Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0010170

Physical Location & Seq

Genomic Coordinates Forward (+)

63318178 .. 63325239

Gene Structure 7062 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG454900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 648 bp

ATGTTCTACCGTAGCCGAATTGAGCACTCATTGCGTCTGCCTCCTTCTCTGCTTAGCCTTCGTCTACAAGATGCAGTTAAGGGAGAGCTTGAGAAGCTATTCTTAGATAAGGTTATCTCGAATTTGGGACTTTGCATTTCTGTCTATGATATCCAATCCATTAAAGATCACTTCATCTTGCCAAATGATGGTCATCCAACTCTAACGGTGGTGTTCACACTGATTATGTTTCGTCCATTTGTGGGAGAGATAATTACTGCAAAAGTCATAGAGTCTACTGCCACTGGTTTACGTTTGTCACTGGGATTTTTTGATGATATTTATATACCTACTCATCGTTTTCCTACACCATGCCACAAGAAGGATGACTCAAAAAAGAATGTTGTCTTATGGTATTGGAAGCCTTCTGATGATGAATTTTCAATTGATTTGAAGGACCAGATACGATTCCAGGTTGAAAGTGTAAACTATCCTAAAATTCCAATTGAGCAGCCAGAAAACTCAAAACCATTTGCCCCTATGGAGGTTAAAGTAAGTTCATGCTTTGAACCTTATCATATGACTTGTCGCTGCATATCTAGCTGGACATTTCCTAATTCCTCGCTCTCTACCATTCTGAGTGAACTTTGTAAATATGCTGCTTCCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0000785 GO:0000790 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005694 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044454 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rbc25 SHS2_Rpb7-N

Protein Analysis

215

Amino Acids

24.7

Weight (kDa)

6.59

Isoelectric Point (pI)

48.97

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	8 - 64	6.2e-12	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
RNA_pol_Rbc25	PF08292	83 - 167	1.7e-16	RNA polymerase III subunit Rpc25

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: OG0010170)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G06790 AT1G06790
fragaria_vesca	FvH4_1g22880
malus_domestica	MD08G1227600.v1.1
prunus_persica	Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.7G016800_v2.0.a1
rosa_chinensis	RchiOBHm_Chr5g0063451
rosa_laevigata	RLG00000022776 RLG00000035635
rosa_multiflora	Rmu_sc0016394.1_g000005
rosa_roxburghii	Rroxscaffold_1G00017270
rosa_rugosa	Rorug05G0357400
rosa_samantha	Rh5AG416500 Rh5BG431600 Rh5CG454900 Rh5DG445100
rosa_wichuraiana	Rw5G039120

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	188
AccI	GTMKAC	2 cut(s)	64, 275
AcsI	RAATTY	3 cut(s)	121, 416, 477
AfiI	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
AgsI	TTSAA	4 cut(s)	423, 433, 458, 548
AjnI	CCWGG	1 cut(s)	450
AluBI	AGCT	3 cut(s)	88, 97, 582
AluI	AGCT	3 cut(s)	88, 97, 582
Alw21I	GWGCWC	1 cut(s)	27
ApeKI	GCWGC	3 cut(s)	490, 570, 638
ApoI	RAATTY	3 cut(s)	121, 416, 477
Asp700I	GAANNNNTTC	1 cut(s)	98
AspS9I	GGNCC	1 cut(s)	436
AvaII	GGWCC	1 cut(s)	436
Bbv12I	GWGCWC	1 cut(s)	27
BbvI	GCAGC	3 cut(s)	502, 557, 625
BccI	CCATC	1 cut(s)	182
BciT130I	CCWGG	1 cut(s)	452
BfaI	CTAG	1 cut(s)	579
BisI	GCNGC	3 cut(s)	491, 571, 639
BlpI	GCTNAGC	1 cut(s)	53
BlsI	GCNGC	3 cut(s)	492, 572, 640
Bme1390I	CCNGG	1 cut(s)	452
Bme18I	GGWCC	1 cut(s)	436
BmgT120I	GGNCC	1 cut(s)	436
BmrFI	CCNGG	1 cut(s)	452
BmrI	ACTGGG	1 cut(s)	311
BmsI	GCATC	1 cut(s)	61
BmuI	ACTGGG	1 cut(s)	311
Bpu1102I	GCTNAGC	1 cut(s)	53
BpuEI	CTTGAG	1 cut(s)	110
BsaBI	GATNNNNATC	1 cut(s)	192
Bsc4I	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
Bse1I	ACTGG	2 cut(s)	289, 306
Bse3DI	GCAATG	1 cut(s)	29
Bse8I	GATNNNNATC	1 cut(s)	192
BseBI	CCWGG	1 cut(s)	452
BseGI	GGATG	2 cut(s)	193, 370
BseJI	GATNNNNATC	1 cut(s)	192
BseLI	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
BseMI	GCAATG	1 cut(s)	29
BseMII	CTCAG	1 cut(s)	608
BseNI	ACTGG	2 cut(s)	289, 306
BseXI	GCAGC	3 cut(s)	502, 557, 625
BsiHKAI	GWGCWC	1 cut(s)	27
BslFI	GGGAC	1 cut(s)	141
BslI	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
BsmFI	GGGAC	1 cut(s)	141
Bsp1286I	GDGCHC	1 cut(s)	27
Bsp143I	GATC	1 cut(s)	166
Bsp1720I	GCTNAGC	1 cut(s)	53
BspCNI	CTCAG	1 cut(s)	609
BsrDI	GCAATG	1 cut(s)	29
BsrI	ACTGG	2 cut(s)	289, 306
BssMI	GATC	1 cut(s)	166
Bst2UI	CCWGG	1 cut(s)	452
Bst4CI	ACNGT	2 cut(s)	11, 208
BstAPI	GCANNNNNTGC	1 cut(s)	31
BstDEI	CTNAG	3 cut(s)	53, 103, 617
BstF5I	GGATG	2 cut(s)	193, 370
BstKTI	GATC	1 cut(s)	169
BstMBI	GATC	1 cut(s)	166
BstMWI	GCNNNNNNNGC	3 cut(s)	31, 94, 579
BstNI	CCWGG	1 cut(s)	452
BstSCI	CCNGG	1 cut(s)	450
BstV1I	GCAGC	3 cut(s)	502, 557, 625
BtsCI	GGATG	2 cut(s)	193, 370
BtsIMutI	CAGTG	3 cut(s)	218, 282, 299
Cfr13I	GGNCC	1 cut(s)	436
CseI	GACGC	1 cut(s)	23
CviAII	CATG	2 cut(s)	351, 540
CviJI	RGCY	7 cut(s)	15, 57, 88, 97, 403, 493, 582
CviKI_1	RGCY	7 cut(s)	15, 57, 88, 97, 403, 493, 582
DdeI	CTNAG	3 cut(s)	53, 103, 617
DpnI	GATC	1 cut(s)	168
DpnII	GATC	1 cut(s)	166
Eco32I	GATATC	1 cut(s)	151
Eco47I	GGWCC	1 cut(s)	436
EcoRII	CCWGG	1 cut(s)	450
EcoRV	GATATC	1 cut(s)	151
FaeI	CATG	2 cut(s)	354, 543
FalI	AAGNNNNNCTT	2 cut(s)	86, 118
FaqI	GGGAC	1 cut(s)	141
FatI	CATG	2 cut(s)	350, 539
FauNDI	CATATG	1 cut(s)	558
FblI	GTMKAC	2 cut(s)	64, 275
Fnu4HI	GCNGC	3 cut(s)	491, 571, 639
FokI	GGATG	2 cut(s)	180, 377
Fsp4HI	GCNGC	3 cut(s)	491, 571, 639
FspBI	CTAG	1 cut(s)	579
GluI	GCNGC	3 cut(s)	491, 571, 639
HgaI	GACGC	1 cut(s)	23
Hin1II	CATG	2 cut(s)	354, 543
HinfI	GANTC	3 cut(s)	272, 368, 447
Hpy166II	GTNNAC	6 cut(s)	65, 216, 276, 290, 466, 623
Hpy188I	TCNGA	2 cut(s)	409, 618
Hpy188III	TCNNGA	2 cut(s)	118, 645
Hpy8I	GTNNAC	6 cut(s)	65, 216, 276, 290, 466, 623
HpyAV	CCTTC	5 cut(s)	54, 68, 355, 414, 427
HpyCH4III	ACNGT	2 cut(s)	11, 208
HpyCH4IV	ACGT	1 cut(s)	292
HpyCH4V	TGCA	4 cut(s)	74, 135, 260, 573
HpyF10VI	GCNNNNNNNGC	3 cut(s)	31, 94, 579
HpyF3I	CTNAG	3 cut(s)	53, 103, 617
HpySE526I	ACGT	1 cut(s)	292
Hsp92II	CATG	2 cut(s)	354, 543
Kzo9I	GATC	1 cut(s)	166
LpnPI	CCDG	7 cut(s)	270, 287, 437, 452, 464, 507, 568
Lsp1109I	GCAGC	3 cut(s)	502, 557, 625
LweI	GCATC	1 cut(s)	61
MaeI	CTAG	1 cut(s)	579
MaeII	ACGT	1 cut(s)	292
MaeIII	GTNAC	1 cut(s)	297
MalI	GATC	1 cut(s)	168
MboI	GATC	1 cut(s)	166
MfeI	CAATTG	2 cut(s)	423, 483
MhlI	GDGCHC	1 cut(s)	27
MluCI	AATT	8 cut(s)	18, 121, 252, 416, 423, 477, 483, 595
MlyI	GAGTC	2 cut(s)	281, 362
MmeI	TCCRAC	1 cut(s)	221
MnlI	CCTC	3 cut(s)	51, 517, 610
MroXI	GAANNNNTTC	1 cut(s)	98
MseI	TTAA	3 cut(s)	78, 162, 528
MspR9I	CCNGG	1 cut(s)	452
MunI	CAATTG	2 cut(s)	423, 483
MvaI	CCWGG	1 cut(s)	452
MwoI	GCNNNNNNNGC	3 cut(s)	31, 94, 579
NdeI	CATATG	1 cut(s)	558
NdeII	GATC	1 cut(s)	166
NlaIII	CATG	2 cut(s)	354, 543
NmuCI	GTSAC	1 cut(s)	297
PdmI	GAANNNNTTC	1 cut(s)	98
PfeI	GAWTC	1 cut(s)	447
PflMI	CCANNNNNTGG	1 cut(s)	188
PkrI	GCNGC	3 cut(s)	492, 572, 640
PleI	GAGTC	2 cut(s)	280, 362
PpsI	GAGTC	2 cut(s)	280, 362
Psp6I	CCWGG	1 cut(s)	450
PspGI	CCWGG	1 cut(s)	450
PspPI	GGNCC	1 cut(s)	436
SaqAI	TTAA	3 cut(s)	78, 162, 528
SatI	GCNGC	3 cut(s)	491, 571, 639
Sau3AI	GATC	1 cut(s)	166
Sau96I	GGNCC	1 cut(s)	436
SchI	GAGTC	2 cut(s)	281, 362
ScrFI	CCNGG	1 cut(s)	452
SduI	GDGCHC	1 cut(s)	27
SetI	ASST	9 cut(s)	90, 99, 114, 295, 331, 456, 528, 553, 584
SfaNI	GCATC	1 cut(s)	61
SinI	GGWCC	1 cut(s)	436
SmlI	CTYRAG	1 cut(s)	89
SmoI	CTYRAG	1 cut(s)	89
Sse9I	AATT	8 cut(s)	18, 121, 252, 416, 423, 477, 483, 595
SspMI	CTAG	1 cut(s)	579
StyD4I	CCNGG	1 cut(s)	450
TaaI	ACNGT	2 cut(s)	11, 208
TaiI	ACGT	1 cut(s)	295
TaqI	TCGA	1 cut(s)	119
TasI	AATT	8 cut(s)	18, 121, 252, 416, 423, 477, 483, 595
TfiI	GAWTC	1 cut(s)	447
Tru1I	TTAA	3 cut(s)	78, 162, 528
Tru9I	TTAA	3 cut(s)	78, 162, 528
TscAI	CASTG	3 cut(s)	225, 289, 306
TseFI	GTSAC	1 cut(s)	297
TseI	GCWGC	3 cut(s)	490, 570, 638
Tsp45I	GTSAC	1 cut(s)	297
TspDTI	ATGAA	3 cut(s)	163, 429, 528
TspRI	CASTG	3 cut(s)	225, 289, 306
Van91I	CCANNNNNTGG	1 cut(s)	188
VpaK11BI	GGWCC	1 cut(s)	436
XapI	RAATTY	3 cut(s)	121, 416, 477
XmiI	GTMKAC	2 cut(s)	64, 275
XmnI	GAANNNNTTC	1 cut(s)	98
XspI	CTAG	1 cut(s)	579

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