Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000002

Orthogroup ID

OG0006876

Physical Location & Seq

Genomic Coordinates Forward (+)

5238436 .. 5241389

Gene Structure 2954 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_2G00082380.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 678 bp

ATGGACGGCACCACCGAAACGGATTACACCGCCGATGAGACGCCGAATATCAGTTATGTAAATGTGCATGCTGTGCTGGACGCCCGGCGAAACCGCGCTAAAACGCTGTCGTCTGATGACCCTAATTCTCCTCAGGCTCAGGGACCGAGGGTGATTGTCGTGGGACCTTCGGATTCTGGGAAAAGTACATTGTCGAAAATGCTGCTTAGTTGGGCAGCTAAGCAGGGATGGAAACCTACTTTTGTCGACTTGGATATTGGACAAGGAGCTATAACAATTCCAGGATGCATTGCTGCTACTCCTATCGAAATGCCTATTGATCCGGTGGAAGGGATTCCCCTTGACATGCCCCTCGTTTATTTCTATGGGCACACAACTCCCATGAGCAATGTGGATTTGTACAGAGTGCTTGTGAAGGAGCTTTCTCAAATGGTGGAGAGACAATTTACTGGTAATGCTGAATCTCAAGCTGCTGGATTGGTCATCAACACCATGGGATGGATAGAAGGTGCCGGCTATGAGTTGCTTCTTCATGCAATTGACACATTCAATGCTAATGTTGTCTTGGTTTTGGGTCAGGAAAAGCTTTGCAGCATGCTCAGAGATGTATTAAAGAACAAGCCCAACGTGGATGTTGTTAAACTTCAAAAATCAGGGGAGTTGTATCCAGGAATGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000394 GO:0003006 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006378 GO:0006379 GO:0006388 GO:0006396 GO:0006397 GO:0006399 GO:0006725 GO:0006793 GO:0006796 GO:0006807 GO:0007275 GO:0008033 GO:0008150 GO:0008152 GO:0008380 GO:0009791 GO:0009908 GO:0009987 GO:0010228 GO:0010467 GO:0016070 GO:0016071 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016773 GO:0019205 GO:0022414 GO:0031123 GO:0031124 GO:0032501 GO:0032502 GO:0034470 GO:0034641 GO:0034660 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043631 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0048367 GO:0048608 GO:0048731 GO:0048827 GO:0048856 GO:0051731 GO:0061458 GO:0071704 GO:0090304 GO:0090305 GO:0090501 GO:0090567 GO:0099402 GO:1901360

KEGG Pathways

Metabolic & Signaling

ko03015 map03015

Pfam Domains

Protein Families

CLP1_N CLP1_P Clp1

Protein Analysis

225

Amino Acids

24.45

Weight (kDa)

4.85

Isoelectric Point (pI)

32.15

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CLP1_P	PF16575	55 - 221	1.8e-61	mRNA cleavage and polyadenylation factor CLP1 P-loop

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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0006876)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G04680 AT3G04680 AT3G04680
fragaria_vesca	FvH4_6g49260 FvH4_6g49260
malus_domestica	MD09G1046200.v1.1 MD09G1046500.v1.1 MD17G1047000.v1.1
prunus_persica	Prupe.3G272100_v2.0.a1
pyrus_communis	pycom09g03810 pycom09g04270 pycom111g03580 pycom111g03600 pycom111g03650 pycom17g04190
rosa_chinensis	RchiOBHm_Chr2g0169161
rosa_laevigata	RLG00000021838
rosa_multiflora	Rmu_ssc0000440.1_g000003
rosa_roxburghii	Rroxscaffold_2G00082380
rosa_rugosa	Rorug02G0537700 Rorug02G0537800
rosa_samantha	Rh2AG609300 Rh2BG622300 Rh2CG591000 Rh2DG633000
rosa_wichuraiana	Rw2G050540

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	2 cut(s)	8, 509
AccB7I	CCANNNNNTGG	1 cut(s)	498
AccI	GTMKAC	1 cut(s)	246
AccII	CGCG	1 cut(s)	96
AciI	CCGC	2 cut(s)	30, 94
AclWI	GGATC	1 cut(s)	314
AcyI	GRCGYC	2 cut(s)	41, 81
AfaI	GTAC	2 cut(s)	187, 401
AfiI	CCNNNNNNNGG	2 cut(s)	329, 498
AgsI	TTSAA	2 cut(s)	550, 647
AjnI	CCWGG	2 cut(s)	280, 667
AluBI	AGCT	5 cut(s)	218, 269, 421, 470, 586
AluI	AGCT	5 cut(s)	218, 269, 421, 470, 586
Alw26I	GTCTC	2 cut(s)	32, 433
AlwI	GGATC	1 cut(s)	314
ApeKI	GCWGC	5 cut(s)	202, 215, 293, 470, 591
Asp700I	GAANNNNTTC	1 cut(s)	333
AspLEI	GCGC	1 cut(s)	98
AspS9I	GGNCC	2 cut(s)	143, 164
AsuC2I	CCSGG	1 cut(s)	85
AsuHPI	GGTGA	1 cut(s)	163
AvaII	GGWCC	2 cut(s)	143, 164
AxyI	CCTNAGG	1 cut(s)	132
BaeGI	GKGCMC	1 cut(s)	372
BanI	GGYRCC	2 cut(s)	8, 509
BbvI	GCAGC	5 cut(s)	189, 227, 280, 457, 603
BccI	CCATC	2 cut(s)	222, 492
BceAI	ACGGC	1 cut(s)	22
BcgI	CGANNNNNNTGC	2 cut(s)	184, 218
BciT130I	CCWGG	2 cut(s)	282, 669
BciVI	GTATCC	1 cut(s)	675
BcnI	CCSGG	1 cut(s)	85
BcoDI	GTCTC	2 cut(s)	32, 433
BfuI	GTATCC	1 cut(s)	675
BisI	GCNGC	5 cut(s)	203, 216, 294, 471, 592
BlpI	GCTNAGC	1 cut(s)	219
BlsI	GCNGC	5 cut(s)	204, 217, 295, 472, 593
Bme1390I	CCNGG	3 cut(s)	85, 282, 669
Bme18I	GGWCC	2 cut(s)	143, 164
BmgT120I	GGNCC	2 cut(s)	143, 164
BmiI	GGNNCC	4 cut(s)	10, 144, 165, 511
BmrFI	CCNGG	3 cut(s)	85, 282, 669
BmsI	GCATC	1 cut(s)	275
Bpu10I	CCTNAGC	1 cut(s)	138
Bpu1102I	GCTNAGC	1 cut(s)	219
BpuEI	CTTGAG	1 cut(s)	450
BpuMI	CCSGG	1 cut(s)	85
BsaHI	GRCGYC	2 cut(s)	41, 81
BsaJI	CCNNGG	2 cut(s)	146, 492
BsaWI	WCCGGW	1 cut(s)	322
Bsc4I	CCNNNNNNNGG	2 cut(s)	329, 498
Bse118I	RCCGGY	1 cut(s)	512
Bse1I	ACTGG	1 cut(s)	454
Bse21I	CCTNAGG	1 cut(s)	132
Bse3DI	GCAATG	2 cut(s)	288, 394
BseBI	CCWGG	2 cut(s)	282, 669
BseDI	CCNNGG	2 cut(s)	146, 492
BseGI	GGATG	4 cut(s)	233, 290, 503, 637
BseLI	CCNNNNNNNGG	2 cut(s)	329, 498
BseMI	GCAATG	2 cut(s)	288, 394
BseMII	CTCAG	3 cut(s)	146, 152, 613
BseNI	ACTGG	1 cut(s)	454
BseRI	GAGGAG	1 cut(s)	120
BseSI	GKGCMC	1 cut(s)	372
BseXI	GCAGC	5 cut(s)	189, 227, 280, 457, 603
Bsh1236I	CGCG	1 cut(s)	96
BshNI	GGYRCC	2 cut(s)	8, 509
BsiSI	CCGG	3 cut(s)	85, 323, 513
BslFI	GGGAC	2 cut(s)	156, 177
BslI	CCNNNNNNNGG	2 cut(s)	329, 498
BsmAI	GTCTC	2 cut(s)	32, 433
BsmBI	CGTCTC	1 cut(s)	32
BsmFI	GGGAC	2 cut(s)	156, 177
Bsp1286I	GDGCHC	1 cut(s)	372
Bsp1407I	TGTACA	1 cut(s)	399
Bsp143I	GATC	1 cut(s)	319
Bsp1720I	GCTNAGC	1 cut(s)	219
Bsp19I	CCATGG	1 cut(s)	492
BspACI	CCGC	2 cut(s)	30, 94
BspCNI	CTCAG	3 cut(s)	145, 151, 612
BspFNI	CGCG	1 cut(s)	96
BspLI	GGNNCC	4 cut(s)	10, 144, 165, 511
BspPI	GGATC	1 cut(s)	314
BspT107I	GGYRCC	2 cut(s)	8, 509
BsrDI	GCAATG	2 cut(s)	288, 394
BsrFI	RCCGGY	1 cut(s)	512
BsrGI	TGTACA	1 cut(s)	399
BsrI	ACTGG	1 cut(s)	454
BssAI	RCCGGY	1 cut(s)	512
BssECI	CCNNGG	2 cut(s)	146, 492
BssMI	GATC	1 cut(s)	319
BssNI	GRCGYC	2 cut(s)	41, 81
BssT1I	CCWWGG	1 cut(s)	492
Bst2UI	CCWGG	2 cut(s)	282, 669
BstACI	GRCGYC	2 cut(s)	41, 81
BstAPI	GCANNNNNTGC	1 cut(s)	73
BstAUI	TGTACA	1 cut(s)	399
BstC8I	GCNNGC	3 cut(s)	69, 514, 596
BstDEI	CTNAG	5 cut(s)	132, 138, 206, 219, 599
BstDSI	CCRYGG	1 cut(s)	492
BstF5I	GGATG	4 cut(s)	233, 290, 503, 637
BstFNI	CGCG	1 cut(s)	96
BstHHI	GCGC	1 cut(s)	98
BstKTI	GATC	1 cut(s)	322
BstMAI	GTCTC	2 cut(s)	32, 433
BstMBI	GATC	1 cut(s)	319
BstMWI	GCNNNNNNNGC	1 cut(s)	73
BstNI	CCWGG	2 cut(s)	282, 669
BstNSI	RCATGY	3 cut(s)	71, 349, 598
BstSCI	CCNGG	3 cut(s)	83, 280, 667
BstSLI	GKGCMC	1 cut(s)	372
BstUI	CGCG	1 cut(s)	96
BstV1I	GCAGC	5 cut(s)	189, 227, 280, 457, 603
Bsu36I	CCTNAGG	1 cut(s)	132
BsuI	GTATCC	1 cut(s)	675
BtgI	CCRYGG	1 cut(s)	492
BtsCI	GGATG	4 cut(s)	233, 290, 503, 637
Cac8I	GCNNGC	3 cut(s)	69, 514, 596
CfoI	GCGC	1 cut(s)	98
Cfr10I	RCCGGY	1 cut(s)	512
Cfr13I	GGNCC	2 cut(s)	143, 164
CseI	GACGC	2 cut(s)	49, 89
Csp6I	GTAC	2 cut(s)	186, 400
CviAII	CATG	6 cut(s)	68, 346, 382, 493, 533, 595
CviJI	RGCY	8 cut(s)	137, 218, 269, 421, 470, 516, 586, 622
CviKI_1	RGCY	8 cut(s)	137, 218, 269, 421, 470, 516, 586, 622
CviQI	GTAC	2 cut(s)	186, 400
DdeI	CTNAG	5 cut(s)	132, 138, 206, 219, 599
DpnI	GATC	1 cut(s)	321
DpnII	GATC	1 cut(s)	319
Eco130I	CCWWGG	1 cut(s)	492
Eco47I	GGWCC	2 cut(s)	143, 164
Eco81I	CCTNAGG	1 cut(s)	132
EcoO109I	RGGNCCY	1 cut(s)	164
EcoRII	CCWGG	2 cut(s)	280, 667
EcoT14I	CCWWGG	1 cut(s)	492
EcoT22I	ATGCAT	1 cut(s)	290
ErhI	CCWWGG	1 cut(s)	492
Esp3I	CGTCTC	1 cut(s)	32
FaeI	CATG	6 cut(s)	71, 349, 385, 496, 536, 598
FaqI	GGGAC	2 cut(s)	156, 177
FatI	CATG	6 cut(s)	67, 345, 381, 492, 532, 594
FblI	GTMKAC	1 cut(s)	246
Fnu4HI	GCNGC	5 cut(s)	203, 216, 294, 471, 592
FokI	GGATG	4 cut(s)	240, 297, 510, 644
Fsp4HI	GCNGC	5 cut(s)	203, 216, 294, 471, 592
GlaI	GCGC	1 cut(s)	97
GluI	GCNGC	5 cut(s)	203, 216, 294, 471, 592
HapII	CCGG	3 cut(s)	85, 323, 513
HgaI	GACGC	2 cut(s)	49, 89
HhaI	GCGC	1 cut(s)	98
Hin1I	GRCGYC	2 cut(s)	41, 81
Hin1II	CATG	6 cut(s)	71, 349, 385, 496, 536, 598
Hin6I	GCGC	1 cut(s)	96
HinP1I	GCGC	1 cut(s)	96
HincII	GTYRAC	1 cut(s)	247
HindII	GTYRAC	1 cut(s)	247
HindIII	AAGCTT	1 cut(s)	584
HinfI	GANTC	3 cut(s)	173, 334, 461
HpaII	CCGG	3 cut(s)	85, 323, 513
HphI	GGTGA	1 cut(s)	163
Hpy166II	GTNNAC	1 cut(s)	247
Hpy188I	TCNGA	3 cut(s)	115, 172, 602
Hpy188III	TCNNGA	1 cut(s)	578
Hpy8I	GTNNAC	1 cut(s)	247
HpyAV	CCTTC	4 cut(s)	177, 323, 409, 500
HpyCH4IV	ACGT	1 cut(s)	627
HpyCH4V	TGCA	4 cut(s)	67, 288, 536, 591
HpyF10VI	GCNNNNNNNGC	1 cut(s)	73
HpyF3I	CTNAG	5 cut(s)	132, 138, 206, 219, 599
HpySE526I	ACGT	1 cut(s)	627
Hsp92I	GRCGYC	2 cut(s)	41, 81
Hsp92II	CATG	6 cut(s)	71, 349, 385, 496, 536, 598
HspAI	GCGC	1 cut(s)	96
KroI	GCCGGC	1 cut(s)	512
KroNI	GCCGGC	1 cut(s)	514
Kzo9I	GATC	1 cut(s)	319
LmnI	GCTCC	2 cut(s)	266, 418
Lsp1109I	GCAGC	5 cut(s)	189, 227, 280, 457, 603
LweI	GCATC	1 cut(s)	275
MaeII	ACGT	1 cut(s)	627
MalI	GATC	1 cut(s)	321
MboI	GATC	1 cut(s)	319
MboII	GAAGA	1 cut(s)	521
MfeI	CAATTG	1 cut(s)	537
MhlI	GDGCHC	1 cut(s)	372
MluCI	AATT	4 cut(s)	124, 276, 443, 537
MnlI	CCTC	3 cut(s)	141, 141, 362
Mph1103I	ATGCAT	1 cut(s)	290
MroNI	GCCGGC	1 cut(s)	512
MroXI	GAANNNNTTC	1 cut(s)	333
MseI	TTAA	2 cut(s)	611, 639
MspI	CCGG	3 cut(s)	85, 323, 513
MspR9I	CCNGG	3 cut(s)	85, 282, 669
MunI	CAATTG	1 cut(s)	537
MvaI	CCWGG	2 cut(s)	282, 669
MvnI	CGCG	1 cut(s)	96
MwoI	GCNNNNNNNGC	1 cut(s)	73
NaeI	GCCGGC	1 cut(s)	514
NciI	CCSGG	1 cut(s)	85
NcoI	CCATGG	1 cut(s)	492
NdeII	GATC	1 cut(s)	319
NgoMIV	GCCGGC	1 cut(s)	512
NlaIII	CATG	6 cut(s)	71, 349, 385, 496, 536, 598
NlaIV	GGNNCC	4 cut(s)	10, 144, 165, 511
NsiI	ATGCAT	1 cut(s)	290
NspI	RCATGY	3 cut(s)	71, 349, 598
PaeI	GCATGC	2 cut(s)	71, 598
PcsI	WCGNNNNNNNCGW	1 cut(s)	12
PdiI	GCCGGC	1 cut(s)	514
PdmI	GAANNNNTTC	1 cut(s)	333
PfeI	GAWTC	3 cut(s)	173, 334, 461
PflMI	CCANNNNNTGG	1 cut(s)	498
PfoI	TCCNGGA	2 cut(s)	280, 667
PkrI	GCNGC	5 cut(s)	204, 217, 295, 472, 593
PpuMI	RGGWCCY	1 cut(s)	164
Psp5II	RGGWCCY	1 cut(s)	164
Psp6I	CCWGG	2 cut(s)	280, 667
PspGI	CCWGG	2 cut(s)	280, 667
PspN4I	GGNNCC	4 cut(s)	10, 144, 165, 511
PspPI	GGNCC	2 cut(s)	143, 164
PspPPI	RGGWCCY	1 cut(s)	164
RsaI	GTAC	2 cut(s)	187, 401
RsaNI	GTAC	2 cut(s)	186, 400
SalI	GTCGAC	1 cut(s)	245
SaqAI	TTAA	2 cut(s)	611, 639
SatI	GCNGC	5 cut(s)	203, 216, 294, 471, 592
Sau3AI	GATC	1 cut(s)	319
Sau96I	GGNCC	2 cut(s)	143, 164
ScrFI	CCNGG	3 cut(s)	85, 282, 669
SduI	GDGCHC	1 cut(s)	372
SetI	ASST	9 cut(s)	169, 220, 238, 271, 423, 472, 511, 588, 630
SfaNI	GCATC	1 cut(s)	275
SinI	GGWCC	2 cut(s)	143, 164
SmlI	CTYRAG	1 cut(s)	465
SmoI	CTYRAG	1 cut(s)	465
SphI	GCATGC	2 cut(s)	71, 598
Sse9I	AATT	4 cut(s)	124, 276, 443, 537
SsiI	CCGC	2 cut(s)	30, 94
StyD4I	CCNGG	3 cut(s)	83, 280, 667
StyI	CCWWGG	1 cut(s)	492
TaiI	ACGT	1 cut(s)	630
TaqI	TCGA	3 cut(s)	194, 246, 306
TaqII	GACCGA	1 cut(s)	160
TasI	AATT	4 cut(s)	124, 276, 443, 537
TatI	WGTACW	2 cut(s)	185, 399
TfiI	GAWTC	3 cut(s)	173, 334, 461
Tru1I	TTAA	2 cut(s)	611, 639
Tru9I	TTAA	2 cut(s)	611, 639
TseI	GCWGC	5 cut(s)	202, 215, 293, 470, 591
TspDTI	ATGAA	1 cut(s)	521
TspGWI	ACGGA	1 cut(s)	35
Van91I	CCANNNNNTGG	1 cut(s)	498
VpaK11BI	GGWCC	2 cut(s)	143, 164
XceI	RCATGY	3 cut(s)	71, 349, 598
XcmI	CCANNNNNNNNNTGG	1 cut(s)	388
XmiI	GTMKAC	1 cut(s)	246
XmnI	GAANNNNTTC	1 cut(s)	333
Zsp2I	ATGCAT	1 cut(s)	290

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