Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0002801

Physical Location & Seq

Genomic Coordinates Forward (+)

73097987 .. 73100920

Gene Structure 2934 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG439300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 465 bp

ATGAATTTCCACTTGCTTTTTGGGGGGTTTGGTGGATGTATGTATCTTCTGATTTTGATTCCTTTTCTGTGCAGGAAGAAATCGTCACAACCAAATGCCAAGAGAGCCAAGACTGACAAAGTGAACAAGAGCAAGGATCCAAATGCACCCAAGCGCCCCCTCACTGCCTTCTTCCTTTTCATGAATGATTTTAGGAAAGCCTACAAGGAAGCTAATCCTGATTCCAAGGGTGTTAAGATGGTTGCAAAGGAGGGTGGTGAAAAGTGGAATCTTATGACTGATGAGGAGAAGAAGCCTTATATGGACAAAGCTGCTGAGCTTAAAGATGAGTACAAAAAGACCTTAGAGACTGAAGCTGATGATGCTGAAGGTGAGGCTGAAGATGTTTCAGAAAAGCTAGTGCCAGAGAAGGAAGTAGAGGAAGCTTCAGAAAAGGAAGTGGAGGAAGCATCAGATGGGGAGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000741 GO:0003674 GO:0003676 GO:0003677 GO:0003700 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006355 GO:0006996 GO:0006997 GO:0007275 GO:0008150 GO:0009553 GO:0009559 GO:0009561 GO:0009889 GO:0009987 GO:0010197 GO:0010468 GO:0010556 GO:0016043 GO:0019219 GO:0019222 GO:0030154 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0048229 GO:0048284 GO:0048856 GO:0048869 GO:0050789 GO:0050794 GO:0051171 GO:0051252 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

154

Amino Acids

17.45

Weight (kDa)

5.11

Isoelectric Point (pI)

42.75

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HMG_box_2	PF09011	47 - 116	1.4e-13	HMG-box domain
HMG_box	PF00505	50 - 114	3.1e-19	HMG (high mobility group) box
HMG_WDHD1	PF24815	53 - 103	2.9e-14	WDHD1 HMG box

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

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Orthologous Genes (Group: OG0002801)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G23420 AT5G23420
fragaria_vesca	FvH4_4g14340 FvH4_4g25270 FvH4_4g37280 FvH4_5g24080 FvH4_7g08880
malus_domestica	MD00G1127400.v1.1 MD13G1001900.v1.1
prunus_persica	Prupe.1G350700_v2.0.a1
pyrus_communis	pycom13g00150 pycom16g00050
rosa_chinensis	RchiOBHm_Chr4g0447101
rosa_laevigata	RLG00000005605 RLG00000017187 RLG00000019927 RLG00000024815
rosa_multiflora	Rmu_co7979696.1_g000001 Rmu_sc0010825.1_g000009 Rmu_ssc0000178.1_g000012
rosa_roxburghii	Rroxscaffold_2G00150280 Rroxscaffold_5G00357540 Rroxscaffold_5G00387440
rosa_rugosa	Rorug02G0403700 Rorug04G0378200 Rorug07G0307000
rosa_samantha	Rh1BG046400 Rh2AG305400 Rh2BG280600 Rh2DG275400 Rh2DG329200 Rh4AG439300 Rh4BG448400 Rh4CG465400 Rh4DG446800 Rh5BG556800 Rh5CG579600 Rh7DG482600
rosa_wichuraiana	Rw4G037580

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AclWI	GGATC	2 cut(s)	131, 144
AcsI	RAATTY	1 cut(s)	4
AcuI	CTGAAG	4 cut(s)	372, 387, 399, 411
AfaI	GTAC	1 cut(s)	332
AluBI	AGCT	6 cut(s)	212, 311, 319, 356, 397, 425
AluI	AGCT	6 cut(s)	212, 311, 319, 356, 397, 425
Alw26I	GTCTC	1 cut(s)	341
AlwI	GGATC	2 cut(s)	131, 144
ApeKI	GCWGC	1 cut(s)	311
ApoI	RAATTY	1 cut(s)	4
AspLEI	GCGC	1 cut(s)	156
AsuHPI	GGTGA	2 cut(s)	269, 383
BamHI	GGATCC	1 cut(s)	136
BbvI	GCAGC	1 cut(s)	298
BccI	CCATC	2 cut(s)	232, 449
BcoDI	GTCTC	1 cut(s)	341
BfaI	CTAG	1 cut(s)	398
BfoI	RGCGCY	1 cut(s)	157
BisI	GCNGC	1 cut(s)	312
BlpI	GCTNAGC	1 cut(s)	315
BlsI	GCNGC	1 cut(s)	313
BmiI	GGNNCC	1 cut(s)	138
BmsI	GCATC	2 cut(s)	352, 458
Bpu1102I	GCTNAGC	1 cut(s)	315
BsaJI	CCNNGG	1 cut(s)	225
BseDI	CCNNGG	1 cut(s)	225
BseGI	GGATG	1 cut(s)	41
BseMII	CTCAG	1 cut(s)	306
BseRI	GAGGAG	1 cut(s)	299
BseXI	GCAGC	1 cut(s)	298
BsgI	GTGCAG	1 cut(s)	91
BsmAI	GTCTC	1 cut(s)	341
Bsp143I	GATC	1 cut(s)	136
Bsp1720I	GCTNAGC	1 cut(s)	315
BspCNI	CTCAG	1 cut(s)	307
BspHI	TCATGA	1 cut(s)	180
BspLI	GGNNCC	1 cut(s)	138
BspPI	GGATC	2 cut(s)	131, 144
BssECI	CCNNGG	1 cut(s)	225
BssMI	GATC	1 cut(s)	136
BssT1I	CCWWGG	1 cut(s)	225
BstDEI	CTNAG	2 cut(s)	315, 343
BstF5I	GGATG	1 cut(s)	41
BstH2I	RGCGCY	1 cut(s)	157
BstHHI	GCGC	1 cut(s)	156
BstKTI	GATC	1 cut(s)	139
BstMAI	GTCTC	1 cut(s)	341
BstMBI	GATC	1 cut(s)	136
BstMWI	GCNNNNNNNGC	2 cut(s)	104, 362
BstV1I	GCAGC	1 cut(s)	298
BstX2I	RGATCY	1 cut(s)	136
BstYI	RGATCY	1 cut(s)	136
BtsCI	GGATG	1 cut(s)	41
BtsI	GCAGTG	1 cut(s)	162
BtsIMutI	CAGTG	1 cut(s)	162
CciI	TCATGA	1 cut(s)	180
CfoI	GCGC	1 cut(s)	156
Csp6I	GTAC	1 cut(s)	331
CviAII	CATG	1 cut(s)	181
CviQI	GTAC	1 cut(s)	331
DdeI	CTNAG	2 cut(s)	315, 343
DpnI	GATC	1 cut(s)	138
DpnII	GATC	1 cut(s)	136
Eco130I	CCWWGG	1 cut(s)	225
Eco57I	CTGAAG	4 cut(s)	372, 387, 399, 411
EcoT14I	CCWWGG	1 cut(s)	225
ErhI	CCWWGG	1 cut(s)	225
FaeI	CATG	1 cut(s)	184
FaiI	YATR	5 cut(s)	41, 182, 275, 300, 302
FatI	CATG	1 cut(s)	180
Fnu4HI	GCNGC	1 cut(s)	312
FokI	GGATG	1 cut(s)	48
Fsp4HI	GCNGC	1 cut(s)	312
FspBI	CTAG	1 cut(s)	398
GlaI	GCGC	1 cut(s)	155
GluI	GCNGC	1 cut(s)	312
HaeII	RGCGCY	1 cut(s)	157
HhaI	GCGC	1 cut(s)	156
Hin1II	CATG	1 cut(s)	184
Hin6I	GCGC	1 cut(s)	154
HinP1I	GCGC	1 cut(s)	154
HindIII	AAGCTT	1 cut(s)	423
HinfI	GANTC	3 cut(s)	58, 221, 268
HphI	GGTGA	2 cut(s)	269, 383
Hpy166II	GTNNAC	1 cut(s)	124
Hpy188I	TCNGA	4 cut(s)	51, 391, 430, 454
Hpy188III	TCNNGA	2 cut(s)	181, 218
Hpy8I	GTNNAC	1 cut(s)	124
HpyAV	CCTTC	3 cut(s)	178, 362, 403
HpyCH4V	TGCA	3 cut(s)	72, 146, 245
HpyF10VI	GCNNNNNNNGC	2 cut(s)	104, 362
HpyF3I	CTNAG	2 cut(s)	315, 343
Hsp92II	CATG	1 cut(s)	184
HspAI	GCGC	1 cut(s)	154
Kzo9I	GATC	1 cut(s)	136
LpnPI	CCDG	3 cut(s)	58, 231, 417
Lsp1109I	GCAGC	1 cut(s)	298
LweI	GCATC	2 cut(s)	352, 458
MaeI	CTAG	1 cut(s)	398
MaeIII	GTNAC	1 cut(s)	84
MalI	GATC	1 cut(s)	138
MboI	GATC	1 cut(s)	136
MboII	GAAGA	5 cut(s)	38, 88, 163, 301, 392
MflI	RGATCY	1 cut(s)	136
MluCI	AATT	1 cut(s)	4
MnlI	CCTC	6 cut(s)	170, 244, 277, 367, 412, 436
MseI	TTAA	2 cut(s)	234, 321
MwoI	GCNNNNNNNGC	2 cut(s)	104, 362
NdeII	GATC	1 cut(s)	136
NlaIII	CATG	1 cut(s)	184
NlaIV	GGNNCC	1 cut(s)	138
NmuCI	GTSAC	1 cut(s)	84
PagI	TCATGA	1 cut(s)	180
PfeI	GAWTC	3 cut(s)	58, 221, 268
PkrI	GCNGC	1 cut(s)	313
PspN4I	GGNNCC	1 cut(s)	138
PsuI	RGATCY	1 cut(s)	136
RsaI	GTAC	1 cut(s)	332
RsaNI	GTAC	1 cut(s)	331
SaqAI	TTAA	2 cut(s)	234, 321
SatI	GCNGC	1 cut(s)	312
Sau3AI	GATC	1 cut(s)	136
SetI	ASST	8 cut(s)	214, 313, 321, 344, 358, 373, 399, 427
SfaNI	GCATC	2 cut(s)	352, 458
Sse9I	AATT	1 cut(s)	4
SspMI	CTAG	1 cut(s)	398
StyI	CCWWGG	1 cut(s)	225
TasI	AATT	1 cut(s)	4
TatI	WGTACW	1 cut(s)	330
TfiI	GAWTC	3 cut(s)	58, 221, 268
Tru1I	TTAA	2 cut(s)	234, 321
Tru9I	TTAA	2 cut(s)	234, 321
TscAI	CASTG	1 cut(s)	169
TseFI	GTSAC	1 cut(s)	84
TseI	GCWGC	1 cut(s)	311
Tsp45I	GTSAC	1 cut(s)	84
TspDTI	ATGAA	3 cut(s)	17, 169, 197
TspRI	CASTG	1 cut(s)	169
XapI	RAATTY	1 cut(s)	4
XcmI	CCANNNNNNNNNTGG	1 cut(s)	17
XspI	CTAG	1 cut(s)	398

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