsnI	GGCC	3 cut(s)	421, 581, 968
Bsp1286I	GDGCHC	3 cut(s)	675, 897, 914
Bsp1407I	TGTACA	1 cut(s)	529
Bsp143I	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
Bsp19I	CCATGG	1 cut(s)	969
BspACI	CCGC	6 cut(s)	276, 338, 502, 965, 987, 998
BspANI	GGCC	3 cut(s)	421, 581, 968
BspCNI	CTCAG	2 cut(s)	64, 301
BspFNI	CGCG	1 cut(s)	1000
BspLI	GGNNCC	1 cut(s)	954
BspPI	GGATC	1 cut(s)	469
BsrGI	TGTACA	1 cut(s)	529
BsrI	ACTGG	2 cut(s)	694, 919
BssECI	CCNNGG	3 cut(s)	576, 789, 969
BssMI	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
BssT1I	CCWWGG	3 cut(s)	576, 789, 969
Bst2UI	CCWGG	1 cut(s)	323
Bst4CI	ACNGT	3 cut(s)	190, 717, 835
Bst6I	CTCTTC	1 cut(s)	940
BstAPI	GCANNNNNTGC	1 cut(s)	366
BstAUI	TGTACA	1 cut(s)	529
BstC8I	GCNNGC	1 cut(s)	160
BstDEI	CTNAG	5 cut(s)	72, 100, 125, 309, 961
BstDSI	CCRYGG	1 cut(s)	969
BstF5I	GGATG	6 cut(s)	39, 205, 272, 355, 498, 877
BstFNI	CGCG	1 cut(s)	1000
BstH2I	RGCGCY	2 cut(s)	316, 445
BstHHI	GCGC	2 cut(s)	315, 444
BstKTI	GATC	8 cut(s)	95, 261, 355, 381, 413, 464, 775, 850
BstMAI	GTCTC	1 cut(s)	378
BstMBI	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
BstMWI	GCNNNNNNNGC	3 cut(s)	88, 366, 971
BstNI	CCWGG	1 cut(s)	323
BstSCI	CCNGG	1 cut(s)	321
BstSFI	CTRYAG	1 cut(s)	660
BstUI	CGCG	1 cut(s)	1000
BstV1I	GCAGC	3 cut(s)	69, 516, 923
BstX2I	RGATCY	1 cut(s)	461
BstYI	RGATCY	1 cut(s)	461
BsuRI	GGCC	3 cut(s)	421, 581, 968
BtgI	CCRYGG	1 cut(s)	969
BtsCI	GGATG	6 cut(s)	39, 205, 272, 355, 498, 877
BtsI	GCAGTG	1 cut(s)	18
BtsIMutI	CAGTG	4 cut(s)	18, 186, 306, 912
Cac8I	GCNNGC	1 cut(s)	160
CaiI	CAGNNNCTG	1 cut(s)	868
CfoI	GCGC	2 cut(s)	315, 444
Cfr13I	GGNCC	1 cut(s)	419
Csp6I	GTAC	3 cut(s)	530, 696, 1014
CviAII	CATG	4 cut(s)	476, 655, 970, 984
CviQI	GTAC	3 cut(s)	530, 696, 1014
DdeI	CTNAG	5 cut(s)	72, 100, 125, 309, 961
DpnI	GATC	8 cut(s)	94, 260, 354, 380, 412, 463, 774, 849
DpnII	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
EaeI	YGGCCR	1 cut(s)	966
Eam1104I	CTCTTC	1 cut(s)	940
EarI	CTCTTC	1 cut(s)	940
Ecl136II	GAGCTC	1 cut(s)	895
Eco130I	CCWWGG	3 cut(s)	576, 789, 969
Eco24I	GRGCYC	2 cut(s)	675, 897
Eco47III	AGCGCT	1 cut(s)	443
Eco53kI	GAGCTC	1 cut(s)	895
Eco57I	CTGAAG	3 cut(s)	51, 408, 920
EcoICRI	GAGCTC	1 cut(s)	895
EcoO109I	RGGNCCY	1 cut(s)	419
EcoRII	CCWGG	1 cut(s)	321
EcoT14I	CCWWGG	3 cut(s)	576, 789, 969
EcoT38I	GRGCYC	2 cut(s)	675, 897
ErhI	CCWWGG	3 cut(s)	576, 789, 969
FaeI	CATG	4 cut(s)	479, 658, 973, 987
FalI	AAGNNNNNCTT	2 cut(s)	135, 167
FatI	CATG	4 cut(s)	475, 654, 969, 983
FbaI	TGATCA	2 cut(s)	378, 772
Fnu4HI	GCNGC	4 cut(s)	83, 505, 937, 966
FokI	GGATG	6 cut(s)	26, 212, 259, 362, 485, 884
FriOI	GRGCYC	2 cut(s)	675, 897
Fsp4HI	GCNGC	4 cut(s)	83, 505, 937, 966
FspBI	CTAG	3 cut(s)	44, 110, 242
GlaI	GCGC	2 cut(s)	314, 443
GluI	GCNGC	4 cut(s)	83, 505, 937, 966
GsuI	CTGGAG	1 cut(s)	542
HaeII	RGCGCY	2 cut(s)	316, 445
HaeIII	GGCC	3 cut(s)	421, 581, 968
HhaI	GCGC	2 cut(s)	315, 444
Hin1II	CATG	4 cut(s)	479, 658, 973, 987
Hin6I	GCGC	2 cut(s)	313, 442
HinP1I	GCGC	2 cut(s)	313, 442
HincII	GTYRAC	1 cut(s)	838
HindII	GTYRAC	1 cut(s)	838
HinfI	GANTC	4 cut(s)	449, 555, 865, 990
HpaI	GTTAAC	1 cut(s)	838
HphI	GGTGA	3 cut(s)	268, 769, 919
Hpy166II	GTNNAC	3 cut(s)	175, 184, 838
Hpy188I	TCNGA	5 cut(s)	31, 253, 383, 847, 1076
Hpy188III	TCNNGA	6 cut(s)	459, 559, 776, 851, 869, 898
Hpy8I	GTNNAC	3 cut(s)	175, 184, 838
HpyAV	CCTTC	7 cut(s)	26, 217, 277, 432, 673, 754, 895
HpyCH4III	ACNGT	3 cut(s)	190, 717, 835
HpyCH4IV	ACGT	2 cut(s)	52, 288
HpyCH4V	TGCA	3 cut(s)	85, 360, 939
HpyF10VI	GCNNNNNNNGC	3 cut(s)	88, 366, 971
HpyF3I	CTNAG	5 cut(s)	72, 100, 125, 309, 961
HpySE526I	ACGT	2 cut(s)	52, 288
Hsp92II	CATG	4 cut(s)	479, 658, 973, 987
HspAI	GCGC	2 cut(s)	313, 442
Ksp22I	TGATCA	2 cut(s)	378, 772
KspAI	GTTAAC	1 cut(s)	838
Kzo9I	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
LmnI	GCTCC	2 cut(s)	113, 900
Lsp1109I	GCAGC	3 cut(s)	69, 516, 923
LweI	GCATC	3 cut(s)	216, 484, 862
MaeI	CTAG	3 cut(s)	44, 110, 242
MaeII	ACGT	2 cut(s)	52, 288
MalI	GATC	8 cut(s)	94, 260, 354, 380, 412, 463, 774, 849
MboI	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
MboII	GAAGA	5 cut(s)	148, 155, 253, 832, 957
MflI	RGATCY	1 cut(s)	461
MhlI	GDGCHC	3 cut(s)	675, 897, 914
MluCI	AATT	5 cut(s)	363, 565, 625, 798, 810
MlyI	GAGTC	2 cut(s)	549, 999
MmeI	TCCRAC	1 cut(s)	1047
MnlI	CCTC	8 cut(s)	67, 247, 312, 534, 610, 636, 685, 941
MseI	TTAA	4 cut(s)	432, 621, 837, 1005
MspA1I	CMGCKG	1 cut(s)	278
MspR9I	CCNGG	1 cut(s)	323
Mva1269I	GAATGC	1 cut(s)	787
MvaI	CCWGG	1 cut(s)	323
MvnI	CGCG	1 cut(s)	1000
MwoI	GCNNNNNNNGC	3 cut(s)	88, 366, 971
NcoI	CCATGG	1 cut(s)	969
NdeII	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
NlaIII	CATG	4 cut(s)	479, 658, 973, 987
NlaIV	GGNNCC	1 cut(s)	954
PctI	GAATGC	1 cut(s)	787
PfeI	GAWTC	2 cut(s)	449, 865
PfoI	TCCNGGA	1 cut(s)	321
PkrI	GCNGC	4 cut(s)	84, 506, 938, 967
PleI	GAGTC	2 cut(s)	549, 998
PpsI	GAGTC	2 cut(s)	549, 998
PshBI	ATTAAT	1 cut(s)	1005
PsiI	TTATAA	3 cut(s)	269, 734, 930
Psp124BI	GAGCTC	1 cut(s)	897
Psp1406I	AACGTT	1 cut(s)	52
Psp6I	CCWGG	1 cut(s)	321
PspGI	CCWGG	1 cut(s)	321
PspN4I	GGNNCC	1 cut(s)	954
PspPI	GGNCC	1 cut(s)	419
PstNI	CAGNNNCTG	1 cut(s)	868
PsuI	RGATCY	1 cut(s)	461
RsaI	GTAC	3 cut(s)	531, 697, 1015
RsaNI	GTAC	3 cut(s)	530, 696, 1014
SacI	GAGCTC	1 cut(s)	897
SaqAI	TTAA	4 cut(s)	432, 621, 837, 1005
SatI	GCNGC	4 cut(s)	83, 505, 937, 966
Sau3AI	GATC	8 cut(s)	92, 258, 352, 378, 410, 461, 772, 847
Sau96I	GGNCC	1 cut(s)	419
SchI	GAGTC	2 cut(s)	549, 999
ScrFI	CCNGG	1 cut(s)	323
SduI	GDGCHC	3 cut(s)	675, 897, 914
SfaNI	GCATC	3 cut(s)	216, 484, 862
SfcI	CTRYAG	1 cut(s)	660
SmlI	CTYRAG	1 cut(s)	538
SmoI	CTYRAG	1 cut(s)	538
Sse9I	AATT	5 cut(s)	363, 565, 625, 798, 810
SsiI	CCGC	6 cut(s)	276, 338, 502, 965, 987, 998
SspMI	CTAG	3 cut(s)	44, 110, 242
SstI	GAGCTC	1 cut(s)	897
StyD4I	CCNGG	1 cut(s)	321
StyI	CCWWGG	3 cut(s)	576, 789, 969
TaaI	ACNGT	3 cut(s)	190, 717, 835
TaiI	ACGT	2 cut(s)	55, 291
TaqI	TCGA	1 cut(s)	677
TasI	AATT	5 cut(s)	363, 565, 625, 798, 810
TatI	WGTACW	1 cut(s)	529
TauI	GCSGC	1 cut(s)	968
TfiI	GAWTC	2 cut(s)	449, 865
Tru1I	TTAA	4 cut(s)	432, 621, 837, 1005
Tru9I	TTAA	4 cut(s)	432, 621, 837, 1005
TscAI	CASTG	4 cut(s)	18, 193, 313, 919
TseI	GCWGC	3 cut(s)	82, 504, 936
TspDTI	ATGAA	3 cut(s)	156, 252, 492
TspGWI	ACGGA	1 cut(s)	451
TspRI	CASTG	4 cut(s)	18, 193, 313, 919
VspI	ATTAAT	1 cut(s)	1005
XapI	RAATTY	3 cut(s)	363, 625, 798
XspI	CTAG	3 cut(s)	44, 110, 242

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