Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0012428

Physical Location & Seq

Genomic Coordinates Reverse (-)

31088896 .. 31092380

Gene Structure 3485 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000013404

Sequence Viewer

CDS Protein Promoter (2k)

Length: 429 bp

ATGGCTGATGATGATTACAATGAGATGGATATTGGATATGAGGATGAGCCGGTGGAGCCAGAGATTGAAGAAGGGGCAGAGGAGGAGGATGTGGATAACAATGATGATCTTGCAGGAGATGCCATTGAAACTGATGACAAGGAAGAACAAGTACCAGTGGAACGGCCTCGCAAAACATCAAAATTTATGACCAAATATGAACGGGCTAGAATCTTGGGTACCCGTGCTGTACAAATTAGCATGAATGCCCCTGTGATGGTTGAGTTGGAGGGTGAGACTGACCCGCTTGAGATTGCTATGAAGGAGCTTCGTGAGCGGAAGATACCCTTTACCATCCGCCGCTACCTGCCTGATGGAAGTTATGAAGATTGGGGAGTTGATGAACTGATTGTGGAAGATTCCTGGAAGAGGCAGGTGGGAGGTAACTGA

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:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006360 GO:0006366 GO:0006383 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb6

Protein Analysis

143

Amino Acids

16.37

Weight (kDa)

4.14

Isoelectric Point (pI)

49.66

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb6	PF01192	59 - 110	6.4e-12	RNA polymerase Rpb6

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

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Orthologous Genes (Group: OG0012428)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G04630 AT5G51940
fragaria_vesca	FvH4_2g14180
malus_domestica	MD09G1242800.v1.1 MD12G1011200.v1.1 MD17G1234800.v1.1
prunus_persica	Prupe.3G134400_v2.0.a1 Prupe.7G013200_v2.0.a1
pyrus_communis	pycom09g16110 pycom12g00870 pycom17g23820
rosa_chinensis	RchiOBHm_Chr6g0276321
rosa_laevigata	RLG00000013404
rosa_multiflora	Rmu_sc0003665.1_g000006
rosa_roxburghii	Rroxscaffold_7G00192390
rosa_rugosa	Rorug06G0099900 Rorug06G0100000
rosa_samantha	Rh6DG207900
rosa_wichuraiana	Rw6G018430

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	403
Acc36I	ACCTGC	2 cut(s)	354, 403
Acc65I	GGTACC	1 cut(s)	218
AccB1I	GGYRCC	1 cut(s)	218
AccBSI	CCGCTC	1 cut(s)	316
AciI	CCGC	4 cut(s)	284, 316, 337, 340
AcsI	RAATTY	1 cut(s)	182
AfaI	GTAC	3 cut(s)	153, 220, 231
AfiI	CCNNNNNNNGG	2 cut(s)	256, 408
AgsI	TTSAA	2 cut(s)	68, 128
AjnI	CCWGG	1 cut(s)	401
AluBI	AGCT	1 cut(s)	307
AluI	AGCT	1 cut(s)	307
Alw26I	GTCTC	1 cut(s)	269
AoxI	GGCC	1 cut(s)	164
ApoI	RAATTY	1 cut(s)	182
Asp718I	GGTACC	1 cut(s)	218
AsuHPI	GGTGA	1 cut(s)	284
BanI	GGYRCC	1 cut(s)	218
BarI	GAAGNNNNNNTAC	2 cut(s)	135, 167
BccI	CCATC	4 cut(s)	19, 250, 341, 347
BceAI	ACGGC	1 cut(s)	179
BciT130I	CCWGG	1 cut(s)	403
BcoDI	GTCTC	1 cut(s)	269
BfaI	CTAG	1 cut(s)	207
BfuAI	ACCTGC	2 cut(s)	354, 403
BisI	GCNGC	1 cut(s)	340
BlsI	GCNGC	1 cut(s)	341
Bme1390I	CCNGG	1 cut(s)	403
BmiI	GGNNCC	2 cut(s)	57, 220
BmrFI	CCNGG	1 cut(s)	403
BmsI	GCATC	1 cut(s)	109
BpuEI	CTTGAG	1 cut(s)	308
Bsc4I	CCNNNNNNNGG	2 cut(s)	256, 408
Bse118I	RCCGGY	1 cut(s)	49
Bse1I	ACTGG	1 cut(s)	155
BseBI	CCWGG	1 cut(s)	403
BseGI	GGATG	3 cut(s)	49, 94, 333
BseLI	CCNNNNNNNGG	2 cut(s)	256, 408
BseNI	ACTGG	1 cut(s)	155
BseRI	GAGGAG	2 cut(s)	95, 98
BshFI	GGCC	1 cut(s)	166
BshNI	GGYRCC	1 cut(s)	218
BsiSI	CCGG	1 cut(s)	50
BslI	CCNNNNNNNGG	2 cut(s)	256, 408
BsmAI	GTCTC	1 cut(s)	269
BsmI	GAATGC	1 cut(s)	250
BsnI	GGCC	1 cut(s)	166
Bsp1407I	TGTACA	1 cut(s)	229
Bsp143I	GATC	1 cut(s)	106
BspACI	CCGC	4 cut(s)	284, 316, 337, 340
BspANI	GGCC	1 cut(s)	166
BspLI	GGNNCC	2 cut(s)	57, 220
BspMI	ACCTGC	2 cut(s)	354, 403
BspT107I	GGYRCC	1 cut(s)	218
BsrBI	CCGCTC	1 cut(s)	316
BsrFI	RCCGGY	1 cut(s)	49
BsrGI	TGTACA	1 cut(s)	229
BsrI	ACTGG	1 cut(s)	155
BssAI	RCCGGY	1 cut(s)	49
BssMI	GATC	1 cut(s)	106
Bst2UI	CCWGG	1 cut(s)	403
Bst6I	CTCTTC	1 cut(s)	401
BstAPI	GCANNNNNTGC	1 cut(s)	119
BstAUI	TGTACA	1 cut(s)	229
BstENI	CCTNNNNNAGG	1 cut(s)	406
BstF5I	GGATG	3 cut(s)	49, 94, 333
BstKTI	GATC	1 cut(s)	109
BstMAI	GTCTC	1 cut(s)	269
BstMBI	GATC	1 cut(s)	106
BstMWI	GCNNNNNNNGC	3 cut(s)	55, 119, 313
BstNI	CCWGG	1 cut(s)	403
BstSCI	CCNGG	1 cut(s)	401
BsuRI	GGCC	1 cut(s)	166
BtsCI	GGATG	3 cut(s)	49, 94, 333
BtsIMutI	CAGTG	1 cut(s)	162
BveI	ACCTGC	2 cut(s)	354, 403
Cfr10I	RCCGGY	1 cut(s)	49
Csp6I	GTAC	3 cut(s)	152, 219, 230
CviAII	CATG	1 cut(s)	241
CviJI	RGCY	6 cut(s)	5, 49, 58, 166, 206, 307
CviKI_1	RGCY	6 cut(s)	5, 49, 58, 166, 206, 307
CviQI	GTAC	3 cut(s)	152, 219, 230
DpnI	GATC	1 cut(s)	108
DpnII	GATC	1 cut(s)	106
Eam1104I	CTCTTC	1 cut(s)	401
EarI	CTCTTC	1 cut(s)	401
EciI	GGCGGA	1 cut(s)	326
EcoNI	CCTNNNNNAGG	1 cut(s)	406
EcoRII	CCWGG	1 cut(s)	401
FaeI	CATG	1 cut(s)	244
FaiI	YATR	6 cut(s)	39, 188, 198, 242, 299, 363
FalI	AAGNNNNNCTT	2 cut(s)	311, 343
FatI	CATG	1 cut(s)	240
FauI	CCCGC	1 cut(s)	291
Fnu4HI	GCNGC	1 cut(s)	340
FokI	GGATG	3 cut(s)	56, 101, 320
Fsp4HI	GCNGC	1 cut(s)	340
FspBI	CTAG	1 cut(s)	207
GluI	GCNGC	1 cut(s)	340
HaeIII	GGCC	1 cut(s)	166
HapII	CCGG	1 cut(s)	50
Hin1II	CATG	1 cut(s)	244
HinfI	GANTC	2 cut(s)	210, 398
HpaII	CCGG	1 cut(s)	50
HphI	GGTGA	1 cut(s)	284
Hpy188III	TCNNGA	1 cut(s)	311
HpyAV	CCTTC	2 cut(s)	65, 295
HpyCH4V	TGCA	1 cut(s)	113
HpyF10VI	GCNNNNNNNGC	3 cut(s)	55, 119, 313
Hsp92II	CATG	1 cut(s)	244
KpnI	GGTACC	1 cut(s)	222
Kzo9I	GATC	1 cut(s)	106
LmnI	GCTCC	2 cut(s)	55, 304
LweI	GCATC	1 cut(s)	109
MaeI	CTAG	1 cut(s)	207
MaeIII	GTNAC	1 cut(s)	422
MalI	GATC	1 cut(s)	108
MbiI	CCGCTC	1 cut(s)	316
MboI	GATC	1 cut(s)	106
MboII	GAAGA	6 cut(s)	80, 155, 331, 377, 407, 418
MluCI	AATT	2 cut(s)	182, 234
MmeI	TCCRAC	1 cut(s)	246
MnlI	CCTC	8 cut(s)	34, 73, 76, 79, 177, 262, 402, 413
MspI	CCGG	1 cut(s)	50
MspR9I	CCNGG	1 cut(s)	403
Mva1269I	GAATGC	1 cut(s)	250
MvaI	CCWGG	1 cut(s)	403
MwoI	GCNNNNNNNGC	3 cut(s)	55, 119, 313
NdeII	GATC	1 cut(s)	106
NlaIII	CATG	1 cut(s)	244
NlaIV	GGNNCC	2 cut(s)	57, 220
PaqCI	CACCTGC	1 cut(s)	403
PctI	GAATGC	1 cut(s)	250
PfeI	GAWTC	2 cut(s)	210, 398
PfoI	TCCNGGA	1 cut(s)	401
PkrI	GCNGC	1 cut(s)	341
Psp6I	CCWGG	1 cut(s)	401
PspGI	CCWGG	1 cut(s)	401
PspN4I	GGNNCC	2 cut(s)	57, 220
RsaI	GTAC	3 cut(s)	153, 220, 231
RsaNI	GTAC	3 cut(s)	152, 219, 230
SatI	GCNGC	1 cut(s)	340
Sau3AI	GATC	1 cut(s)	106
ScrFI	CCNGG	1 cut(s)	403
SetI	ASST	4 cut(s)	309, 348, 417, 424
SfaNI	GCATC	1 cut(s)	109
SmlI	CTYRAG	1 cut(s)	287
SmoI	CTYRAG	1 cut(s)	287
Sse9I	AATT	2 cut(s)	182, 234
SsiI	CCGC	4 cut(s)	284, 316, 337, 340
SspMI	CTAG	1 cut(s)	207
StyD4I	CCNGG	1 cut(s)	401
TasI	AATT	2 cut(s)	182, 234
TatI	WGTACW	1 cut(s)	229
TauI	GCSGC	1 cut(s)	342
TfiI	GAWTC	2 cut(s)	210, 398
TscAI	CASTG	1 cut(s)	162
TspDTI	ATGAA	5 cut(s)	213, 257, 314, 378, 396
TspRI	CASTG	1 cut(s)	162
XagI	CCTNNNNNAGG	1 cut(s)	406
XapI	RAATTY	1 cut(s)	182
XspI	CTAG	1 cut(s)	207

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