Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0002801

Physical Location & Seq

Genomic Coordinates Forward (+)

64621811 .. 64626933

Gene Structure 5123 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG446800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 501 bp

ATGTATGTATGTATTCAGTTTGCCTGTGAGCGTTGCTTATTATTTTTATGTTCAGAGGCTCAAGTCGTGGAAAAGCCCAGTGAAGTGACTAAGAAGCCTCCCACAGAGAGGAAGAAATCGTCACAACCAAATGCCAAGAGAGCCAAGACTGACAAAGTGAACAAGAGCAAGGATCCAAATGCACCCAAGCGCCCCCTCACTGCCTTCTTCCTTTTCATGAATGATTTTAGGAAAGCCTACAAGGAAGCTAATCCTGATTCCAAGGGTGTTAAGATGGTTGCAAAGGAGGGTGGTGAAAAGTGGAATCTTATGACTGATGAGGAGAAGAAGCCTTATATGGACAAAGCTGCTGAGCTTAAAGATGAGTACAAAAAGACCTTAGAGACTGAAGCTGATGATGCTGAAGGTGAGGCTGAAGATGTTTCAGAAAAGCAAGTGCCAGAGAAGGAAGTAGAGGAAGCTTCAGAAAAGGAAGTGGAGGAAGCATCAGATGGGGAGTAG

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

166

Amino Acids

18.87

Weight (kDa)

5.03

Isoelectric Point (pI)

44.45

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HMG_box_2	PF09011	59 - 128	1.7e-13	HMG-box domain
HMG_box	PF00505	62 - 126	3.7e-19	HMG (high mobility group) box
HMG_WDHD1	PF24815	65 - 115	3.4e-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)	167, 180
AcuI	CTGAAG	4 cut(s)	408, 423, 435, 447
AfaI	GTAC	1 cut(s)	368
AfiI	CCNNNNNNNGG	1 cut(s)	108
AluBI	AGCT	5 cut(s)	248, 347, 355, 392, 461
AluI	AGCT	5 cut(s)	248, 347, 355, 392, 461
Alw26I	GTCTC	1 cut(s)	377
AlwI	GGATC	2 cut(s)	167, 180
ApeKI	GCWGC	1 cut(s)	347
AspLEI	GCGC	1 cut(s)	192
AsuHPI	GGTGA	2 cut(s)	305, 419
BamHI	GGATCC	1 cut(s)	172
BbvI	GCAGC	1 cut(s)	334
BccI	CCATC	2 cut(s)	268, 485
BcoDI	GTCTC	1 cut(s)	377
BfoI	RGCGCY	1 cut(s)	193
BisI	GCNGC	1 cut(s)	348
BlpI	GCTNAGC	1 cut(s)	351
BlsI	GCNGC	1 cut(s)	349
BmiI	GGNNCC	1 cut(s)	174
BmrI	ACTGGG	1 cut(s)	72
BmsI	GCATC	2 cut(s)	388, 494
BmuI	ACTGGG	1 cut(s)	72
Bpu1102I	GCTNAGC	1 cut(s)	351
BpuEI	CTTGAG	1 cut(s)	45
BsaJI	CCNNGG	1 cut(s)	261
Bsc4I	CCNNNNNNNGG	1 cut(s)	108
Bse1I	ACTGG	1 cut(s)	78
BseDI	CCNNGG	1 cut(s)	261
BseLI	CCNNNNNNNGG	1 cut(s)	108
BseMII	CTCAG	1 cut(s)	342
BseNI	ACTGG	1 cut(s)	78
BseRI	GAGGAG	1 cut(s)	335
BseXI	GCAGC	1 cut(s)	334
BslI	CCNNNNNNNGG	1 cut(s)	108
BsmAI	GTCTC	1 cut(s)	377
Bsp143I	GATC	1 cut(s)	172
Bsp1720I	GCTNAGC	1 cut(s)	351
BspCNI	CTCAG	1 cut(s)	343
BspHI	TCATGA	1 cut(s)	216
BspLI	GGNNCC	1 cut(s)	174
BspPI	GGATC	2 cut(s)	167, 180
BsrI	ACTGG	1 cut(s)	78
BssECI	CCNNGG	1 cut(s)	261
BssMI	GATC	1 cut(s)	172
BssT1I	CCWWGG	1 cut(s)	261
BstDEI	CTNAG	3 cut(s)	90, 351, 379
BstH2I	RGCGCY	1 cut(s)	193
BstHHI	GCGC	1 cut(s)	192
BstKTI	GATC	1 cut(s)	175
BstMAI	GTCTC	1 cut(s)	377
BstMBI	GATC	1 cut(s)	172
BstMWI	GCNNNNNNNGC	2 cut(s)	140, 398
BstV1I	GCAGC	1 cut(s)	334
BstX2I	RGATCY	1 cut(s)	172
BstYI	RGATCY	1 cut(s)	172
BtsI	GCAGTG	1 cut(s)	198
BtsIMutI	CAGTG	2 cut(s)	85, 198
CciI	TCATGA	1 cut(s)	216
CfoI	GCGC	1 cut(s)	192
Csp6I	GTAC	1 cut(s)	367
CviAII	CATG	1 cut(s)	217
CviQI	GTAC	1 cut(s)	367
DdeI	CTNAG	3 cut(s)	90, 351, 379
DpnI	GATC	1 cut(s)	174
DpnII	GATC	1 cut(s)	172
Eco130I	CCWWGG	1 cut(s)	261
Eco57I	CTGAAG	4 cut(s)	408, 423, 435, 447
EcoT14I	CCWWGG	1 cut(s)	261
ErhI	CCWWGG	1 cut(s)	261
FaeI	CATG	1 cut(s)	220
FaiI	YATR	7 cut(s)	6, 10, 49, 218, 311, 336, 338
FatI	CATG	1 cut(s)	216
Fnu4HI	GCNGC	1 cut(s)	348
Fsp4HI	GCNGC	1 cut(s)	348
GlaI	GCGC	1 cut(s)	191
GluI	GCNGC	1 cut(s)	348
HaeII	RGCGCY	1 cut(s)	193
HhaI	GCGC	1 cut(s)	192
Hin1II	CATG	1 cut(s)	220
Hin6I	GCGC	1 cut(s)	190
HinP1I	GCGC	1 cut(s)	190
HindIII	AAGCTT	1 cut(s)	459
HinfI	GANTC	2 cut(s)	257, 304
HphI	GGTGA	2 cut(s)	305, 419
Hpy166II	GTNNAC	1 cut(s)	160
Hpy188I	TCNGA	4 cut(s)	55, 427, 466, 490
Hpy188III	TCNNGA	2 cut(s)	217, 254
Hpy8I	GTNNAC	1 cut(s)	160
HpyAV	CCTTC	3 cut(s)	214, 398, 439
HpyCH4V	TGCA	2 cut(s)	182, 281
HpyF10VI	GCNNNNNNNGC	2 cut(s)	140, 398
HpyF3I	CTNAG	3 cut(s)	90, 351, 379
Hsp92II	CATG	1 cut(s)	220
HspAI	GCGC	1 cut(s)	190
Kzo9I	GATC	1 cut(s)	172
LpnPI	CCDG	4 cut(s)	37, 91, 267, 453
Lsp1109I	GCAGC	1 cut(s)	334
LweI	GCATC	2 cut(s)	388, 494
MaeIII	GTNAC	2 cut(s)	85, 120
MalI	GATC	1 cut(s)	174
MboI	GATC	1 cut(s)	172
MboII	GAAGA	4 cut(s)	124, 199, 337, 428
MflI	RGATCY	1 cut(s)	172
MnlI	CCTC	9 cut(s)	49, 102, 108, 206, 280, 313, 403, 448, 472
MseI	TTAA	2 cut(s)	270, 357
MwoI	GCNNNNNNNGC	2 cut(s)	140, 398
NdeII	GATC	1 cut(s)	172
NlaIII	CATG	1 cut(s)	220
NlaIV	GGNNCC	1 cut(s)	174
NmuCI	GTSAC	2 cut(s)	85, 120
PagI	TCATGA	1 cut(s)	216
PfeI	GAWTC	2 cut(s)	257, 304
PkrI	GCNGC	1 cut(s)	349
PspN4I	GGNNCC	1 cut(s)	174
PsuI	RGATCY	1 cut(s)	172
RsaI	GTAC	1 cut(s)	368
RsaNI	GTAC	1 cut(s)	367
SaqAI	TTAA	2 cut(s)	270, 357
SatI	GCNGC	1 cut(s)	348
Sau3AI	GATC	1 cut(s)	172
SetI	ASST	7 cut(s)	250, 349, 357, 380, 394, 409, 463
SfaNI	GCATC	2 cut(s)	388, 494
SmlI	CTYRAG	1 cut(s)	60
SmoI	CTYRAG	1 cut(s)	60
StyI	CCWWGG	1 cut(s)	261
TatI	WGTACW	1 cut(s)	366
TfiI	GAWTC	2 cut(s)	257, 304
Tru1I	TTAA	2 cut(s)	270, 357
Tru9I	TTAA	2 cut(s)	270, 357
TscAI	CASTG	2 cut(s)	85, 205
TseFI	GTSAC	2 cut(s)	85, 120
TseI	GCWGC	1 cut(s)	347
Tsp45I	GTSAC	2 cut(s)	85, 120
TspDTI	ATGAA	2 cut(s)	205, 233
TspRI	CASTG	2 cut(s)	85, 205

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