Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0001626

Physical Location & Seq

Genomic Coordinates Reverse (-)

10330354 .. 10334863

Gene Structure 4510 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG125300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 600 bp

ATGGGAGATAGAGGTTTTATTGAGATTCCTCTTTTCAAAGACGCTAATCTCGGAACAATGAGGGCTGCCAAGGCTAAGGCGGGAGCAAGAGCCCTGAAACCTGTCGATGATGGGAGAGTTGGGAAACGAAAGGCTGCTGCTGCTCCAGTTGATAAGAGTAGCAAAGGAAAGGCCAAGCAGACAAAGAAGGCCAAGAAAGACCCCAACAAGCCTAAGAGGCCACCTAGTGCCTTTTTCGTGTTCCTTGGTCAGTTCAGGGAAGAGTTCAAGAAAAAGAACCCTAATGTGAAAGGGGTAGCAGCTGTTGGAAAAGCTGGAGGAGAAAAGTGGAGATCCCTGTCTGATGCTGAAAAAGCTCCATATGAAGCTGAGTCTGCAAAAGCAAAGACTGAGTATGAAAAGCAGCTGAAAATCTATGACAAAAAGCAGAGTGCACCTGATGATGGTGATGAAGAGTCAGAGAGGTCAAGATCTGAAGTGCATGATGAAGACGATGAGGCTAGTGGGGAGGTAGTCCTATATATACTACTTTTGCTTGGACTTCGGTTCTTCTTTCTTCTCATGGCAATACCCTTTATTTTAGTCATGAGAAGCGCATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000785 GO:0003674 GO:0003676 GO:0003677 GO:0003682 GO:0003700 GO:0005198 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0006325 GO:0006333 GO:0006355 GO:0006996 GO:0008150 GO:0009889 GO:0009987 GO:0010468 GO:0010556 GO:0016043 GO:0019219 GO:0019222 GO:0030527 GO:0031323 GO:0031326 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0044422 GO:0044424 GO:0044427 GO:0044446 GO:0044464 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0051276 GO:0060255 GO:0065007 GO:0071840 GO:0080090 GO:0097159 GO:0140110 GO:1901363 GO:1903506 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

ko03410 ko04140 ko04217 map03410 map04140 map04217

Pfam Domains

Protein Families

HMG_box

Protein Analysis

199

Amino Acids

21.96

Weight (kDa)

9.64

Isoelectric Point (pI)

43.09

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HMG_box_2	PF09011	68 - 139	7.5e-15	HMG-box domain
HMG_box	PF00505	71 - 139	3.8e-22	HMG (high mobility group) box
HMG_WDHD1	PF24815	74 - 121	6e-11	WDHD1 HMG box

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: OG0001626)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G51880 AT3G51880 AT3G51880 AT3G51880 AT3G51880
fragaria_vesca	FvH4_6g11530 FvH4_6g11530 FvH4_6g11530 FvH4_6g11530 FvH4_7g24360 FvH4_7g24360 FvH4_7g24360
malus_domestica	MD01G1132900.v1.1 MD07G1220600.v1.1
prunus_persica	Prupe.2G249000_v2.0.a1 Prupe.2G249000_v2.0.a1 Prupe.6G276300_v2.0.a1 Prupe.6G276300_v2.0.a1 Prupe.6G276300_v2.0.a1 Prupe.6G276300_v2.0.a1
pyrus_communis	pycom01g16950 pycom07g19960
rosa_chinensis	RchiOBHm_Chr1g0370021 RchiOBHm_Chr3g0463231
rosa_laevigata	RLG00000024799
rosa_multiflora	Rmu_co8427781.1_g000001 Rmu_sc0005056.1_g000014 Rmu_sc0008079.1_g000019 Rmu_sc0022743.1_g000005 Rmu_sc0022743.1_g000006
rosa_roxburghii	Rroxscaffold_4G00286860 Rroxscaffold_4G00287170 Rroxscaffold_6G00416770
rosa_rugosa	Rorug01G0353500 Rorug03G0062700 Rorug03G0062700 Rorug03G0062700 Rorug03G0062800 Rorug03G0062800
rosa_samantha	Rh1AG362200 Rh1BG325400 Rh1CG338700 Rh1DG355900 Rh3AG120800 Rh3BG125300 Rh3CG127300 Rh3DG126500
rosa_wichuraiana	Rw1G031870 Rw3G010260

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	80
AclWI	GGATC	1 cut(s)	327
AcuI	CTGAAG	1 cut(s)	495
AdeI	CACNNNGTG	1 cut(s)	227
AfiI	CCNNNNNNNGG	1 cut(s)	443
AgsI	TTSAA	2 cut(s)	37, 268
AluBI	AGCT	5 cut(s)	302, 314, 356, 368, 406
AluI	AGCT	5 cut(s)	302, 314, 356, 368, 406
Alw21I	GWGCWC	1 cut(s)	436
Alw44I	GTGCAC	1 cut(s)	432
AlwI	GGATC	1 cut(s)	327
AoxI	GGCC	3 cut(s)	171, 189, 218
ApaLI	GTGCAC	1 cut(s)	432
ApeKI	GCWGC	6 cut(s)	65, 134, 137, 140, 299, 403
AspLEI	GCGC	1 cut(s)	596
AsuHPI	GGTGA	1 cut(s)	458
BaeGI	GKGCMC	1 cut(s)	436
BanII	GRGCYC	1 cut(s)	94
BbsI	GAAGAC	1 cut(s)	495
Bbv12I	GWGCWC	1 cut(s)	436
BbvI	GCAGC	6 cut(s)	52, 121, 124, 127, 311, 415
BccI	CCATC	2 cut(s)	104, 437
BfaI	CTAG	2 cut(s)	225, 501
BglI	GCCNNNNNGGC	1 cut(s)	217
BglII	AGATCT	1 cut(s)	470
BisI	GCNGC	6 cut(s)	66, 135, 138, 141, 300, 404
BlsI	GCNGC	6 cut(s)	67, 136, 139, 142, 301, 405
BmsI	GCATC	1 cut(s)	334
BpiI	GAAGAC	1 cut(s)	495
BpmI	CTGGAG	2 cut(s)	129, 336
Bpu10I	CCTNAGC	1 cut(s)	75
BsaJI	CCNNGG	2 cut(s)	69, 244
Bsc4I	CCNNNNNNNGG	1 cut(s)	443
Bse1I	ACTGG	1 cut(s)	146
BseDI	CCNNGG	2 cut(s)	69, 244
BseLI	CCNNNNNNNGG	1 cut(s)	443
BseMII	CTCAG	2 cut(s)	360, 381
BseNI	ACTGG	1 cut(s)	146
BseRI	GAGGAG	1 cut(s)	333
BseSI	GKGCMC	1 cut(s)	436
BseXI	GCAGC	6 cut(s)	52, 121, 124, 127, 311, 415
BshFI	GGCC	3 cut(s)	173, 191, 220
BsiHKAI	GWGCWC	1 cut(s)	436
BslI	CCNNNNNNNGG	1 cut(s)	443
BsnI	GGCC	3 cut(s)	173, 191, 220
Bsp1286I	GDGCHC	2 cut(s)	94, 436
Bsp143I	GATC	2 cut(s)	332, 470
BspACI	CCGC	1 cut(s)	80
BspANI	GGCC	3 cut(s)	173, 191, 220
BspCNI	CTCAG	2 cut(s)	361, 382
BspHI	TCATGA	1 cut(s)	585
BspPI	GGATC	1 cut(s)	327
BsrI	ACTGG	1 cut(s)	146
BssECI	CCNNGG	2 cut(s)	69, 244
BssMI	GATC	2 cut(s)	332, 470
BssT1I	CCWWGG	2 cut(s)	69, 244
Bst6I	CTCTTC	2 cut(s)	255, 447
BstDEI	CTNAG	4 cut(s)	75, 213, 369, 390
BstHHI	GCGC	1 cut(s)	596
BstKTI	GATC	2 cut(s)	335, 473
BstMBI	GATC	2 cut(s)	332, 470
BstMWI	GCNNNNNNNGC	5 cut(s)	71, 140, 217, 353, 374
BstSLI	GKGCMC	1 cut(s)	436
BstV1I	GCAGC	6 cut(s)	52, 121, 124, 127, 311, 415
BstV2I	GAAGAC	1 cut(s)	495
BstX2I	RGATCY	2 cut(s)	332, 470
BstYI	RGATCY	2 cut(s)	332, 470
BsuRI	GGCC	3 cut(s)	173, 191, 220
CciI	TCATGA	1 cut(s)	585
CfoI	GCGC	1 cut(s)	596
CseI	GACGC	1 cut(s)	50
CviAII	CATG	3 cut(s)	482, 562, 586
DdeI	CTNAG	4 cut(s)	75, 213, 369, 390
DpnI	GATC	2 cut(s)	334, 472
DpnII	GATC	2 cut(s)	332, 470
DraIII	CACNNNGTG	1 cut(s)	227
Eam1104I	CTCTTC	2 cut(s)	255, 447
EarI	CTCTTC	2 cut(s)	255, 447
Eco130I	CCWWGG	2 cut(s)	69, 244
Eco24I	GRGCYC	1 cut(s)	94
Eco57I	CTGAAG	1 cut(s)	495
EcoT14I	CCWWGG	2 cut(s)	69, 244
EcoT38I	GRGCYC	1 cut(s)	94
ErhI	CCWWGG	2 cut(s)	69, 244
FaeI	CATG	3 cut(s)	485, 565, 589
FatI	CATG	3 cut(s)	481, 561, 585
FauI	CCCGC	1 cut(s)	73
FauNDI	CATATG	1 cut(s)	361
Fnu4HI	GCNGC	6 cut(s)	66, 135, 138, 141, 300, 404
FriOI	GRGCYC	1 cut(s)	94
Fsp4HI	GCNGC	6 cut(s)	66, 135, 138, 141, 300, 404
FspBI	CTAG	2 cut(s)	225, 501
GlaI	GCGC	1 cut(s)	595
GluI	GCNGC	6 cut(s)	66, 135, 138, 141, 300, 404
GsuI	CTGGAG	2 cut(s)	129, 336
HaeIII	GGCC	3 cut(s)	173, 191, 220
HgaI	GACGC	1 cut(s)	50
HhaI	GCGC	1 cut(s)	596
Hin1II	CATG	3 cut(s)	485, 565, 589
Hin6I	GCGC	1 cut(s)	594
HinP1I	GCGC	1 cut(s)	594
HinfI	GANTC	3 cut(s)	25, 371, 455
HphI	GGTGA	1 cut(s)	458
Hpy166II	GTNNAC	1 cut(s)	434
Hpy188I	TCNGA	4 cut(s)	53, 343, 460, 475
Hpy188III	TCNNGA	3 cut(s)	268, 468, 586
Hpy8I	GTNNAC	1 cut(s)	434
HpyAV	CCTTC	1 cut(s)	181
HpyCH4V	TGCA	3 cut(s)	377, 434, 481
HpyF10VI	GCNNNNNNNGC	5 cut(s)	71, 140, 217, 353, 374
HpyF3I	CTNAG	4 cut(s)	75, 213, 369, 390
Hsp92II	CATG	3 cut(s)	485, 565, 589
HspAI	GCGC	1 cut(s)	594
Kzo9I	GATC	2 cut(s)	332, 470
LmnI	GCTCC	3 cut(s)	83, 148, 361
LpnPI	CCDG	7 cut(s)	107, 114, 159, 241, 300, 350, 450
Lsp1109I	GCAGC	6 cut(s)	52, 121, 124, 127, 311, 415
LweI	GCATC	1 cut(s)	334
MaeI	CTAG	2 cut(s)	225, 501
MalI	GATC	2 cut(s)	334, 472
MboI	GATC	2 cut(s)	332, 470
MboII	GAAGA	5 cut(s)	272, 464, 500, 541, 548
MflI	RGATCY	2 cut(s)	332, 470
MhlI	GDGCHC	2 cut(s)	94, 436
MlyI	GAGTC	2 cut(s)	380, 464
MmeI	TCCRAC	1 cut(s)	286
MnlI	CCTC	8 cut(s)	5, 39, 54, 210, 311, 456, 490, 502
MspA1I	CMGCKG	2 cut(s)	302, 406
MwoI	GCNNNNNNNGC	5 cut(s)	71, 140, 217, 353, 374
NdeI	CATATG	1 cut(s)	361
NdeII	GATC	2 cut(s)	332, 470
NlaIII	CATG	3 cut(s)	485, 565, 589
PagI	TCATGA	1 cut(s)	585
PfeI	GAWTC	1 cut(s)	25
PkrI	GCNGC	6 cut(s)	67, 136, 139, 142, 301, 405
PleI	GAGTC	2 cut(s)	379, 463
PpsI	GAGTC	2 cut(s)	379, 463
PsuI	RGATCY	2 cut(s)	332, 470
PvuII	CAGCTG	2 cut(s)	302, 406
SatI	GCNGC	6 cut(s)	66, 135, 138, 141, 300, 404
Sau3AI	GATC	2 cut(s)	332, 470
SchI	GAGTC	2 cut(s)	380, 464
SduI	GDGCHC	2 cut(s)	94, 436
SfaNI	GCATC	1 cut(s)	334
SsiI	CCGC	1 cut(s)	80
SspMI	CTAG	2 cut(s)	225, 501
StyI	CCWWGG	2 cut(s)	69, 244
TaqI	TCGA	1 cut(s)	105
TfiI	GAWTC	1 cut(s)	25
TseI	GCWGC	6 cut(s)	65, 134, 137, 140, 299, 403
TspDTI	ATGAA	4 cut(s)	378, 411, 465, 501
VneI	GTGCAC	1 cut(s)	432
XspI	CTAG	2 cut(s)	225, 501

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