Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0001238

Physical Location & Seq

Genomic Coordinates Reverse (-)

70508726 .. 70509719

Gene Structure 994 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG402600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 579 bp

ATGGCCACCGAGGAGTCCAACGAGCAACCGCCACCGTCGCCGGCACCGCCTAATCCGGCTCCGTCCCTCCCTGAGTACCCAAAGATGATTATGGCGGCGATTGAGGCGCTTAATGAGAGCGAGGGGTCGAACAAGACCTCAATCGCGCAGCAAATCGAGTCCACCTACGGCGATCTGCCTCCGGCTCACGCCACGCTTCTGGCGCACCACCTCAACAAGATGAAGCAGAGCGGCGAGCTCGTTTTCGTCAAGAACAACTACATGAAGCCCGACCCCAACGCGCCGCCCAAGCGGGGCCGTGGCCGCCCGCCCAAGCCCAAGGTCCCGGCGCCGGAAGGAGCAGCCGTGGTCTCCTCGCCTCCGAGGCCACGTGGCAGACCTCCCAAGCCTAGGGATCCGTTTTTCCCGCTCCCAATTGCCAAGAGCTCGACATCAACCGGGTCCGGCAGGCCACGTGGCCGCCCTCCGAAGAAGGCCAAGACAAGTCCGACCTCGACTCCGGCTCCGGCGAGTGGTGCCCCTAGAGGTAGAGGCAGGCCACCGAAAGTCAAGCCCTCCGTAGCTCCGGTGGGTTGCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003677 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005730 GO:0031974 GO:0031981 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0070013 GO:0097159 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

AT_hook Linker_histone

Protein Analysis

192

Amino Acids

20.21

Weight (kDa)

10.41

Isoelectric Point (pI)

77.95

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Linker_histone	PF00538	24 - 85	5.1e-09	linker histone H1 and H5 family

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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0001238)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G14900
fragaria_vesca	FvH4_1g28760 FvH4_3g22350 FvH4_4g10240 FvH4_4g16250 FvH4_4g34011 FvH4_4g34030 FvH4_5g06490
malus_domestica	MD09G1263200.v1.1 MD13G1021100.v1.1 MD16G1022400.v1.1 MD17G1258400.v1.1
prunus_persica	Prupe.1G330600_v2.0.a1 Prupe.3G161100_v2.0.a1
pyrus_communis	pycom09g17750 pycom13g02000 pycom16g01970 pycom17g26030
rosa_chinensis	RchiOBHm_Chr3g0493151 RchiOBHm_Chr4g0443521
rosa_laevigata	RLG00000005921 RLG00000022725
rosa_multiflora	Rmu_sc0004094.1_g000037 Rmu_sc0009488.1_g000002 Rmu_sc0009954.1_g000002
rosa_roxburghii	Rroxscaffold_1G00033110 Rroxscaffold_5G00353160 Rroxscaffold_5G00384060 Rroxscaffold_6G00391770
rosa_rugosa	Rorug03G0259500 Rorug04G0347000
rosa_samantha	Rh2BG493600 Rh2BG493700 Rh2DG502600 Rh2DG502700 Rh3AG308500 Rh3BG344600 Rh3CG341800 Rh3DG343900 Rh4AG402600 Rh4BG208400 Rh4BG414100 Rh4CG429900 Rh4DG241300 Rh4DG409800 Rh4DG411100 Rh5BG528400 Rh5CG552800 Rh5DG132000 Rh5DG289700 Rh6CG100400
rosa_wichuraiana	Rw0G017400 Rw3G027130 Rw4G007110 Rw4G007140 Rw4G034710

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	3 cut(s)	43, 328, 515
AccBSI	CCGCTC	2 cut(s)	231, 409
AccII	CGCG	2 cut(s)	146, 281
AclWI	GGATC	2 cut(s)	389, 402
AcoI	YGGCCR	3 cut(s)	3, 301, 457
AcvI	CACGTG	2 cut(s)	371, 455
AcyI	GRCGYC	1 cut(s)	329
AfaI	GTAC	1 cut(s)	77
AfiI	CCNNNNNNNGG	4 cut(s)	293, 331, 390, 512
AluBI	AGCT	3 cut(s)	238, 426, 563
AluI	AGCT	3 cut(s)	238, 426, 563
Alw21I	GWGCWC	2 cut(s)	240, 428
Alw26I	GTCTC	1 cut(s)	355
AlwI	GGATC	2 cut(s)	389, 402
AoxI	GGCC	8 cut(s)	3, 295, 301, 365, 449, 457, 474, 536
ApeKI	GCWGC	2 cut(s)	148, 341
AspA2I	CCTAGG	1 cut(s)	389
AspLEI	GCGC	5 cut(s)	109, 148, 205, 283, 331
AspS9I	GGNCC	3 cut(s)	295, 322, 441
AsuC2I	CCSGG	2 cut(s)	326, 439
AvaII	GGWCC	2 cut(s)	322, 441
AvrII	CCTAGG	1 cut(s)	389
BaeGI	GKGCMC	1 cut(s)	520
BalI	TGGCCA	1 cut(s)	5
BamHI	GGATCC	1 cut(s)	394
BanI	GGYRCC	3 cut(s)	43, 328, 515
BanII	GRGCYC	2 cut(s)	240, 428
BbrPI	CACGTG	2 cut(s)	371, 455
Bbv12I	GWGCWC	2 cut(s)	240, 428
BbvI	GCAGC	2 cut(s)	160, 353
BceAI	ACGGC	3 cut(s)	184, 282, 329
BcnI	CCSGG	2 cut(s)	326, 439
BcoDI	GTCTC	1 cut(s)	355
BfaI	CTAG	2 cut(s)	390, 522
BfoI	RGCGCY	2 cut(s)	110, 332
BglI	GCCNNNNNGGC	1 cut(s)	364
BisI	GCNGC	7 cut(s)	96, 149, 232, 284, 304, 342, 460
BlnI	CCTAGG	1 cut(s)	389
BlsI	GCNGC	7 cut(s)	97, 150, 233, 285, 305, 343, 461
Bme1390I	CCNGG	2 cut(s)	326, 439
Bme18I	GGWCC	2 cut(s)	322, 441
BmgT120I	GGNCC	3 cut(s)	295, 322, 441
BmiI	GGNNCC	9 cut(s)	45, 60, 296, 324, 330, 396, 442, 504, 517
BmrFI	CCNGG	2 cut(s)	326, 439
BpuMI	CCSGG	2 cut(s)	326, 439
BsaAI	YACGTR	2 cut(s)	371, 455
BsaHI	GRCGYC	1 cut(s)	329
BsaI	GGTCTC	1 cut(s)	355
BsaJI	CCNNGG	6 cut(s)	9, 298, 318, 345, 362, 389
BsaWI	WCCGGW	1 cut(s)	565
BsaXI	ACNNNNNCTCC	6 cut(s)	330, 360, 481, 487, 511, 517
Bsc4I	CCNNNNNNNGG	4 cut(s)	293, 331, 390, 512
Bse118I	RCCGGY	1 cut(s)	40
BseDI	CCNNGG	6 cut(s)	9, 298, 318, 345, 362, 389
BseLI	CCNNNNNNNGG	4 cut(s)	293, 331, 390, 512
BseMII	CTCAG	1 cut(s)	63
BseRI	GAGGAG	2 cut(s)	26, 343
BseSI	GKGCMC	1 cut(s)	520
BseXI	GCAGC	2 cut(s)	160, 353
Bsh1236I	CGCG	2 cut(s)	146, 281
BshFI	GGCC	8 cut(s)	5, 297, 303, 367, 451, 459, 476, 538
BshNI	GGYRCC	3 cut(s)	43, 328, 515
BsiHKAI	GWGCWC	2 cut(s)	240, 428
BslFI	GGGAC	2 cut(s)	49, 308
BslI	CCNNNNNNNGG	4 cut(s)	293, 331, 390, 512
BsmAI	GTCTC	1 cut(s)	355
BsmFI	GGGAC	2 cut(s)	49, 308
BsnI	GGCC	8 cut(s)	5, 297, 303, 367, 451, 459, 476, 538
Bso31I	GGTCTC	1 cut(s)	355
Bsp1286I	GDGCHC	3 cut(s)	240, 428, 520
Bsp143I	GATC	2 cut(s)	172, 394
BspANI	GGCC	8 cut(s)	5, 297, 303, 367, 451, 459, 476, 538
BspCNI	CTCAG	1 cut(s)	64
BspFNI	CGCG	2 cut(s)	146, 281
BspLI	GGNNCC	9 cut(s)	45, 60, 296, 324, 330, 396, 442, 504, 517
BspPI	GGATC	2 cut(s)	389, 402
BspT107I	GGYRCC	3 cut(s)	43, 328, 515
BspTNI	GGTCTC	1 cut(s)	355
BsrBI	CCGCTC	2 cut(s)	231, 409
BsrFI	RCCGGY	1 cut(s)	40
BssAI	RCCGGY	1 cut(s)	40
BssECI	CCNNGG	6 cut(s)	9, 298, 318, 345, 362, 389
BssMI	GATC	2 cut(s)	172, 394
BssNI	GRCGYC	1 cut(s)	329
BssT1I	CCWWGG	2 cut(s)	318, 389
Bst4CI	ACNGT	1 cut(s)	36
BstACI	GRCGYC	1 cut(s)	329
BstBAI	YACGTR	2 cut(s)	371, 455
BstC8I	GCNNGC	5 cut(s)	42, 236, 308, 449, 536
BstDEI	CTNAG	1 cut(s)	72
BstDSI	CCRYGG	2 cut(s)	298, 345
BstFNI	CGCG	2 cut(s)	146, 281
BstH2I	RGCGCY	2 cut(s)	110, 332
BstHHI	GCGC	5 cut(s)	109, 148, 205, 283, 331
BstKTI	GATC	2 cut(s)	175, 397
BstMAI	GTCTC	1 cut(s)	355
BstMBI	GATC	2 cut(s)	172, 394
BstMWI	GCNNNNNNNGC	8 cut(s)	37, 46, 104, 202, 289, 303, 364, 515
BstSCI	CCNGG	2 cut(s)	324, 437
BstSLI	GKGCMC	1 cut(s)	520
BstUI	CGCG	2 cut(s)	146, 281
BstV1I	GCAGC	2 cut(s)	160, 353
BstX2I	RGATCY	1 cut(s)	394
BstXI	CCANNNNNNTGG	1 cut(s)	199
BstYI	RGATCY	1 cut(s)	394
BsuRI	GGCC	8 cut(s)	5, 297, 303, 367, 451, 459, 476, 538
BtgI	CCRYGG	2 cut(s)	298, 345
Cac8I	GCNNGC	5 cut(s)	42, 236, 308, 449, 536
CfoI	GCGC	5 cut(s)	109, 148, 205, 283, 331
Cfr10I	RCCGGY	1 cut(s)	40
Cfr13I	GGNCC	3 cut(s)	295, 322, 441
Csp6I	GTAC	1 cut(s)	76
CviAII	CATG	1 cut(s)	262
CviQI	GTAC	1 cut(s)	76
DdeI	CTNAG	1 cut(s)	72
DinI	GGCGCC	1 cut(s)	330
DpnI	GATC	2 cut(s)	174, 396
DpnII	GATC	2 cut(s)	172, 394
EaeI	YGGCCR	3 cut(s)	3, 301, 457
Ecl136II	GAGCTC	2 cut(s)	238, 426
Eco130I	CCWWGG	2 cut(s)	318, 389
Eco24I	GRGCYC	2 cut(s)	240, 428
Eco31I	GGTCTC	1 cut(s)	355
Eco47I	GGWCC	2 cut(s)	322, 441
Eco53kI	GAGCTC	2 cut(s)	238, 426
Eco72I	CACGTG	2 cut(s)	371, 455
EcoICRI	GAGCTC	2 cut(s)	238, 426
EcoO109I	RGGNCCY	1 cut(s)	322
EcoT14I	CCWWGG	2 cut(s)	318, 389
EcoT38I	GRGCYC	2 cut(s)	240, 428
EgeI	GGCGCC	1 cut(s)	330
EheI	GGCGCC	1 cut(s)	330
ErhI	CCWWGG	2 cut(s)	318, 389
FaeI	CATG	1 cut(s)	265
FaiI	YATR	2 cut(s)	92, 263
FaqI	GGGAC	2 cut(s)	49, 308
FatI	CATG	1 cut(s)	261
FauI	CCCGC	3 cut(s)	285, 315, 414
Fnu4HI	GCNGC	7 cut(s)	96, 149, 232, 284, 304, 342, 460
FriOI	GRGCYC	2 cut(s)	240, 428
Fsp4HI	GCNGC	7 cut(s)	96, 149, 232, 284, 304, 342, 460
FspBI	CTAG	2 cut(s)	390, 522
GlaI	GCGC	5 cut(s)	108, 147, 204, 282, 330
GluI	GCNGC	7 cut(s)	96, 149, 232, 284, 304, 342, 460
HaeII	RGCGCY	2 cut(s)	110, 332
HaeIII	GGCC	8 cut(s)	5, 297, 303, 367, 451, 459, 476, 538
HhaI	GCGC	5 cut(s)	109, 148, 205, 283, 331
Hin1I	GRCGYC	1 cut(s)	329
Hin1II	CATG	1 cut(s)	265
Hin6I	GCGC	5 cut(s)	107, 146, 203, 281, 329
HinP1I	GCGC	5 cut(s)	107, 146, 203, 281, 329
HinfI	GANTC	3 cut(s)	14, 158, 496
Hpy166II	GTNNAC	1 cut(s)	162
Hpy188I	TCNGA	3 cut(s)	363, 468, 489
Hpy188III	TCNNGA	1 cut(s)	250
Hpy8I	GTNNAC	1 cut(s)	162
Hpy99I	CGWCG	1 cut(s)	40
HpyAV	CCTTC	2 cut(s)	329, 466
HpyCH4III	ACNGT	1 cut(s)	36
HpyCH4IV	ACGT	2 cut(s)	370, 454
HpyF10VI	GCNNNNNNNGC	8 cut(s)	37, 46, 104, 202, 289, 303, 364, 515
HpyF3I	CTNAG	1 cut(s)	72
HpySE526I	ACGT	2 cut(s)	370, 454
Hsp92I	GRCGYC	1 cut(s)	329
Hsp92II	CATG	1 cut(s)	265
HspAI	GCGC	5 cut(s)	107, 146, 203, 281, 329
KasI	GGCGCC	1 cut(s)	328
KroI	GCCGGC	1 cut(s)	40
KroNI	GCCGGC	1 cut(s)	42
Kzo9I	GATC	2 cut(s)	172, 394
LmnI	GCTCC	5 cut(s)	64, 338, 414, 508, 568
Lsp1109I	GCAGC	2 cut(s)	160, 353
MaeI	CTAG	2 cut(s)	390, 522
MaeII	ACGT	2 cut(s)	370, 454
MalI	GATC	2 cut(s)	174, 396
MbiI	CCGCTC	2 cut(s)	231, 409
MboI	GATC	2 cut(s)	172, 394
MboII	GAAGA	1 cut(s)	481
MfeI	CAATTG	1 cut(s)	414
MflI	RGATCY	1 cut(s)	394
MhlI	GDGCHC	3 cut(s)	240, 428, 520
MlsI	TGGCCA	1 cut(s)	5
MluCI	AATT	1 cut(s)	414
MluNI	TGGCCA	1 cut(s)	5
Mly113I	GGCGCC	1 cut(s)	329
MlyI	GAGTC	3 cut(s)	23, 167, 490
MmeI	TCCRAC	2 cut(s)	42, 512
Mox20I	TGGCCA	1 cut(s)	5
MroNI	GCCGGC	1 cut(s)	40
MscI	TGGCCA	1 cut(s)	5
MseI	TTAA	1 cut(s)	111
Msp20I	TGGCCA	1 cut(s)	5
MspR9I	CCNGG	2 cut(s)	326, 439
MunI	CAATTG	1 cut(s)	414
MvnI	CGCG	2 cut(s)	146, 281
MwoI	GCNNNNNNNGC	8 cut(s)	37, 46, 104, 202, 289, 303, 364, 515
NaeI	GCCGGC	1 cut(s)	42
NarI	GGCGCC	1 cut(s)	329
NciI	CCSGG	2 cut(s)	326, 439
NdeII	GATC	2 cut(s)	172, 394
NgoMIV	GCCGGC	1 cut(s)	40
NlaIII	CATG	1 cut(s)	265
NlaIV	GGNNCC	9 cut(s)	45, 60, 296, 324, 330, 396, 442, 504, 517
PdiI	GCCGGC	1 cut(s)	42
PkrI	GCNGC	7 cut(s)	97, 150, 233, 285, 305, 343, 461
PleI	GAGTC	3 cut(s)	22, 166, 490
PluTI	GGCGCC	1 cut(s)	332
PmaCI	CACGTG	2 cut(s)	371, 455
PmlI	CACGTG	2 cut(s)	371, 455
PpsI	GAGTC	3 cut(s)	22, 166, 490
Ppu21I	YACGTR	2 cut(s)	371, 455
PpuMI	RGGWCCY	1 cut(s)	322
Psp124BI	GAGCTC	2 cut(s)	240, 428
Psp5II	RGGWCCY	1 cut(s)	322
PspCI	CACGTG	2 cut(s)	371, 455
PspN4I	GGNNCC	9 cut(s)	45, 60, 296, 324, 330, 396, 442, 504, 517
PspPI	GGNCC	3 cut(s)	295, 322, 441
PspPPI	RGGWCCY	1 cut(s)	322
PsuI	RGATCY	1 cut(s)	394
RsaI	GTAC	1 cut(s)	77
RsaNI	GTAC	1 cut(s)	76
SacI	GAGCTC	2 cut(s)	240, 428
SaqAI	TTAA	1 cut(s)	111
SatI	GCNGC	7 cut(s)	96, 149, 232, 284, 304, 342, 460
Sau3AI	GATC	2 cut(s)	172, 394
Sau96I	GGNCC	3 cut(s)	295, 322, 441
SchI	GAGTC	3 cut(s)	23, 167, 490
ScrFI	CCNGG	2 cut(s)	326, 439
SduI	GDGCHC	3 cut(s)	240, 428, 520
SfoI	GGCGCC	1 cut(s)	330
SinI	GGWCC	2 cut(s)	322, 441
Sse9I	AATT	1 cut(s)	414
SspDI	GGCGCC	1 cut(s)	328
SspMI	CTAG	2 cut(s)	390, 522
SstI	GAGCTC	2 cut(s)	240, 428
StyD4I	CCNGG	2 cut(s)	324, 437
StyI	CCWWGG	2 cut(s)	318, 389
TaaI	ACNGT	1 cut(s)	36
TaiI	ACGT	2 cut(s)	373, 457
TaqI	TCGA	4 cut(s)	128, 156, 428, 494
TasI	AATT	1 cut(s)	414
TauI	GCSGC	5 cut(s)	98, 234, 286, 306, 462
Tru1I	TTAA	1 cut(s)	111
Tru9I	TTAA	1 cut(s)	111
TseI	GCWGC	2 cut(s)	148, 341
TspDTI	ATGAA	2 cut(s)	236, 278
TspGWI	ACGGA	3 cut(s)	51, 387, 547
VpaK11BI	GGWCC	2 cut(s)	322, 441
XmaJI	CCTAGG	1 cut(s)	389
XspI	CTAG	2 cut(s)	390, 522

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