Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0002122

Physical Location & Seq

Genomic Coordinates Forward (+)

40063195 .. 40071991

Gene Structure 8797 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG157300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 960 bp

ATGGTGAGGATAAGACTAGGGAGAGGAAAGGAAGAACACCTTTGTCTGCCTCTTCTTGATTCTTGTTCCTCTCTTGCTAGCATGGCCGCCGAGTCCGCATTTGTCAGAAATGGCGGGAGCAGCAGCAGCGCCACTACTGCTGCCTTATTCGGCAGCTCAACGTGGAAACATTCCAAGAGAAAGACCCAGCAGTCTCTACACACTCACTGCGCCCATGACAAGAACAGGTTCTACAAACAACTGGGATTATTTTCATTGAAAAAGAAGATTGAAGATGCTGTTCTCCGAGCTGAGATGTTGGCCCCATTGGCACTGGAGCTTGAAGAAGAAAGACGGAATGAGCAGGAACAACTGATGCGCGACTATGACCTATGGGATGACACTGCTGAGTCCAATGAGGTTCTTGCTAAATTGGCTGATAGTGTTAGAGTGGTTGACGCTCTCAGAGACTTGACATATAAGGCTGAAGAAGCAAAACTTATTACACAGTTAGCAGAGATAGATGCTATCAATTATGGGCTTTTTAGGCAAGCATATGATGCATCTCTGGATATGAGCAAGATTTTGAATAAATATGAGATTTCCAAGCTTCTTAAGGGACCATATGACATGGAGGGAGCATGTCTAATTATAAAAGCTGGTGGCACAGGCTACCCTGAGGTTTGGGTAAAACAACTACTAAGCATGTATACCAAATGGGCCAGAAAGCTAGGTTACAAAGGGAGGGTAGTAGAGATGCATTCTTCCACGAATGGTGGCATCAAGTCAGCAACTATTGAGTTTGAACATGAGTTTGCTTTTGGTTATCTATCAGGAGAGGCAGGTGTGCACTACATCATAAATTCTGAAAACGGATCTGCTGTGCACGAGGTACAACTCTGTCTTGTTGATATCAATCCAATATTAAAGTTTTCAGAATTGCTCGTATTTTCTTTTCCTAAAAAAAGATGTCACTGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003677 GO:0003723 GO:0003729 GO:0003730 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006996 GO:0008150 GO:0009507 GO:0009532 GO:0009536 GO:0009570 GO:0009657 GO:0009658 GO:0009894 GO:0009987 GO:0010468 GO:0010608 GO:0016043 GO:0019219 GO:0019222 GO:0031323 GO:0031329 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043487 GO:0043488 GO:0043565 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0060255 GO:0061013 GO:0065007 GO:0065008 GO:0071840 GO:0080090 GO:0097159 GO:1901363 GO:1903311

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PCRF RF-1

Protein Analysis

319

Amino Acids

35.91

Weight (kDa)

6.8

Isoelectric Point (pI)

44.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PCRF	PF03462	110 - 278	1.7e-23	PCRF 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: OG0002122)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G57190
fragaria_vesca	FvH4_4g12020 FvH4_4g12020
prunus_persica	Prupe.7G049700_v2.0.a1 Prupe.7G049700_v2.0.a1 Prupe.7G049700_v2.0.a1
pyrus_communis	pycom12g07340
rosa_chinensis	RchiOBHm_Chr1g0343471 RchiOBHm_Chr2g0168541 RchiOBHm_Chr4g0409641 RchiOBHm_Chr5g0045081 RchiOBHm_Chr5g0071051 RchiOBHm_Chr6g0273161 RchiOBHm_Chr7g0240011
rosa_laevigata	RLG00000008537
rosa_multiflora	Rmu_sc0000652.1_g000001 Rmu_sc0002310.1_g000022 Rmu_sc0015305.1_g000010 Rmu_sc0015338.1_g000005 Rmu_sc0018973.1_g000001
rosa_roxburghii	Rroxscaffold_5G00354180
rosa_rugosa	Rorug04G0095700 Rorug04G0095800 Rorug05G0498600
rosa_samantha	Rh2BG617100 Rh2CG585200 Rh3DG274500 Rh4AG157300 Rh4BG156900 Rh4CG024300 Rh4CG167500 Rh4DG151200 Rh4DG161700 Rh5BG221000 Rh5BG274800 Rh5BG309900 Rh5CG332800 Rh5DG283000 Rh5DG320400
rosa_wichuraiana	Rw0G003500 Rw2G050080 Rw3G022130 Rw4G012870 Rw4G012980

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	632
AarI	CACCTGC	1 cut(s)	812
AasI	GACNNNNNNGTC	1 cut(s)	190
Acc36I	ACCTGC	1 cut(s)	812
AccI	GTMKAC	1 cut(s)	689
AccII	CGCG	1 cut(s)	360
AciI	CCGC	3 cut(s)	87, 96, 114
AclWI	GGATC	1 cut(s)	862
AcoI	YGGCCR	1 cut(s)	84
AcsI	RAATTY	1 cut(s)	841
AcuI	CTGAAG	1 cut(s)	486
AfaI	GTAC	1 cut(s)	873
AflII	CTTAAG	1 cut(s)	593
AgsI	TTSAA	5 cut(s)	259, 272, 323, 568, 785
AluBI	AGCT	6 cut(s)	156, 290, 319, 589, 638, 709
AluI	AGCT	6 cut(s)	156, 290, 319, 589, 638, 709
Alw21I	GWGCWC	2 cut(s)	831, 867
Alw26I	GTCTC	2 cut(s)	198, 441
Alw44I	GTGCAC	2 cut(s)	827, 863
AlwI	GGATC	1 cut(s)	862
AoxI	GGCC	3 cut(s)	84, 300, 699
ApaLI	GTGCAC	2 cut(s)	827, 863
ApeKI	GCWGC	5 cut(s)	120, 123, 126, 140, 153
ApoI	RAATTY	1 cut(s)	841
Asp700I	GAANNNNTTC	1 cut(s)	227
AspLEI	GCGC	3 cut(s)	131, 212, 360
AspS9I	GGNCC	3 cut(s)	301, 599, 699
AsuHPI	GGTGA	1 cut(s)	16
AsuNHI	GCTAGC	1 cut(s)	77
AvaII	GGWCC	1 cut(s)	599
AxyI	CCTNAGG	1 cut(s)	657
BaeGI	GKGCMC	2 cut(s)	831, 867
BauI	CACGAG	1 cut(s)	866
Bbv12I	GWGCWC	2 cut(s)	831, 867
BbvI	GCAGC	5 cut(s)	127, 132, 135, 138, 165
BcoDI	GTCTC	2 cut(s)	198, 441
BfaI	CTAG	3 cut(s)	17, 78, 710
BfoI	RGCGCY	1 cut(s)	132
BfrI	CTTAAG	1 cut(s)	593
BfuAI	ACCTGC	1 cut(s)	812
BglI	GCCNNNNNGGC	1 cut(s)	308
BisI	GCNGC	6 cut(s)	87, 121, 124, 127, 141, 154
BlsI	GCNGC	6 cut(s)	88, 122, 125, 128, 142, 155
Bme18I	GGWCC	1 cut(s)	599
BmgT120I	GGNCC	3 cut(s)	301, 599, 699
BmiI	GGNNCC	2 cut(s)	303, 600
BmrI	ACTGGG	1 cut(s)	251
BmsI	GCATC	7 cut(s)	265, 345, 493, 529, 551, 726, 768
BmtI	GCTAGC	1 cut(s)	81
BmuI	ACTGGG	1 cut(s)	251
BpmI	CTGGAG	1 cut(s)	335
BsaBI	GATNNNNATC	1 cut(s)	894
Bse1I	ACTGG	3 cut(s)	246, 318, 959
Bse21I	CCTNAGG	1 cut(s)	657
Bse8I	GATNNNNATC	1 cut(s)	894
BseGI	GGATG	1 cut(s)	382
BseJI	GATNNNNATC	1 cut(s)	894
BseMII	CTCAG	4 cut(s)	282, 378, 457, 648
BseNI	ACTGG	3 cut(s)	246, 318, 959
BseSI	GKGCMC	2 cut(s)	831, 867
BseXI	GCAGC	5 cut(s)	127, 132, 135, 138, 165
BseYI	CCCAGC	1 cut(s)	186
Bsh1236I	CGCG	1 cut(s)	360
BshFI	GGCC	3 cut(s)	86, 302, 701
BsiHKAI	GWGCWC	2 cut(s)	831, 867
BslFI	GGGAC	1 cut(s)	612
BsmAI	GTCTC	2 cut(s)	198, 441
BsmFI	GGGAC	1 cut(s)	612
BsmI	GAATGC	1 cut(s)	739
BsnI	GGCC	3 cut(s)	86, 302, 701
Bsp1286I	GDGCHC	2 cut(s)	831, 867
Bsp143I	GATC	1 cut(s)	854
BspACI	CCGC	3 cut(s)	87, 96, 114
BspANI	GGCC	3 cut(s)	86, 302, 701
BspCNI	CTCAG	4 cut(s)	283, 379, 456, 649
BspFNI	CGCG	1 cut(s)	360
BspLI	GGNNCC	2 cut(s)	303, 600
BspMI	ACCTGC	1 cut(s)	812
BspOI	GCTAGC	1 cut(s)	81
BspPI	GGATC	1 cut(s)	862
BspTI	CTTAAG	1 cut(s)	593
BsrI	ACTGG	3 cut(s)	246, 318, 959
BssMI	GATC	1 cut(s)	854
BssNAI	GTATAC	1 cut(s)	690
BssSI	CACGAG	1 cut(s)	866
Bst1107I	GTATAC	1 cut(s)	690
Bst2BI	CACGAG	1 cut(s)	866
Bst4CI	ACNGT	1 cut(s)	489
Bst6I	CTCTTC	1 cut(s)	57
BstAFI	CTTAAG	1 cut(s)	593
BstAPI	GCANNNNNTGC	1 cut(s)	539
BstC8I	GCNNGC	2 cut(s)	79, 531
BstDEI	CTNAG	5 cut(s)	291, 387, 443, 657, 680
BstF5I	GGATG	1 cut(s)	382
BstFNI	CGCG	1 cut(s)	360
BstH2I	RGCGCY	1 cut(s)	132
BstHHI	GCGC	3 cut(s)	131, 212, 360
BstKTI	GATC	1 cut(s)	857
BstMAI	GTCTC	2 cut(s)	198, 441
BstMBI	GATC	1 cut(s)	854
BstNSI	RCATGY	2 cut(s)	624, 688
BstSLI	GKGCMC	2 cut(s)	831, 867
BstUI	CGCG	1 cut(s)	360
BstV1I	GCAGC	5 cut(s)	127, 132, 135, 138, 165
BstX2I	RGATCY	1 cut(s)	854
BstYI	RGATCY	1 cut(s)	854
BstZ17I	GTATAC	1 cut(s)	690
Bsu36I	CCTNAGG	1 cut(s)	657
BsuRI	GGCC	3 cut(s)	86, 302, 701
BtsCI	GGATG	1 cut(s)	382
BtsI	GCAGTG	2 cut(s)	205, 381
BtsIMutI	CAGTG	4 cut(s)	205, 311, 381, 952
BveI	ACCTGC	1 cut(s)	812
Cac8I	GCNNGC	2 cut(s)	79, 531
CfoI	GCGC	3 cut(s)	131, 212, 360
Cfr13I	GGNCC	3 cut(s)	301, 599, 699
CseI	GACGC	1 cut(s)	446
Csp6I	GTAC	1 cut(s)	872
CviAII	CATG	6 cut(s)	82, 215, 610, 621, 685, 788
CviQI	GTAC	1 cut(s)	872
DdeI	CTNAG	5 cut(s)	291, 387, 443, 657, 680
DpnI	GATC	1 cut(s)	856
DpnII	GATC	1 cut(s)	854
DrdI	GACNNNNNNGTC	1 cut(s)	190
DseDI	GACNNNNNNGTC	1 cut(s)	190
EaeI	YGGCCR	1 cut(s)	84
Eam1104I	CTCTTC	1 cut(s)	57
EarI	CTCTTC	1 cut(s)	57
Eco32I	GATATC	1 cut(s)	892
Eco47I	GGWCC	1 cut(s)	599
Eco57I	CTGAAG	1 cut(s)	486
Eco81I	CCTNAGG	1 cut(s)	657
EcoRV	GATATC	1 cut(s)	892
EcoT22I	ATGCAT	2 cut(s)	544, 741
FaeI	CATG	6 cut(s)	85, 218, 613, 624, 688, 791
FalI	AAGNNNNNCTT	4 cut(s)	24, 56, 462, 494
FaqI	GGGAC	1 cut(s)	612
FatI	CATG	6 cut(s)	81, 214, 609, 620, 684, 787
FauI	CCCGC	1 cut(s)	107
FauNDI	CATATG	2 cut(s)	535, 604
FblI	GTMKAC	1 cut(s)	689
Fnu4HI	GCNGC	6 cut(s)	87, 121, 124, 127, 141, 154
FokI	GGATG	1 cut(s)	389
Fsp4HI	GCNGC	6 cut(s)	87, 121, 124, 127, 141, 154
FspBI	CTAG	3 cut(s)	17, 78, 710
GlaI	GCGC	3 cut(s)	130, 211, 359
GluI	GCNGC	6 cut(s)	87, 121, 124, 127, 141, 154
GsaI	CCCAGC	1 cut(s)	190
GsuI	CTGGAG	1 cut(s)	335
HaeII	RGCGCY	1 cut(s)	132
HaeIII	GGCC	3 cut(s)	86, 302, 701
HgaI	GACGC	1 cut(s)	446
HhaI	GCGC	3 cut(s)	131, 212, 360
Hin1II	CATG	6 cut(s)	85, 218, 613, 624, 688, 791
Hin6I	GCGC	3 cut(s)	129, 210, 358
HinP1I	GCGC	3 cut(s)	129, 210, 358
HincII	GTYRAC	1 cut(s)	436
HindII	GTYRAC	1 cut(s)	436
HindIII	AAGCTT	1 cut(s)	587
HinfI	GANTC	3 cut(s)	59, 92, 389
HphI	GGTGA	1 cut(s)	16
Hpy166II	GTNNAC	4 cut(s)	436, 690, 829, 865
Hpy188I	TCNGA	5 cut(s)	107, 287, 446, 847, 916
Hpy188III	TCNNGA	3 cut(s)	56, 548, 813
Hpy8I	GTNNAC	4 cut(s)	436, 690, 829, 865
HpyCH4III	ACNGT	1 cut(s)	489
HpyCH4IV	ACGT	1 cut(s)	161
HpyCH4V	TGCA	4 cut(s)	542, 739, 829, 865
HpyF3I	CTNAG	5 cut(s)	291, 387, 443, 657, 680
HpySE526I	ACGT	1 cut(s)	161
Hsp92II	CATG	6 cut(s)	85, 218, 613, 624, 688, 791
HspAI	GCGC	3 cut(s)	129, 210, 358
Kzo9I	GATC	1 cut(s)	854
LmnI	GCTCC	3 cut(s)	117, 316, 617
Lsp1109I	GCAGC	5 cut(s)	127, 132, 135, 138, 165
LweI	GCATC	7 cut(s)	265, 345, 493, 529, 551, 726, 768
MaeI	CTAG	3 cut(s)	17, 78, 710
MaeII	ACGT	1 cut(s)	161
MaeIII	GTNAC	2 cut(s)	713, 950
MalI	GATC	1 cut(s)	856
MboI	GATC	1 cut(s)	854
MboII	GAAGA	8 cut(s)	44, 44, 277, 284, 335, 338, 479, 735
MflI	RGATCY	1 cut(s)	854
MhlI	GDGCHC	2 cut(s)	831, 867
MluCI	AATT	5 cut(s)	410, 511, 627, 841, 917
MlyI	GAGTC	2 cut(s)	101, 398
MnlI	CCTC	9 cut(s)	17, 60, 79, 391, 607, 652, 717, 811, 862
Mph1103I	ATGCAT	2 cut(s)	544, 741
MroXI	GAANNNNTTC	1 cut(s)	227
MseI	TTAA	2 cut(s)	594, 905
MspCI	CTTAAG	1 cut(s)	593
Mva1269I	GAATGC	1 cut(s)	739
MvnI	CGCG	1 cut(s)	360
NdeI	CATATG	2 cut(s)	535, 604
NdeII	GATC	1 cut(s)	854
NheI	GCTAGC	1 cut(s)	77
NlaIII	CATG	6 cut(s)	85, 218, 613, 624, 688, 791
NlaIV	GGNNCC	2 cut(s)	303, 600
NmeAIII	GCCGAG	1 cut(s)	115
NmuCI	GTSAC	1 cut(s)	950
NsiI	ATGCAT	2 cut(s)	544, 741
NspI	RCATGY	2 cut(s)	624, 688
PaqCI	CACCTGC	1 cut(s)	812
PctI	GAATGC	1 cut(s)	739
PdmI	GAANNNNTTC	1 cut(s)	227
PfeI	GAWTC	1 cut(s)	59
PkrI	GCNGC	6 cut(s)	88, 122, 125, 128, 142, 155
PleI	GAGTC	2 cut(s)	100, 397
PpsI	GAGTC	2 cut(s)	100, 397
PsiI	TTATAA	1 cut(s)	632
PspFI	CCCAGC	1 cut(s)	186
PspN4I	GGNNCC	2 cut(s)	303, 600
PspPI	GGNCC	3 cut(s)	301, 599, 699
PsrI	GAACNNNNNNTAC	2 cut(s)	215, 247
PsuI	RGATCY	1 cut(s)	854
RsaI	GTAC	1 cut(s)	873
RsaNI	GTAC	1 cut(s)	872
SaqAI	TTAA	2 cut(s)	594, 905
SatI	GCNGC	6 cut(s)	87, 121, 124, 127, 141, 154
Sau3AI	GATC	1 cut(s)	854
Sau96I	GGNCC	3 cut(s)	301, 599, 699
SchI	GAGTC	2 cut(s)	101, 398
SduI	GDGCHC	2 cut(s)	831, 867
SfaNI	GCATC	7 cut(s)	265, 345, 493, 529, 551, 726, 768
SinI	GGWCC	1 cut(s)	599
SmlI	CTYRAG	1 cut(s)	593
SmoI	CTYRAG	1 cut(s)	593
Sse9I	AATT	5 cut(s)	410, 511, 627, 841, 917
SsiI	CCGC	3 cut(s)	87, 96, 114
SspI	AATATT	1 cut(s)	903
SspMI	CTAG	3 cut(s)	17, 78, 710
TaaI	ACNGT	1 cut(s)	489
TaiI	ACGT	1 cut(s)	164
TasI	AATT	5 cut(s)	410, 511, 627, 841, 917
TauI	GCSGC	1 cut(s)	89
TfiI	GAWTC	1 cut(s)	59
Tru1I	TTAA	2 cut(s)	594, 905
Tru9I	TTAA	2 cut(s)	594, 905
TscAI	CASTG	4 cut(s)	212, 318, 388, 959
TseFI	GTSAC	1 cut(s)	950
TseI	GCWGC	5 cut(s)	120, 123, 126, 140, 153
Tsp45I	GTSAC	1 cut(s)	950
TspDTI	ATGAA	1 cut(s)	243
TspGWI	ACGGA	2 cut(s)	349, 867
TspRI	CASTG	4 cut(s)	212, 318, 388, 959
Vha464I	CTTAAG	1 cut(s)	593
VneI	GTGCAC	2 cut(s)	827, 863
VpaK11BI	GGWCC	1 cut(s)	599
XapI	RAATTY	1 cut(s)	841
XceI	RCATGY	2 cut(s)	624, 688
XmiI	GTMKAC	1 cut(s)	689
XmnI	GAANNNNTTC	1 cut(s)	227
XspI	CTAG	3 cut(s)	17, 78, 710
Zsp2I	ATGCAT	2 cut(s)	544, 741

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