Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4B

Orthogroup ID

OG0002288

Physical Location & Seq

Genomic Coordinates Reverse (-)

29176126 .. 29177601

Gene Structure 1476 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4BG161900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 576 bp

ATGAGTCGAGGTGATACACAAGAATATTCGAATCTGAATAAGTTTGCTAGACGGTTCCTAAAAGGCAGCCGGAATTCTGTGGAAGGGGAAGCCAAAGATGCTCCTTCACGGGCTTACGTTCAAGAAGTTGTTGAAGAAATACACAAGGGGGAACAGGGAGAATGTCCAATATGTCTTGAAGCATTTGAAGATGCAGTATTGACACCTTGTGCTCATCACTTATGCCGTGAATGTCTCTTGGCAAGTTGGCGGAATTCAACTTCTGGCTTGTGTCCGGTTTGCAGGAAGAGTGTAAGCAAGCAAGATCTAATTACAGCACCAACTGAGAGTCGGTTCTATGTTGATATTGAGAAAAACTGGGTGGAATCATCCAAAATAGTTCTTCTTTTGCGTGTGCTTGAATGTCTTCGTTCGTCAGGCTCAAAGAGCATTGTCTTCAGCCAGTGGACGGCCTTTCTGGACCTCCTGCAGATATCTCTTTCTCGGAGTAACATTCCATTTCTTCACCTGGATGGGACTCTGAATCAACAGCAGCGCGAAAAAGTGTTAAAACAGTTTGTTCTGACATTCTGGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000724 GO:0000725 GO:0006139 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009292 GO:0009294 GO:0009987 GO:0033554 GO:0034641 GO:0043170 GO:0044237 GO:0044238 GO:0044260 GO:0044764 GO:0045003 GO:0046483 GO:0050896 GO:0051704 GO:0051716 GO:0071704 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

HIRAN Helicase_C SNF2_N zf-C3HC4_2 zf-C3HC4_3

Protein Analysis

191

Amino Acids

21.76

Weight (kDa)

7.56

Isoelectric Point (pI)

64.12

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
zf-C3HC4_3	PF13920	52 - 100	4.1e-10	Zinc finger, C3HC4 type (RING finger)
zf-RING_2	PF13639	54 - 95	1.7e-09	Ring finger domain
zf-C3HC4_2	PF13923	54 - 94	7e-09	Zinc finger, C3HC4 type (RING finger)
zf-RING_5	PF14634	54 - 96	2.7e-06	zinc-RING finger domain
zf-RING_UBOX	PF13445	55 - 92	3.5e-10	RING-type zinc-finger
zf-C3HC4	PF00097	55 - 94	2.9e-09	Zinc finger, C3HC4 type (RING finger)
Prok-RING_4	PF14447	55 - 102	1.8e-07	Prokaryotic RING finger family 4
zf-C3HC4_4	PF15227	55 - 94	1.8e-06	zinc finger of C3HC4-type, RING
RING_XB3-XBAT31	PF24921	55 - 99	6.5e-06	E3 ubiquitin-protein ligase XB3/XBAT31 RING finger
Helicase_C	PF00271	126 - 186	1.9e-07	Helicase conserved C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0002288)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G22750
fragaria_vesca	FvH4_6g52660 FvH4_6g52660 FvH4_6g52660 FvH4_6g52660 FvH4_6g52660 FvH4_6g52660 FvH4_6g52660 FvH4_6g52660 FvH4_6g52660 FvH4_6g52660
malus_domestica	MD17G1018000.v1.1
prunus_persica	Prupe.3G300100_v2.0.a1 Prupe.3G300100_v2.0.a1 Prupe.3G300100_v2.0.a1 Prupe.3G300100_v2.0.a1
pyrus_communis	pycom17g01450
rosa_chinensis	RchiOBHm_Chr2g0174191 RchiOBHm_Chr4g0410751
rosa_laevigata	RLG00000022255 RLG00000022256 RLG00000029588
rosa_multiflora	Rmu_sc0000954.1_g000002 Rmu_ssc0000198.1_g000002
rosa_roxburghii	Rroxscaffold_2G00078340 Rroxscaffold_2G00078370 Rroxscaffold_5G00355500
rosa_rugosa	Rorug02G0575800 Rorug02G0575900 Rorug02G0576000 Rorug04G0376700
rosa_samantha	Rh2AG655200 Rh2BG666400 Rh2CG630600 Rh2DG681000 Rh4AG162800 Rh4BG161900 Rh4BG162000 Rh4DG158500 Rh7CG048600
rosa_wichuraiana	Rw2G053780 Rw4G013570

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	537
AciI	CCGC	1 cut(s)	250
AcsI	RAATTY	2 cut(s)	73, 253
AcuI	CTGAAG	1 cut(s)	421
AdeI	CACNNNGTG	1 cut(s)	209
AfiI	CCNNNNNNNGG	1 cut(s)	448
AgsI	TTSAA	6 cut(s)	122, 134, 179, 188, 258, 401
AjnI	CCWGG	1 cut(s)	507
Alw21I	GWGCWC	1 cut(s)	214
Alw26I	GTCTC	1 cut(s)	239
AoxI	GGCC	1 cut(s)	450
ApeKI	GCWGC	2 cut(s)	66, 532
ApoI	RAATTY	2 cut(s)	73, 253
Asp700I	GAANNNNTTC	1 cut(s)	405
AspLEI	GCGC	1 cut(s)	537
AspS9I	GGNCC	1 cut(s)	460
AsuHPI	GGTGA	2 cut(s)	23, 497
AsuII	TTCGAA	1 cut(s)	29
AvaII	GGWCC	1 cut(s)	460
BbsI	GAAGAC	2 cut(s)	398, 427
Bbv12I	GWGCWC	1 cut(s)	214
BbvI	GCAGC	2 cut(s)	78, 544
BccI	CCATC	1 cut(s)	506
BceAI	ACGGC	2 cut(s)	210, 465
BciT130I	CCWGG	1 cut(s)	509
BcoDI	GTCTC	1 cut(s)	239
BfaI	CTAG	1 cut(s)	48
BfmI	CTRYAG	1 cut(s)	467
BglII	AGATCT	1 cut(s)	304
BisI	GCNGC	2 cut(s)	67, 533
BlsI	GCNGC	2 cut(s)	68, 534
Bme1390I	CCNGG	1 cut(s)	509
Bme18I	GGWCC	1 cut(s)	460
BmgT120I	GGNCC	1 cut(s)	460
BmiI	GGNNCC	1 cut(s)	56
BmrFI	CCNGG	1 cut(s)	509
BmrI	ACTGGG	1 cut(s)	367
BmsI	GCATC	2 cut(s)	88, 181
BmuI	ACTGGG	1 cut(s)	367
BpiI	GAAGAC	2 cut(s)	398, 427
Bpu14I	TTCGAA	1 cut(s)	29
BsaWI	WCCGGW	1 cut(s)	274
Bsc4I	CCNNNNNNNGG	1 cut(s)	448
Bse1I	ACTGG	2 cut(s)	362, 442
BseBI	CCWGG	1 cut(s)	509
BseGI	GGATG	2 cut(s)	368, 517
BseLI	CCNNNNNNNGG	1 cut(s)	448
BseMII	CTCAG	1 cut(s)	315
BseNI	ACTGG	2 cut(s)	362, 442
BseXI	GCAGC	2 cut(s)	78, 544
Bsh1236I	CGCG	1 cut(s)	537
BshFI	GGCC	1 cut(s)	452
BsiHKAI	GWGCWC	1 cut(s)	214
BsiSI	CCGG	2 cut(s)	70, 275
BslFI	GGGAC	1 cut(s)	529
BslI	CCNNNNNNNGG	1 cut(s)	448
BsmAI	GTCTC	1 cut(s)	239
BsmFI	GGGAC	1 cut(s)	529
BsnI	GGCC	1 cut(s)	452
Bsp119I	TTCGAA	1 cut(s)	29
Bsp1286I	GDGCHC	1 cut(s)	214
Bsp143I	GATC	1 cut(s)	304
BspACI	CCGC	1 cut(s)	250
BspANI	GGCC	1 cut(s)	452
BspCNI	CTCAG	1 cut(s)	316
BspFNI	CGCG	1 cut(s)	537
BspLI	GGNNCC	1 cut(s)	56
BspMAI	CTGCAG	1 cut(s)	471
BspT104I	TTCGAA	1 cut(s)	29
BsrI	ACTGG	2 cut(s)	362, 442
BssMI	GATC	1 cut(s)	304
Bst2UI	CCWGG	1 cut(s)	509
Bst4CI	ACNGT	2 cut(s)	54, 555
Bst6I	CTCTTC	1 cut(s)	281
BstBI	TTCGAA	1 cut(s)	29
BstC8I	GCNNGC	1 cut(s)	299
BstDEI	CTNAG	1 cut(s)	324
BstF5I	GGATG	2 cut(s)	368, 517
BstFNI	CGCG	1 cut(s)	537
BstHHI	GCGC	1 cut(s)	537
BstKTI	GATC	1 cut(s)	307
BstMAI	GTCTC	1 cut(s)	239
BstMBI	GATC	1 cut(s)	304
BstMWI	GCNNNNNNNGC	2 cut(s)	98, 426
BstNI	CCWGG	1 cut(s)	509
BstSCI	CCNGG	1 cut(s)	507
BstSFI	CTRYAG	1 cut(s)	467
BstUI	CGCG	1 cut(s)	537
BstV1I	GCAGC	2 cut(s)	78, 544
BstV2I	GAAGAC	2 cut(s)	398, 427
BstX2I	RGATCY	1 cut(s)	304
BstYI	RGATCY	1 cut(s)	304
BsuRI	GGCC	1 cut(s)	452
BtsCI	GGATG	2 cut(s)	368, 517
BtsIMutI	CAGTG	1 cut(s)	449
Cac8I	GCNNGC	1 cut(s)	299
CfoI	GCGC	1 cut(s)	537
Cfr13I	GGNCC	1 cut(s)	460
CviJI	RGCY	7 cut(s)	69, 92, 113, 267, 420, 441, 452
CviKI_1	RGCY	7 cut(s)	69, 92, 113, 267, 420, 441, 452
DdeI	CTNAG	1 cut(s)	324
DpnI	GATC	1 cut(s)	306
DpnII	GATC	1 cut(s)	304
DraIII	CACNNNGTG	1 cut(s)	209
Eam1104I	CTCTTC	1 cut(s)	281
EarI	CTCTTC	1 cut(s)	281
EciI	GGCGGA	1 cut(s)	265
Eco32I	GATATC	1 cut(s)	474
Eco47I	GGWCC	1 cut(s)	460
Eco57I	CTGAAG	1 cut(s)	421
EcoRI	GAATTC	2 cut(s)	73, 253
EcoRII	CCWGG	1 cut(s)	507
EcoRV	GATATC	1 cut(s)	474
FaiI	YATR	3 cut(s)	172, 223, 339
FaqI	GGGAC	1 cut(s)	529
Fnu4HI	GCNGC	2 cut(s)	67, 533
FokI	GGATG	2 cut(s)	355, 524
Fsp4HI	GCNGC	2 cut(s)	67, 533
FspBI	CTAG	1 cut(s)	48
GlaI	GCGC	1 cut(s)	536
GluI	GCNGC	2 cut(s)	67, 533
HaeIII	GGCC	1 cut(s)	452
HapII	CCGG	2 cut(s)	70, 275
HhaI	GCGC	1 cut(s)	537
Hin6I	GCGC	1 cut(s)	535
HinP1I	GCGC	1 cut(s)	535
HinfI	GANTC	6 cut(s)	4, 31, 328, 365, 517, 523
HpaII	CCGG	2 cut(s)	70, 275
HphI	GGTGA	2 cut(s)	23, 497
Hpy166II	GTNNAC	1 cut(s)	447
Hpy188I	TCNGA	4 cut(s)	36, 486, 522, 564
Hpy188III	TCNNGA	3 cut(s)	122, 176, 458
Hpy8I	GTNNAC	1 cut(s)	447
HpyAV	CCTTC	2 cut(s)	77, 114
HpyCH4III	ACNGT	2 cut(s)	54, 555
HpyCH4IV	ACGT	1 cut(s)	117
HpyCH4V	TGCA	3 cut(s)	194, 282, 469
HpyF10VI	GCNNNNNNNGC	2 cut(s)	98, 426
HpyF3I	CTNAG	1 cut(s)	324
HpySE526I	ACGT	1 cut(s)	117
HspAI	GCGC	1 cut(s)	535
Kzo9I	GATC	1 cut(s)	304
LmnI	GCTCC	1 cut(s)	106
Lsp1109I	GCAGC	2 cut(s)	78, 544
LweI	GCATC	2 cut(s)	88, 181
MaeI	CTAG	1 cut(s)	48
MaeII	ACGT	1 cut(s)	117
MaeIII	GTNAC	1 cut(s)	488
MalI	GATC	1 cut(s)	306
MboI	GATC	1 cut(s)	304
MboII	GAAGA	7 cut(s)	146, 200, 298, 374, 398, 427, 494
MflI	RGATCY	1 cut(s)	304
MhlI	GDGCHC	1 cut(s)	214
MluCI	AATT	3 cut(s)	73, 253, 309
MlyI	GAGTC	3 cut(s)	13, 337, 511
MnlI	CCTC	1 cut(s)	473
MroXI	GAANNNNTTC	1 cut(s)	405
MseI	TTAA	1 cut(s)	548
MslI	CAYNNNNRTG	1 cut(s)	510
MspI	CCGG	2 cut(s)	70, 275
MspR9I	CCNGG	1 cut(s)	509
MvaI	CCWGG	1 cut(s)	509
MvnI	CGCG	1 cut(s)	537
MwoI	GCNNNNNNNGC	2 cut(s)	98, 426
NdeII	GATC	1 cut(s)	304
NlaIV	GGNNCC	1 cut(s)	56
NspV	TTCGAA	1 cut(s)	29
PdmI	GAANNNNTTC	1 cut(s)	405
PfeI	GAWTC	3 cut(s)	31, 365, 523
PkrI	GCNGC	2 cut(s)	68, 534
PleI	GAGTC	3 cut(s)	12, 336, 511
PpsI	GAGTC	3 cut(s)	12, 336, 511
Psp6I	CCWGG	1 cut(s)	507
PspGI	CCWGG	1 cut(s)	507
PspN4I	GGNNCC	1 cut(s)	56
PspPI	GGNCC	1 cut(s)	460
PstI	CTGCAG	1 cut(s)	471
PsuI	RGATCY	1 cut(s)	304
RseI	CAYNNNNRTG	1 cut(s)	510
SaqAI	TTAA	1 cut(s)	548
SatI	GCNGC	2 cut(s)	67, 533
Sau3AI	GATC	1 cut(s)	304
Sau96I	GGNCC	1 cut(s)	460
SchI	GAGTC	3 cut(s)	13, 337, 511
ScrFI	CCNGG	1 cut(s)	509
SduI	GDGCHC	1 cut(s)	214
SetI	ASST	5 cut(s)	13, 120, 208, 465, 510
SfaNI	GCATC	2 cut(s)	88, 181
SfcI	CTRYAG	1 cut(s)	467
SfuI	TTCGAA	1 cut(s)	29
SinI	GGWCC	1 cut(s)	460
SmiMI	CAYNNNNRTG	1 cut(s)	510
Sse9I	AATT	3 cut(s)	73, 253, 309
SsiI	CCGC	1 cut(s)	250
SspI	AATATT	1 cut(s)	26
SspMI	CTAG	1 cut(s)	48
StyD4I	CCNGG	1 cut(s)	507
TaaI	ACNGT	2 cut(s)	54, 555
TaiI	ACGT	1 cut(s)	120
TaqI	TCGA	2 cut(s)	7, 29
TasI	AATT	3 cut(s)	73, 253, 309
TfiI	GAWTC	3 cut(s)	31, 365, 523
Tru1I	TTAA	1 cut(s)	548
Tru9I	TTAA	1 cut(s)	548
TscAI	CASTG	1 cut(s)	449
TseI	GCWGC	2 cut(s)	66, 532
TspRI	CASTG	1 cut(s)	449
VpaK11BI	GGWCC	1 cut(s)	460
XapI	RAATTY	2 cut(s)	73, 253
XmnI	GAANNNNTTC	1 cut(s)	405
XspI	CTAG	1 cut(s)	48

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