Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0003822

Physical Location & Seq

Genomic Coordinates Reverse (-)

15931244 .. 15932016

Gene Structure 773 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG088800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 408 bp

ATGATCCAGCTGACATTAATCAACACGGGAGCTGGCTCTGGGCCATTGAGAACATTGCTCATGATCAGCCACCTCCCGGCTGACAACGGCCACTCACGATTCAAGGTGCAGGAAGCACCAAGTTTGAGTGCCAACATTTATTATCAAGCTCCGTTGGGCAAGAGACTTCGATCCATGGTGGAAGTCCAAAAGTATTTGATTGAACATCCTGAGTATATGGTGGATGGTCTATCTATGGTGGCACAATTTTCATTTCAAATTCCAAAGCCTGTACAGGAGAAATATGTGAGGAAACGCCCTACGGCTCCTCGGTTGACAGCAGCTGCCCATGCCAGTAGAACTCTTGAACCTACTGAAGATCATTCGCTGTGTATGTCATACGAGTGCCAATCTGCCATGCTTTTCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000166 GO:0003674 GO:0003676 GO:0003677 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0008327 GO:0019899 GO:0036094 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043565 GO:0044424 GO:0044464 GO:0097159 GO:1901265 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

MBD zf-CW

Protein Analysis

135

Amino Acids

15.15

Weight (kDa)

8.98

Isoelectric Point (pI)

54.89

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
MBD	PF01429	43 - 73	7.2e-07	Methyl-CpG binding domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0003822)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G35330 AT5G35330 AT5G35330 AT5G35330
fragaria_vesca	FvH4_4g06240 FvH4_4g06240 FvH4_4g06240 FvH4_4g06240 FvH4_4g06240
malus_domestica	MD13G1234700.v1.1 MD16G1239500.v1.1
prunus_persica	Prupe.1G065600_v2.0.a1 Prupe.1G065600_v2.0.a1
pyrus_communis	pycom16g20040
rosa_chinensis	RchiOBHm_Chr4g0397961
rosa_laevigata	RLG00000009392
rosa_multiflora	Rmu_co8227835.1_g000001 Rmu_co8419633.1_g000001 Rmu_sc0001074.1_g000002 Rmu_sc0001074.1_g000005 Rmu_sc0003773.1_g000027
rosa_roxburghii	Rroxscaffold_5G00342870 Rroxscaffold_5G00342930
rosa_rugosa	Rorug04G0004900 Rorug04G0005000
rosa_samantha	Rh4AG081200 Rh4AG081600 Rh4BG079200 Rh4CG088800 Rh4CG089100 Rh4DG074700
rosa_wichuraiana	Rw0G019360 Rw4G006770 Rw4G006790

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AclWI	GGATC	1 cut(s)	165
AcoI	YGGCCR	1 cut(s)	88
AcsI	RAATTY	1 cut(s)	258
AcuI	CTGAAG	1 cut(s)	375
AfaI	GTAC	1 cut(s)	273
AfiI	CCNNNNNNNGG	1 cut(s)	76
AgsI	TTSAA	4 cut(s)	103, 203, 257, 347
AluBI	AGCT	4 cut(s)	10, 32, 149, 323
AluI	AGCT	4 cut(s)	10, 32, 149, 323
Alw26I	GTCTC	1 cut(s)	157
AlwI	GGATC	1 cut(s)	165
AlwNI	CAGNNNCTG	1 cut(s)	323
AoxI	GGCC	2 cut(s)	41, 88
ApeKI	GCWGC	2 cut(s)	320, 323
ApoI	RAATTY	1 cut(s)	258
AseI	ATTAAT	1 cut(s)	17
AspS9I	GGNCC	1 cut(s)	41
AsuC2I	CCSGG	1 cut(s)	77
BbvI	GCAGC	2 cut(s)	310, 332
BccI	CCATC	1 cut(s)	218
BceAI	ACGGC	2 cut(s)	103, 318
BclI	TGATCA	1 cut(s)	63
BcnI	CCSGG	1 cut(s)	77
BcoDI	GTCTC	1 cut(s)	157
BisI	GCNGC	2 cut(s)	321, 324
BlsI	GCNGC	2 cut(s)	322, 325
Bme1390I	CCNGG	1 cut(s)	77
BmgT120I	GGNCC	1 cut(s)	41
BmiI	GGNNCC	1 cut(s)	306
BmrFI	CCNGG	1 cut(s)	77
BpuMI	CCSGG	1 cut(s)	77
BsaJI	CCNNGG	2 cut(s)	174, 308
Bsc4I	CCNNNNNNNGG	1 cut(s)	76
Bse1I	ACTGG	1 cut(s)	333
Bse3DI	GCAATG	1 cut(s)	53
BseDI	CCNNGG	2 cut(s)	174, 308
BseGI	GGATG	2 cut(s)	205, 229
BseLI	CCNNNNNNNGG	1 cut(s)	76
BseMI	GCAATG	1 cut(s)	53
BseMII	CTCAG	1 cut(s)	201
BseNI	ACTGG	1 cut(s)	333
BseRI	GAGGAG	1 cut(s)	297
BseXI	GCAGC	2 cut(s)	310, 332
BsgI	GTGCAG	1 cut(s)	128
BshFI	GGCC	2 cut(s)	43, 90
BsiSI	CCGG	1 cut(s)	77
BslI	CCNNNNNNNGG	1 cut(s)	76
BsmAI	GTCTC	1 cut(s)	157
BsnI	GGCC	2 cut(s)	43, 90
Bsp1407I	TGTACA	1 cut(s)	271
Bsp143I	GATC	4 cut(s)	3, 63, 170, 358
Bsp19I	CCATGG	1 cut(s)	174
BspANI	GGCC	2 cut(s)	43, 90
BspCNI	CTCAG	1 cut(s)	202
BspHI	TCATGA	1 cut(s)	60
BspLI	GGNNCC	1 cut(s)	306
BspPI	GGATC	1 cut(s)	165
BsrDI	GCAATG	1 cut(s)	53
BsrGI	TGTACA	1 cut(s)	271
BsrI	ACTGG	1 cut(s)	333
BssECI	CCNNGG	2 cut(s)	174, 308
BssMI	GATC	4 cut(s)	3, 63, 170, 358
BssT1I	CCWWGG	1 cut(s)	174
BstAUI	TGTACA	1 cut(s)	271
BstC8I	GCNNGC	1 cut(s)	34
BstDEI	CTNAG	1 cut(s)	210
BstDSI	CCRYGG	1 cut(s)	174
BstF5I	GGATG	2 cut(s)	205, 229
BstKTI	GATC	4 cut(s)	6, 66, 173, 361
BstMAI	GTCTC	1 cut(s)	157
BstMBI	GATC	4 cut(s)	3, 63, 170, 358
BstMWI	GCNNNNNNNGC	1 cut(s)	329
BstSCI	CCNGG	1 cut(s)	75
BstV1I	GCAGC	2 cut(s)	310, 332
BsuRI	GGCC	2 cut(s)	43, 90
BtgI	CCRYGG	1 cut(s)	174
BtsCI	GGATG	2 cut(s)	205, 229
Cac8I	GCNNGC	1 cut(s)	34
CaiI	CAGNNNCTG	1 cut(s)	323
CciI	TCATGA	1 cut(s)	60
Cfr13I	GGNCC	1 cut(s)	41
Csp6I	GTAC	1 cut(s)	272
CviAII	CATG	4 cut(s)	61, 175, 329, 397
CviQI	GTAC	1 cut(s)	272
DdeI	CTNAG	1 cut(s)	210
DpnI	GATC	4 cut(s)	5, 65, 172, 360
DpnII	GATC	4 cut(s)	3, 63, 170, 358
EaeI	YGGCCR	1 cut(s)	88
Eco130I	CCWWGG	1 cut(s)	174
Eco57I	CTGAAG	1 cut(s)	375
EcoT14I	CCWWGG	1 cut(s)	174
ErhI	CCWWGG	1 cut(s)	174
FaeI	CATG	4 cut(s)	64, 178, 332, 400
FatI	CATG	4 cut(s)	60, 174, 328, 396
FbaI	TGATCA	1 cut(s)	63
Fnu4HI	GCNGC	2 cut(s)	321, 324
FokI	GGATG	2 cut(s)	192, 236
Fsp4HI	GCNGC	2 cut(s)	321, 324
GluI	GCNGC	2 cut(s)	321, 324
HaeIII	GGCC	2 cut(s)	43, 90
HapII	CCGG	1 cut(s)	77
Hin1II	CATG	4 cut(s)	64, 178, 332, 400
HincII	GTYRAC	1 cut(s)	315
HindII	GTYRAC	1 cut(s)	315
HinfI	GANTC	1 cut(s)	99
HpaII	CCGG	1 cut(s)	77
Hpy166II	GTNNAC	1 cut(s)	315
Hpy188I	TCNGA	1 cut(s)	407
Hpy188III	TCNNGA	4 cut(s)	61, 96, 209, 344
Hpy8I	GTNNAC	1 cut(s)	315
HpyCH4V	TGCA	1 cut(s)	109
HpyF10VI	GCNNNNNNNGC	1 cut(s)	329
HpyF3I	CTNAG	1 cut(s)	210
Hsp92II	CATG	4 cut(s)	64, 178, 332, 400
Ksp22I	TGATCA	1 cut(s)	63
Kzo9I	GATC	4 cut(s)	3, 63, 170, 358
LmnI	GCTCC	3 cut(s)	29, 154, 310
LpnPI	CCDG	9 cut(s)	18, 20, 24, 90, 95, 222, 260, 282, 346
Lsp1109I	GCAGC	2 cut(s)	310, 332
MalI	GATC	4 cut(s)	5, 65, 172, 360
MboI	GATC	4 cut(s)	3, 63, 170, 358
MboII	GAAGA	1 cut(s)	368
MluCI	AATT	2 cut(s)	245, 258
MnlI	CCTC	3 cut(s)	83, 282, 318
MseI	TTAA	1 cut(s)	17
MslI	CAYNNNNRTG	1 cut(s)	382
MspA1I	CMGCKG	2 cut(s)	10, 323
MspI	CCGG	1 cut(s)	77
MspR9I	CCNGG	1 cut(s)	77
MwoI	GCNNNNNNNGC	1 cut(s)	329
NciI	CCSGG	1 cut(s)	77
NcoI	CCATGG	1 cut(s)	174
NdeII	GATC	4 cut(s)	3, 63, 170, 358
NlaIII	CATG	4 cut(s)	64, 178, 332, 400
NlaIV	GGNNCC	1 cut(s)	306
PagI	TCATGA	1 cut(s)	60
PfeI	GAWTC	1 cut(s)	99
PkrI	GCNGC	2 cut(s)	322, 325
PshBI	ATTAAT	1 cut(s)	17
PspN4I	GGNNCC	1 cut(s)	306
PspPI	GGNCC	1 cut(s)	41
PstNI	CAGNNNCTG	1 cut(s)	323
PvuII	CAGCTG	2 cut(s)	10, 323
RsaI	GTAC	1 cut(s)	273
RsaNI	GTAC	1 cut(s)	272
RseI	CAYNNNNRTG	1 cut(s)	382
SaqAI	TTAA	1 cut(s)	17
SatI	GCNGC	2 cut(s)	321, 324
Sau3AI	GATC	4 cut(s)	3, 63, 170, 358
Sau96I	GGNCC	1 cut(s)	41
ScrFI	CCNGG	1 cut(s)	77
SetI	ASST	7 cut(s)	12, 34, 75, 108, 151, 325, 352
SmiMI	CAYNNNNRTG	1 cut(s)	382
Sse9I	AATT	2 cut(s)	245, 258
StyD4I	CCNGG	1 cut(s)	75
StyI	CCWWGG	1 cut(s)	174
TaqI	TCGA	1 cut(s)	169
TasI	AATT	2 cut(s)	245, 258
TatI	WGTACW	1 cut(s)	271
TfiI	GAWTC	1 cut(s)	99
Tru1I	TTAA	1 cut(s)	17
Tru9I	TTAA	1 cut(s)	17
TseI	GCWGC	2 cut(s)	320, 323
TspDTI	ATGAA	1 cut(s)	240
TspGWI	ACGGA	1 cut(s)	141
VspI	ATTAAT	1 cut(s)	17
XapI	RAATTY	1 cut(s)	258

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