Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0012407

Physical Location & Seq

Genomic Coordinates Forward (+)

24226269 .. 24232510

Gene Structure 6242 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG147400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 996 bp

ATGGGCAAAGACGACGAGGAGATGCGGGGCGAGATTGAGGAGAGGCTAGTCAACGAGGAGTACAAGATATGGAAGAAGAACACTCCCTTTCTCTACGATCTGGTCATAACTCACGCCCTGGAGTGGCCGTCGCTCACCGTCGAGTGGCTGCCTGACCGGGAAGAGCCGCCGGGGAAGGACTACTCGGTGCAGAAGATGATATTGGGGACGCACACCTCGGAAAATGAGCCCAATTATCTTATGCTCGCGCAGGTCCAGCTGCCGTTGGAGGACGCGGAGAACGATGCTCGTAATTATGATGATGATCGTGCGGAGGCTGGAGGTTTCGGCTGCGCTAATGGCAAGGTGCAAATAATCCAGCAAATAAACCATGATGGAGAGGTTAATCGGGCTCGTTATATGCCTCAGAATCCATTTATTATTGCCACGAAAACTGTCAGTGCTGAAGTTTTTGTGTTTGATTATAGCAAACACCCATCTAAGCCTCCTTTAGATGGTGCATGCAGTCCTGATTTGAGGCTCAGGGGTCATAGCACTGAAGGATATGGTTTATCATGGAGTAAGTTCAAGCAGGGTCATTTACTCAGTGGTTCTGATGATGCGCAAATATGTTTGTGGGATATCAATGCAAATTCTAAGAACAAAACCCTGGAGGCTACTCAGATATTTAAGGTCCACGAAGGTGTTGTAGAAGATGTAGCATGGCATTTGAGGCATGAATATTTATTCGGTTCTGTTGGTGATGATCAATACCTTCTGGTATGGGATCTCCGGACCCCATCAGTTACCAAGCCTGTCCAATCTGTAGTTGCTCATCAAAGTGAGGTGAGTGATGTGAATATCCCTCTCCCCCTCTCCCCCTCTCCCTCTCATTTAGATGGACAGCATTGCTATAGATCAATGATGTTTATCCAATTACAGTTTAAAAGTCAATTGTGTAGATTCAGTTCTGTCATGAATTACTTATATTCTAACAATGGCATCTATATGTTCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000151 GO:0003006 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005677 GO:0005737 GO:0006139 GO:0006323 GO:0006325 GO:0006333 GO:0006338 GO:0006349 GO:0006725 GO:0006807 GO:0006996 GO:0007275 GO:0008150 GO:0008152 GO:0008283 GO:0009507 GO:0009536 GO:0009555 GO:0009790 GO:0009791 GO:0009793 GO:0009888 GO:0009909 GO:0009987 GO:0010026 GO:0010154 GO:0010214 GO:0010468 GO:0016043 GO:0017053 GO:0019219 GO:0019222 GO:0022414 GO:0022607 GO:0030154 GO:0031323 GO:0031461 GO:0031497 GO:0031507 GO:0031974 GO:0031981 GO:0032501 GO:0032502 GO:0032991 GO:0034641 GO:0040029 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044085 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045787 GO:0046483 GO:0048229 GO:0048316 GO:0048366 GO:0048367 GO:0048518 GO:0048522 GO:0048580 GO:0048608 GO:0048731 GO:0048827 GO:0048831 GO:0048856 GO:0048869 GO:0050789 GO:0050793 GO:0050794 GO:0051171 GO:0051239 GO:0051276 GO:0051726 GO:0060255 GO:0061458 GO:0065007 GO:0070013 GO:0070828 GO:0071103 GO:0071514 GO:0071704 GO:0071840 GO:0080008 GO:0080090 GO:0090558 GO:0090568 GO:0099402 GO:1901360 GO:1902494 GO:1990234 GO:2000026 GO:2000241 GO:2000653

KEGG Pathways

Metabolic & Signaling

ko04218 map04218

Pfam Domains

Protein Families

CAF1C_H4-bd WD40

Protein Analysis

331

Amino Acids

37.76

Weight (kDa)

5.09

Isoelectric Point (pI)

44.4

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CAF1C_H4-bd	PF12265	19 - 88	1.2e-31	Histone-binding protein RBBP4 or subunit C of CAF1 complex
Beta-prop_THOC3	PF25174	115 - 219	2.3e-06	THOC3 beta-propeller domain
Beta-prop_WDR3_1st	PF25173	123 - 281	9.9e-12	WDR3 first beta-propeller domain
WD40_CDC20-Fz	PF24807	126 - 267	1.5e-08	CDC20/Fizzy WD40 domain
Beta-prop_WDR5	PF25175	170 - 280	1.6e-10	WDR5 beta-propeller domain
Beta-prop_CAF1B_HIR1	PF24105	173 - 273	1.6e-09	CAF1B/HIR1 beta-propeller domain
WD40_Prp19	PF24814	177 - 268	3.5e-06	Prp19 WD40 domain
Beta-prop_THOC3	PF25174	178 - 273	4.8e-12	THOC3 beta-propeller domain
Beta-prop_TEP1_2nd	PF25047	191 - 273	7.9e-06	TEP-1 second beta-propeller

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)

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Orthologous Genes (Group: OG0012407)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G58230
fragaria_vesca	FvH4_7g08380 FvH4_7g08380
malus_domestica	MD02G1228600.v1.1 MD07G1083900.v1.1
prunus_persica	Prupe.2G110700_v2.0.a1
pyrus_communis	pycom02g19730 pycom07g06780
rosa_chinensis	RchiOBHm_Chr1g0340261
rosa_laevigata	RLG00000029008
rosa_multiflora	Rmu_sc0001836.1_g000007 Rmu_sc0005193.1_g000010
rosa_roxburghii	Rroxscaffold_4G00311130
rosa_rugosa	Rorug01G0164500.1
rosa_samantha	Rh1AG179200 Rh1BG147400 Rh1CG166100 Rh1DG179300
rosa_wichuraiana	Rw1G014930

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	603
Acc36I	ACCTGC	1 cut(s)	241
AccII	CGCG	2 cut(s)	248, 275
AccIII	TCCGGA	1 cut(s)	771
AciI	CCGC	4 cut(s)	25, 167, 275, 311
AclWI	GGATC	1 cut(s)	774
AcoI	YGGCCR	1 cut(s)	125
AcsI	RAATTY	1 cut(s)	631
AcuI	CTGAAG	2 cut(s)	465, 558
AfaI	GTAC	1 cut(s)	62
AfiI	CCNNNNNNNGG	3 cut(s)	123, 144, 494
AgsI	TTSAA	1 cut(s)	568
AjnI	CCWGG	2 cut(s)	117, 648
AjuI	GAANNNNNNNTTGG	2 cut(s)	185, 217
AleI	CACNNNNGTG	1 cut(s)	681
AluBI	AGCT	1 cut(s)	259
AluI	AGCT	1 cut(s)	259
AlwI	GGATC	1 cut(s)	774
Aor13HI	TCCGGA	1 cut(s)	771
AoxI	GGCC	1 cut(s)	125
ApeKI	GCWGC	3 cut(s)	148, 259, 330
ApoI	RAATTY	1 cut(s)	631
AspLEI	GCGC	3 cut(s)	250, 335, 604
AspS9I	GGNCC	3 cut(s)	253, 673, 774
AsuC2I	CCSGG	2 cut(s)	158, 171
AsuHPI	GGTGA	3 cut(s)	127, 752, 838
AvaII	GGWCC	3 cut(s)	253, 673, 774
BanII	GRGCYC	2 cut(s)	231, 394
BbvI	GCAGC	3 cut(s)	135, 246, 317
BccI	CCATC	5 cut(s)	368, 484, 488, 787, 872
BceAI	ACGGC	2 cut(s)	112, 247
BciT130I	CCWGG	2 cut(s)	119, 650
BclI	TGATCA	1 cut(s)	745
BcnI	CCSGG	2 cut(s)	158, 171
BfaI	CTAG	1 cut(s)	47
BfmI	CTRYAG	2 cut(s)	804, 892
BfuAI	ACCTGC	1 cut(s)	241
BisI	GCNGC	4 cut(s)	149, 167, 260, 331
BlsI	GCNGC	4 cut(s)	150, 168, 261, 332
Bme1390I	CCNGG	4 cut(s)	119, 158, 171, 650
Bme18I	GGWCC	3 cut(s)	253, 673, 774
BmgT120I	GGNCC	3 cut(s)	253, 673, 774
BmiI	GGNNCC	1 cut(s)	776
BmrFI	CCNGG	4 cut(s)	119, 158, 171, 650
BmsI	GCATC	4 cut(s)	12, 274, 589, 990
BpmI	CTGGAG	3 cut(s)	140, 339, 671
Bpu10I	CCTNAGC	1 cut(s)	521
BpuMI	CCSGG	2 cut(s)	158, 171
BsaBI	GATNNNNATC	2 cut(s)	303, 908
BsaJI	CCNNGG	4 cut(s)	117, 170, 216, 648
BsaWI	WCCGGW	1 cut(s)	771
BsaXI	ACNNNNNCTCC	2 cut(s)	113, 143
Bsc4I	CCNNNNNNNGG	3 cut(s)	123, 144, 494
Bse3DI	GCAATG	1 cut(s)	886
Bse8I	GATNNNNATC	2 cut(s)	303, 908
BseAI	TCCGGA	1 cut(s)	771
BseBI	CCWGG	2 cut(s)	119, 650
BseDI	CCNNGG	4 cut(s)	117, 170, 216, 648
BseJI	GATNNNNATC	2 cut(s)	303, 908
BseLI	CCNNNNNNNGG	3 cut(s)	123, 144, 494
BseMI	GCAATG	1 cut(s)	886
BseMII	CTCAG	4 cut(s)	419, 535, 598, 674
BseRI	GAGGAG	3 cut(s)	32, 53, 71
BseXI	GCAGC	3 cut(s)	135, 246, 317
BsgI	GTGCAG	1 cut(s)	209
Bsh1236I	CGCG	2 cut(s)	248, 275
BshFI	GGCC	1 cut(s)	127
BsiSI	CCGG	3 cut(s)	157, 170, 772
BslFI	GGGAC	1 cut(s)	220
BslI	CCNNNNNNNGG	3 cut(s)	123, 144, 494
BsmFI	GGGAC	1 cut(s)	220
BsnI	GGCC	1 cut(s)	127
Bsp1286I	GDGCHC	2 cut(s)	231, 394
Bsp13I	TCCGGA	1 cut(s)	771
Bsp143I	GATC	5 cut(s)	97, 304, 745, 766, 896
BspACI	CCGC	4 cut(s)	25, 167, 275, 311
BspANI	GGCC	1 cut(s)	127
BspCNI	CTCAG	4 cut(s)	418, 534, 597, 673
BspEI	TCCGGA	1 cut(s)	771
BspFNI	CGCG	2 cut(s)	248, 275
BspHI	TCATGA	1 cut(s)	954
BspLI	GGNNCC	1 cut(s)	776
BspMI	ACCTGC	1 cut(s)	241
BspPI	GGATC	1 cut(s)	774
BspQI	GCTCTTC	1 cut(s)	156
BsrDI	GCAATG	1 cut(s)	886
BssECI	CCNNGG	4 cut(s)	117, 170, 216, 648
BssMI	GATC	5 cut(s)	97, 304, 745, 766, 896
Bst2UI	CCWGG	2 cut(s)	119, 650
Bst4CI	ACNGT	3 cut(s)	139, 436, 921
Bst6I	CTCTTC	1 cut(s)	156
BstC8I	GCNNGC	2 cut(s)	246, 502
BstDEI	CTNAG	6 cut(s)	405, 480, 521, 584, 636, 660
BstFNI	CGCG	2 cut(s)	248, 275
BstHHI	GCGC	3 cut(s)	250, 335, 604
BstKTI	GATC	5 cut(s)	100, 307, 748, 769, 899
BstMBI	GATC	5 cut(s)	97, 304, 745, 766, 896
BstMWI	GCNNNNNNNGC	3 cut(s)	256, 339, 712
BstNI	CCWGG	2 cut(s)	119, 650
BstNSI	RCATGY	1 cut(s)	504
BstSCI	CCNGG	4 cut(s)	117, 156, 169, 648
BstSFI	CTRYAG	2 cut(s)	804, 892
BstUI	CGCG	2 cut(s)	248, 275
BstV1I	GCAGC	3 cut(s)	135, 246, 317
BstX2I	RGATCY	1 cut(s)	766
BstYI	RGATCY	1 cut(s)	766
BsuRI	GGCC	1 cut(s)	127
BtsIMutI	CAGTG	3 cut(s)	445, 534, 592
BveI	ACCTGC	1 cut(s)	241
Cac8I	GCNNGC	2 cut(s)	246, 502
CciI	TCATGA	1 cut(s)	954
CfoI	GCGC	3 cut(s)	250, 335, 604
Cfr13I	GGNCC	3 cut(s)	253, 673, 774
CseI	GACGC	2 cut(s)	217, 281
Csp6I	GTAC	1 cut(s)	61
CviAII	CATG	6 cut(s)	371, 501, 555, 702, 716, 955
CviQI	GTAC	1 cut(s)	61
DdeI	CTNAG	6 cut(s)	405, 480, 521, 584, 636, 660
DpnI	GATC	5 cut(s)	99, 306, 747, 768, 898
DpnII	GATC	5 cut(s)	97, 304, 745, 766, 896
DraI	TTTAAA	1 cut(s)	925
EaeI	YGGCCR	1 cut(s)	125
Eam1104I	CTCTTC	1 cut(s)	156
EarI	CTCTTC	1 cut(s)	156
Eco24I	GRGCYC	2 cut(s)	231, 394
Eco32I	GATATC	1 cut(s)	622
Eco47I	GGWCC	3 cut(s)	253, 673, 774
Eco57I	CTGAAG	2 cut(s)	465, 558
EcoRII	CCWGG	2 cut(s)	117, 648
EcoRV	GATATC	1 cut(s)	622
EcoT38I	GRGCYC	2 cut(s)	231, 394
FaeI	CATG	6 cut(s)	374, 504, 558, 705, 719, 958
FaqI	GGGAC	1 cut(s)	220
FatI	CATG	6 cut(s)	370, 500, 554, 701, 715, 954
FauI	CCCGC	1 cut(s)	18
FbaI	TGATCA	1 cut(s)	745
Fnu4HI	GCNGC	4 cut(s)	149, 167, 260, 331
FriOI	GRGCYC	2 cut(s)	231, 394
Fsp4HI	GCNGC	4 cut(s)	149, 167, 260, 331
FspBI	CTAG	1 cut(s)	47
FspI	TGCGCA	1 cut(s)	603
GlaI	GCGC	3 cut(s)	249, 334, 603
GluI	GCNGC	4 cut(s)	149, 167, 260, 331
GsuI	CTGGAG	3 cut(s)	140, 339, 671
HaeIII	GGCC	1 cut(s)	127
HapII	CCGG	3 cut(s)	157, 170, 772
HgaI	GACGC	2 cut(s)	217, 281
HhaI	GCGC	3 cut(s)	250, 335, 604
Hin1II	CATG	6 cut(s)	374, 504, 558, 705, 719, 958
Hin6I	GCGC	3 cut(s)	248, 333, 602
HinP1I	GCGC	3 cut(s)	248, 333, 602
HincII	GTYRAC	1 cut(s)	52
HindII	GTYRAC	1 cut(s)	52
HinfI	GANTC	2 cut(s)	409, 942
HpaII	CCGG	3 cut(s)	157, 170, 772
HphI	GGTGA	3 cut(s)	127, 752, 838
Hpy166II	GTNNAC	2 cut(s)	52, 676
Hpy188I	TCNGA	4 cut(s)	220, 408, 595, 663
Hpy188III	TCNNGA	3 cut(s)	509, 772, 955
Hpy8I	GTNNAC	2 cut(s)	52, 676
Hpy99I	CGWCG	3 cut(s)	17, 133, 143
HpyAV	CCTTC	4 cut(s)	169, 533, 674, 764
HpyCH4III	ACNGT	3 cut(s)	139, 436, 921
HpyCH4V	TGCA	5 cut(s)	190, 349, 500, 504, 629
HpyF10VI	GCNNNNNNNGC	3 cut(s)	256, 339, 712
HpyF3I	CTNAG	6 cut(s)	405, 480, 521, 584, 636, 660
Hsp92II	CATG	6 cut(s)	374, 504, 558, 705, 719, 958
HspAI	GCGC	3 cut(s)	248, 333, 602
Kpn2I	TCCGGA	1 cut(s)	771
Ksp22I	TGATCA	1 cut(s)	745
Kzo9I	GATC	5 cut(s)	97, 304, 745, 766, 896
LguI	GCTCTTC	1 cut(s)	156
Lsp1109I	GCAGC	3 cut(s)	135, 246, 317
LweI	GCATC	4 cut(s)	12, 274, 589, 990
MaeI	CTAG	1 cut(s)	47
MaeIII	GTNAC	1 cut(s)	784
MalI	GATC	5 cut(s)	99, 306, 747, 768, 898
MboI	GATC	5 cut(s)	97, 304, 745, 766, 896
MboII	GAAGA	5 cut(s)	85, 88, 173, 205, 704
MfeI	CAATTG	1 cut(s)	932
MflI	RGATCY	1 cut(s)	766
MhlI	GDGCHC	2 cut(s)	231, 394
MluCI	AATT	6 cut(s)	232, 292, 631, 914, 932, 958
MmeI	TCCRAC	1 cut(s)	246
MroI	TCCGGA	1 cut(s)	771
MseI	TTAA	3 cut(s)	384, 669, 924
MslI	CAYNNNNRTG	4 cut(s)	681, 819, 876, 986
MspA1I	CMGCKG	1 cut(s)	259
MspI	CCGG	3 cut(s)	157, 170, 772
MspR9I	CCNGG	4 cut(s)	119, 158, 171, 650
MunI	CAATTG	1 cut(s)	932
MvaI	CCWGG	2 cut(s)	119, 650
MvnI	CGCG	2 cut(s)	248, 275
MwoI	GCNNNNNNNGC	3 cut(s)	256, 339, 712
NciI	CCSGG	2 cut(s)	158, 171
NdeII	GATC	5 cut(s)	97, 304, 745, 766, 896
NlaIII	CATG	6 cut(s)	374, 504, 558, 705, 719, 958
NlaIV	GGNNCC	1 cut(s)	776
NsbI	TGCGCA	1 cut(s)	603
NspI	RCATGY	1 cut(s)	504
OliI	CACNNNNGTG	1 cut(s)	681
PaeI	GCATGC	1 cut(s)	504
PagI	TCATGA	1 cut(s)	954
PciSI	GCTCTTC	1 cut(s)	156
PcsI	WCGNNNNNNNCGW	1 cut(s)	279
PfeI	GAWTC	2 cut(s)	409, 942
PkrI	GCNGC	4 cut(s)	150, 168, 261, 332
Psp6I	CCWGG	2 cut(s)	117, 648
PspGI	CCWGG	2 cut(s)	117, 648
PspN4I	GGNNCC	1 cut(s)	776
PspPI	GGNCC	3 cut(s)	253, 673, 774
PsrI	GAACNNNNNNTAC	2 cut(s)	931, 963
PsuI	RGATCY	1 cut(s)	766
PvuII	CAGCTG	1 cut(s)	259
RsaI	GTAC	1 cut(s)	62
RsaNI	GTAC	1 cut(s)	61
RseI	CAYNNNNRTG	4 cut(s)	681, 819, 876, 986
SapI	GCTCTTC	1 cut(s)	156
SaqAI	TTAA	3 cut(s)	384, 669, 924
SatI	GCNGC	4 cut(s)	149, 167, 260, 331
Sau3AI	GATC	5 cut(s)	97, 304, 745, 766, 896
Sau96I	GGNCC	3 cut(s)	253, 673, 774
ScrFI	CCNGG	4 cut(s)	119, 158, 171, 650
SduI	GDGCHC	2 cut(s)	231, 394
SfaNI	GCATC	4 cut(s)	12, 274, 589, 990
SfcI	CTRYAG	2 cut(s)	804, 892
SinI	GGWCC	3 cut(s)	253, 673, 774
SmiMI	CAYNNNNRTG	4 cut(s)	681, 819, 876, 986
SphI	GCATGC	1 cut(s)	504
Sse9I	AATT	6 cut(s)	232, 292, 631, 914, 932, 958
SsiI	CCGC	4 cut(s)	25, 167, 275, 311
SspI	AATATT	1 cut(s)	722
SspMI	CTAG	1 cut(s)	47
StyD4I	CCNGG	4 cut(s)	117, 156, 169, 648
TaaI	ACNGT	3 cut(s)	139, 436, 921
TaqI	TCGA	1 cut(s)	141
TasI	AATT	6 cut(s)	232, 292, 631, 914, 932, 958
TatI	WGTACW	1 cut(s)	60
TauI	GCSGC	1 cut(s)	169
TfiI	GAWTC	2 cut(s)	409, 942
Tru1I	TTAA	3 cut(s)	384, 669, 924
Tru9I	TTAA	3 cut(s)	384, 669, 924
TscAI	CASTG	3 cut(s)	445, 541, 592
TseI	GCWGC	3 cut(s)	148, 259, 330
TspDTI	ATGAA	2 cut(s)	732, 971
TspRI	CASTG	3 cut(s)	445, 541, 592
VpaK11BI	GGWCC	3 cut(s)	253, 673, 774
XapI	RAATTY	1 cut(s)	631
XceI	RCATGY	1 cut(s)	504
XspI	CTAG	1 cut(s)	47

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