Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr7D

Orthogroup ID

OG0005088

Physical Location & Seq

Genomic Coordinates Forward (+)

2297205 .. 2300121

Gene Structure 2917 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh7DG031100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 852 bp

ATGGCTTCAATTTCAGGACCTGAAAACCCGTCGCCGAACATCTACATACCGCCAGAATGGTCCGACGCCGCCGACGCCGTCGCACAAGCCTCCGTCGCTTCGCCGCCGCCCATTGTCTTAGTCTGTGGCGCCAAGAACTGTGGAAAGTCCACCTTCTCCCGCTACCTCCTCAACATTCTTCTCCACCGGTATAAGAAAGTTGGGTACTTGGATACAGATGAGTACTGCAACAGTGATAACTCTAATAATATTGGATTGCCTCTCGTTGTGAATACACCTGGATGGGTGAAAGGTATTGGCTATGATATTTTGGTGGATATGTTGAAGTATATTTCCCCTACCCATGTTGTTAAAATAAACATATCTGCTCAGAGTAAGAATCTACCAGATGGGCGATTCTGGTTAGATGAGGATTATGATGGTATGGTAAATCTAACAGAGATCAGTTCAGCTCGTCAGGACTCTTTGAATAGATCGGTTCTAGTCCAAAAGGATGCACGGCTGCTGCGCGATATACGTTTAATGGCTTATTTCAGGCAGTGCTTTTCAAGTAACTTGAACATTTCTACAATCAAAGAACTTGCTAATGCTTTGGCATCTCACCCTCCTTATGAAGTTCCAATATCTAGCATTAAGATTAGGCATCTCCATTGTCAGGTCCCAGGTACTGAGATCTTCTATAGTTTGAATGGAAGCATTGTTGGCTTGGCAGTTAGCACTGAAGGCTCAAAAGATTTACCATGGTGTGTTGGTCTTGGAATTGTGAGGAGCATTGACACACTCAAAGGCTTGCTATATGTGATAACACCTGTTCCACAAGGCACTCTGGAAAATGTAATTGAACCCATCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000448 GO:0000460 GO:0000463 GO:0000466 GO:0000469 GO:0000470 GO:0000478 GO:0000479 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006364 GO:0006396 GO:0006725 GO:0006793 GO:0006796 GO:0006807 GO:0008150 GO:0008152 GO:0009987 GO:0010467 GO:0016070 GO:0016072 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0016773 GO:0019205 GO:0022613 GO:0034470 GO:0034641 GO:0034660 GO:0042254 GO:0042273 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044085 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0051731 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0090501 GO:0090502 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

CLP1_P

Protein Analysis

283

Amino Acids

31.04

Weight (kDa)

5.96

Isoelectric Point (pI)

43.31

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CLP1_P	PF16575	43 - 73	1.3e-06	mRNA cleavage and polyadenylation factor CLP1 P-loop
CLP1_P	PF16575	85 - 178	2.1e-08	mRNA cleavage and polyadenylation factor CLP1 P-loop
NOL9_C	PF25467	200 - 279	4.9e-27	NOL9-like, C-terminal domain

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: OG0005088)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G11010 AT5G11010 AT5G11010 AT5G11010
fragaria_vesca	FvH4_5g16020 FvH4_5g16020 FvH4_5g16020 FvH4_5g16020
malus_domestica	MD06G1183600.v1.1 MD14G1057100.v1.1 MD14G1189700.v1.1
prunus_persica	Prupe.5G161200_v2.0.a1 Prupe.5G182300_v2.0.a1 Prupe.5G182300_v2.0.a1
pyrus_communis	pycom06g16270 pycom14g15720
rosa_chinensis	RchiOBHm_Chr7g0180051
rosa_laevigata	RLG00000005299
rosa_multiflora	Rmu_co8044072.1_g000001 Rmu_sc0002219.1_g000023 Rmu_sc0017616.1_g000001 Rmu_ssc0000119.1_g000025
rosa_roxburghii	Rroxscaffold_3G00273170
rosa_rugosa	Rorug06G0430200 Rorug06G0430200
rosa_samantha	Rh7AG030400 Rh7BG030300 Rh7CG032100 Rh7DG031100
rosa_wichuraiana	Rw7G002530

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	128
AccII	CGCG	1 cut(s)	510
AciI	CCGC	5 cut(s)	50, 69, 104, 107, 160
AcuI	CTGAAG	1 cut(s)	741
AcyI	GRCGYC	3 cut(s)	66, 75, 129
AfaI	GTAC	3 cut(s)	206, 224, 667
AfiI	CCNNNNNNNGG	1 cut(s)	655
AgeI	ACCGGT	1 cut(s)	186
AgsI	TTSAA	7 cut(s)	9, 325, 469, 549, 559, 688, 842
AjnI	CCWGG	2 cut(s)	277, 661
AluBI	AGCT	1 cut(s)	452
AluI	AGCT	1 cut(s)	452
AlwNI	CAGNNNCTG	2 cut(s)	20, 668
ApeKI	GCWGC	2 cut(s)	502, 505
AsiGI	ACCGGT	1 cut(s)	186
AspLEI	GCGC	2 cut(s)	131, 510
AspS9I	GGNCC	3 cut(s)	17, 60, 658
AsuHPI	GGTGA	2 cut(s)	298, 593
AvaII	GGWCC	3 cut(s)	17, 60, 658
BanI	GGYRCC	1 cut(s)	128
BbvI	GCAGC	2 cut(s)	489, 492
BccI	CCATC	3 cut(s)	276, 383, 413
BceAI	ACGGC	2 cut(s)	62, 515
BciT130I	CCWGG	2 cut(s)	279, 663
BciVI	GTATCC	1 cut(s)	205
BfaI	CTAG	2 cut(s)	482, 627
BfmI	CTRYAG	1 cut(s)	679
BfoI	RGCGCY	1 cut(s)	132
BfuI	GTATCC	1 cut(s)	205
BglII	AGATCT	1 cut(s)	672
BisI	GCNGC	5 cut(s)	69, 104, 107, 503, 506
BlsI	GCNGC	5 cut(s)	70, 105, 108, 504, 507
BmcAI	AGTACT	1 cut(s)	224
Bme1390I	CCNGG	2 cut(s)	279, 663
Bme18I	GGWCC	3 cut(s)	17, 60, 658
BmgT120I	GGNCC	3 cut(s)	17, 60, 658
BmiI	GGNNCC	2 cut(s)	130, 660
BmrFI	CCNGG	2 cut(s)	279, 663
BmsI	GCATC	3 cut(s)	484, 605, 652
BsaHI	GRCGYC	3 cut(s)	66, 75, 129
BsaJI	CCNNGG	2 cut(s)	661, 740
BsaWI	WCCGGW	1 cut(s)	186
Bsc4I	CCNNNNNNNGG	1 cut(s)	655
Bse118I	RCCGGY	1 cut(s)	186
BseBI	CCWGG	2 cut(s)	279, 663
BseDI	CCNNGG	2 cut(s)	661, 740
BseGI	GGATG	2 cut(s)	287, 499
BseLI	CCNNNNNNNGG	1 cut(s)	655
BseMII	CTCAG	2 cut(s)	383, 660
BseRI	GAGGAG	2 cut(s)	158, 781
BseXI	GCAGC	2 cut(s)	489, 492
Bsh1236I	CGCG	1 cut(s)	510
BshNI	GGYRCC	1 cut(s)	128
BshTI	ACCGGT	1 cut(s)	186
BsiSI	CCGG	1 cut(s)	187
BslFI	GGGAC	1 cut(s)	644
BslI	CCNNNNNNNGG	1 cut(s)	655
BsmFI	GGGAC	1 cut(s)	644
Bsp143I	GATC	3 cut(s)	441, 473, 672
Bsp19I	CCATGG	1 cut(s)	740
BspACI	CCGC	5 cut(s)	50, 69, 104, 107, 160
BspCNI	CTCAG	2 cut(s)	382, 661
BspFNI	CGCG	1 cut(s)	510
BspLI	GGNNCC	2 cut(s)	130, 660
BspT107I	GGYRCC	1 cut(s)	128
BsrFI	RCCGGY	1 cut(s)	186
BssAI	RCCGGY	1 cut(s)	186
BssECI	CCNNGG	2 cut(s)	661, 740
BssMI	GATC	3 cut(s)	441, 473, 672
BssNI	GRCGYC	3 cut(s)	66, 75, 129
BssT1I	CCWWGG	1 cut(s)	740
Bst2UI	CCWGG	2 cut(s)	279, 663
Bst4CI	ACNGT	2 cut(s)	140, 233
BstACI	GRCGYC	3 cut(s)	66, 75, 129
BstC8I	GCNNGC	1 cut(s)	791
BstDEI	CTNAG	3 cut(s)	118, 369, 669
BstDSI	CCRYGG	1 cut(s)	740
BstF5I	GGATG	2 cut(s)	287, 499
BstFNI	CGCG	1 cut(s)	510
BstH2I	RGCGCY	1 cut(s)	132
BstHHI	GCGC	2 cut(s)	131, 510
BstKTI	GATC	3 cut(s)	444, 476, 675
BstMBI	GATC	3 cut(s)	441, 473, 672
BstMWI	GCNNNNNNNGC	4 cut(s)	74, 95, 702, 723
BstNI	CCWGG	2 cut(s)	279, 663
BstSCI	CCNGG	2 cut(s)	277, 661
BstSFI	CTRYAG	1 cut(s)	679
BstUI	CGCG	1 cut(s)	510
BstV1I	GCAGC	2 cut(s)	489, 492
BstX2I	RGATCY	1 cut(s)	672
BstYI	RGATCY	1 cut(s)	672
BsuI	GTATCC	1 cut(s)	205
BtgI	CCRYGG	1 cut(s)	740
BtsCI	GGATG	2 cut(s)	287, 499
BtsI	GCAGTG	1 cut(s)	545
BtsIMutI	CAGTG	3 cut(s)	238, 545, 717
Cac8I	GCNNGC	1 cut(s)	791
CaiI	CAGNNNCTG	2 cut(s)	20, 668
CfoI	GCGC	2 cut(s)	131, 510
Cfr10I	RCCGGY	1 cut(s)	186
Cfr13I	GGNCC	3 cut(s)	17, 60, 658
CseI	GACGC	2 cut(s)	74, 83
Csp6I	GTAC	3 cut(s)	205, 223, 666
CspAI	ACCGGT	1 cut(s)	186
CspCI	CAANNNNNGTGG	2 cut(s)	121, 156
CviAII	CATG	2 cut(s)	344, 741
CviJI	RGCY	9 cut(s)	5, 89, 300, 452, 502, 527, 705, 726, 789
CviKI_1	RGCY	9 cut(s)	5, 89, 300, 452, 502, 527, 705, 726, 789
CviQI	GTAC	3 cut(s)	205, 223, 666
DdeI	CTNAG	3 cut(s)	118, 369, 669
DinI	GGCGCC	1 cut(s)	130
DpnI	GATC	3 cut(s)	443, 475, 674
DpnII	GATC	3 cut(s)	441, 473, 672
Eco130I	CCWWGG	1 cut(s)	740
Eco47I	GGWCC	3 cut(s)	17, 60, 658
Eco57I	CTGAAG	1 cut(s)	741
EcoO109I	RGGNCCY	2 cut(s)	17, 658
EcoRII	CCWGG	2 cut(s)	277, 661
EcoT14I	CCWWGG	1 cut(s)	740
EgeI	GGCGCC	1 cut(s)	130
EheI	GGCGCC	1 cut(s)	130
ErhI	CCWWGG	1 cut(s)	740
FaeI	CATG	2 cut(s)	347, 744
FalI	AAGNNNNNCTT	2 cut(s)	137, 169
FaqI	GGGAC	1 cut(s)	644
FatI	CATG	2 cut(s)	343, 740
FauI	CCCGC	1 cut(s)	167
Fnu4HI	GCNGC	5 cut(s)	69, 104, 107, 503, 506
FokI	GGATG	2 cut(s)	294, 506
Fsp4HI	GCNGC	5 cut(s)	69, 104, 107, 503, 506
FspBI	CTAG	2 cut(s)	482, 627
GlaI	GCGC	2 cut(s)	130, 509
GluI	GCNGC	5 cut(s)	69, 104, 107, 503, 506
HaeII	RGCGCY	1 cut(s)	132
HapII	CCGG	1 cut(s)	187
HgaI	GACGC	2 cut(s)	74, 83
HhaI	GCGC	2 cut(s)	131, 510
Hin1I	GRCGYC	3 cut(s)	66, 75, 129
Hin1II	CATG	2 cut(s)	347, 744
Hin6I	GCGC	2 cut(s)	129, 508
HinP1I	GCGC	2 cut(s)	129, 508
HinfI	GANTC	3 cut(s)	379, 396, 461
HpaII	CCGG	1 cut(s)	187
HphI	GGTGA	2 cut(s)	298, 593
Hpy166II	GTNNAC	1 cut(s)	150
Hpy188I	TCNGA	2 cut(s)	64, 372
Hpy188III	TCNNGA	3 cut(s)	15, 458, 827
Hpy8I	GTNNAC	1 cut(s)	150
Hpy99I	CGWCG	5 cut(s)	34, 68, 77, 83, 98
HpyAV	CCTTC	2 cut(s)	163, 716
HpyCH4III	ACNGT	2 cut(s)	140, 233
HpyCH4IV	ACGT	1 cut(s)	517
HpyCH4V	TGCA	2 cut(s)	228, 497
HpyF10VI	GCNNNNNNNGC	4 cut(s)	74, 95, 702, 723
HpyF3I	CTNAG	3 cut(s)	118, 369, 669
HpySE526I	ACGT	1 cut(s)	517
Hsp92I	GRCGYC	3 cut(s)	66, 75, 129
Hsp92II	CATG	2 cut(s)	347, 744
HspAI	GCGC	2 cut(s)	129, 508
KasI	GGCGCC	1 cut(s)	128
Kzo9I	GATC	3 cut(s)	441, 473, 672
LmnI	GCTCC	1 cut(s)	768
Lsp1109I	GCAGC	2 cut(s)	489, 492
LweI	GCATC	3 cut(s)	484, 605, 652
MaeI	CTAG	2 cut(s)	482, 627
MaeII	ACGT	1 cut(s)	517
MaeIII	GTNAC	1 cut(s)	551
MalI	GATC	3 cut(s)	443, 475, 674
MboI	GATC	3 cut(s)	441, 473, 672
MboII	GAAGA	2 cut(s)	170, 667
MflI	RGATCY	1 cut(s)	672
MluCI	AATT	3 cut(s)	9, 759, 837
Mly113I	GGCGCC	1 cut(s)	129
MlyI	GAGTC	1 cut(s)	455
MmeI	TCCRAC	1 cut(s)	87
MnlI	CCTC	7 cut(s)	100, 176, 179, 270, 403, 615, 759
MseI	TTAA	3 cut(s)	351, 521, 633
MslI	CAYNNNNRTG	1 cut(s)	280
MspI	CCGG	1 cut(s)	187
MspR9I	CCNGG	2 cut(s)	279, 663
MvaI	CCWGG	2 cut(s)	279, 663
MvnI	CGCG	1 cut(s)	510
MwoI	GCNNNNNNNGC	4 cut(s)	74, 95, 702, 723
NarI	GGCGCC	1 cut(s)	129
NcoI	CCATGG	1 cut(s)	740
NdeII	GATC	3 cut(s)	441, 473, 672
NlaIII	CATG	2 cut(s)	347, 744
NlaIV	GGNNCC	2 cut(s)	130, 660
PfeI	GAWTC	2 cut(s)	379, 396
PflFI	GACNNNGTC	1 cut(s)	77
PinAI	ACCGGT	1 cut(s)	186
PkrI	GCNGC	5 cut(s)	70, 105, 108, 504, 507
PleI	GAGTC	1 cut(s)	455
PluTI	GGCGCC	1 cut(s)	132
PpsI	GAGTC	1 cut(s)	455
PpuMI	RGGWCCY	2 cut(s)	17, 658
Psp5II	RGGWCCY	2 cut(s)	17, 658
Psp6I	CCWGG	2 cut(s)	277, 661
PspGI	CCWGG	2 cut(s)	277, 661
PspN4I	GGNNCC	2 cut(s)	130, 660
PspPI	GGNCC	3 cut(s)	17, 60, 658
PspPPI	RGGWCCY	2 cut(s)	17, 658
PstNI	CAGNNNCTG	2 cut(s)	20, 668
PsuI	RGATCY	1 cut(s)	672
PsyI	GACNNNGTC	1 cut(s)	77
RsaI	GTAC	3 cut(s)	206, 224, 667
RsaNI	GTAC	3 cut(s)	205, 223, 666
RseI	CAYNNNNRTG	1 cut(s)	280
SaqAI	TTAA	3 cut(s)	351, 521, 633
SatI	GCNGC	5 cut(s)	69, 104, 107, 503, 506
Sau3AI	GATC	3 cut(s)	441, 473, 672
Sau96I	GGNCC	3 cut(s)	17, 60, 658
ScaI	AGTACT	1 cut(s)	224
SchI	GAGTC	1 cut(s)	455
ScrFI	CCNGG	2 cut(s)	279, 663
SfaNI	GCATC	3 cut(s)	484, 605, 652
SfcI	CTRYAG	1 cut(s)	679
SfoI	GGCGCC	1 cut(s)	130
SinI	GGWCC	3 cut(s)	17, 60, 658
SmiMI	CAYNNNNRTG	1 cut(s)	280
Sse9I	AATT	3 cut(s)	9, 759, 837
SsiI	CCGC	5 cut(s)	50, 69, 104, 107, 160
SspDI	GGCGCC	1 cut(s)	128
SspI	AATATT	1 cut(s)	250
SspMI	CTAG	2 cut(s)	482, 627
StyD4I	CCNGG	2 cut(s)	277, 661
StyI	CCWWGG	1 cut(s)	740
TaaI	ACNGT	2 cut(s)	140, 233
TaiI	ACGT	1 cut(s)	520
TasI	AATT	3 cut(s)	9, 759, 837
TatI	WGTACW	1 cut(s)	222
TauI	GCSGC	3 cut(s)	71, 106, 109
TfiI	GAWTC	2 cut(s)	379, 396
Tru1I	TTAA	3 cut(s)	351, 521, 633
Tru9I	TTAA	3 cut(s)	351, 521, 633
TscAI	CASTG	3 cut(s)	238, 545, 724
TseI	GCWGC	2 cut(s)	502, 505
TspDTI	ATGAA	1 cut(s)	627
TspGWI	ACGGA	1 cut(s)	82
TspRI	CASTG	3 cut(s)	238, 545, 724
Tth111I	GACNNNGTC	1 cut(s)	77
VpaK11BI	GGWCC	3 cut(s)	17, 60, 658
XspI	CTAG	2 cut(s)	482, 627
ZrmI	AGTACT	1 cut(s)	224

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