Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0004698

Physical Location & Seq

Genomic Coordinates Reverse (-)

43668100 .. 43671732

Gene Structure 3633 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG331200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 465 bp

ATGAACATCTGCTTTGGAAATTTACAGCATTGCTTTGTTGGTCTACAGATAACAGTTGATGGAGAAGTTATTAGAGACTCGAATACGATCCTCAGGGTTGGTTCACAATTGGTCTATCATAGGCTTCCGTGGAGAGAGCCGGATGCGCCATACTTGCTGGAGGTTCTGTATGAGGATGATGATATGCTTGCTTTGAATAAGCCAGGCGGGCTACAAGTTTTACCTGGAGGTCTTTTCCAGCAACATATAGTTCTAACACAGCTCCTATGGCGGCAAACTCAGAAGATCCATCACTTAGCATGCCAAAAATCACATCTTGTTCATGTTCATCGCCTAGGAAGGGGCACTTCAGGAATACTGCTAGGTGCAAAGATAAATCATGCCAAAAAGCAACTTGCAGCATATTTTGCTGATGGGACATCCCATATTGGAGATGACAGTGACACCAACATGAAGCTTCTTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000154 GO:0000455 GO:0001522 GO:0003674 GO:0003824 GO:0006139 GO:0006364 GO:0006396 GO:0006399 GO:0006400 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009451 GO:0009982 GO:0009987 GO:0010467 GO:0016070 GO:0016072 GO:0016853 GO:0016866 GO:0022613 GO:0031118 GO:0031119 GO:0034470 GO:0034641 GO:0034660 GO:0042254 GO:0043170 GO:0043412 GO:0044085 GO:0044237 GO:0044238 GO:0046483 GO:0071704 GO:0071840 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_2

Protein Analysis

154

Amino Acids

17.27

Weight (kDa)

7.15

Isoelectric Point (pI)

36.53

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	62 - 138	4.8e-07	RNA pseudouridylate synthase

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)

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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: OG0004698)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G52260 AT3G52260 AT3G52260 AT3G52260
fragaria_vesca	FvH4_7g19860
malus_domestica	MD07G1176900.v1.1
prunus_persica	Prupe.2G215700_v2.0.a1 Prupe.2G215700_v2.0.a1
pyrus_communis	pycom07g17100
rosa_chinensis	RchiOBHm_Chr1g0363851 RchiOBHm_Chr2g0104231 RchiOBHm_Chr2g0110391 RchiOBHm_Chr5g0046841
rosa_laevigata	RLG00000027541 RLG00000030372
rosa_multiflora	Rmu_sc0002474.1_g000014
rosa_roxburghii	Rroxscaffold_4G00292920
rosa_rugosa	Rorug01G0309800 Rorug01G0309900
rosa_samantha	Rh1AG318300 Rh1BG281500 Rh1CG297900 Rh1DG312800 Rh3CG345100 Rh4AG103100 Rh4CG111400 Rh5AG515700 Rh5BG320500 Rh5DG331200
rosa_wichuraiana	Rw1G028250 Rw5G039760

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	43
AciI	CCGC	2 cut(s)	207, 271
AclWI	GGATC	2 cut(s)	82, 280
AcsI	RAATTY	1 cut(s)	19
AcuI	CTGAAG	1 cut(s)	333
AfiI	CCNNNNNNNGG	1 cut(s)	340
AgsI	TTSAA	1 cut(s)	196
AjnI	CCWGG	2 cut(s)	202, 223
AluBI	AGCT	2 cut(s)	262, 457
AluI	AGCT	2 cut(s)	262, 457
Alw26I	GTCTC	1 cut(s)	69
AlwI	GGATC	2 cut(s)	82, 280
ApeKI	GCWGC	1 cut(s)	398
ApoI	RAATTY	1 cut(s)	19
AspA2I	CCTAGG	1 cut(s)	334
AspLEI	GCGC	1 cut(s)	148
AvrII	CCTAGG	1 cut(s)	334
AxyI	CCTNAGG	1 cut(s)	92
BaeGI	GKGCMC	1 cut(s)	347
BbvI	GCAGC	1 cut(s)	410
BccI	CCATC	3 cut(s)	53, 297, 407
BciT130I	CCWGG	2 cut(s)	204, 225
BcoDI	GTCTC	1 cut(s)	69
BfaI	CTAG	2 cut(s)	335, 362
BfmI	CTRYAG	1 cut(s)	44
BglI	GCCNNNNNGGC	1 cut(s)	208
BisI	GCNGC	2 cut(s)	272, 399
BlnI	CCTAGG	1 cut(s)	334
BlsI	GCNGC	2 cut(s)	273, 400
Bme1390I	CCNGG	2 cut(s)	204, 225
BmrFI	CCNGG	2 cut(s)	204, 225
BmsI	GCATC	1 cut(s)	133
BpmI	CTGGAG	2 cut(s)	179, 246
BsaJI	CCNNGG	2 cut(s)	128, 334
BsaXI	ACNNNNNCTCC	2 cut(s)	152, 182
Bsc4I	CCNNNNNNNGG	1 cut(s)	340
Bse21I	CCTNAGG	1 cut(s)	92
Bse3DI	GCAATG	1 cut(s)	28
BseBI	CCWGG	2 cut(s)	204, 225
BseDI	CCNNGG	2 cut(s)	128, 334
BseGI	GGATG	3 cut(s)	148, 181, 419
BseLI	CCNNNNNNNGG	1 cut(s)	340
BseMI	GCAATG	1 cut(s)	28
BseMII	CTCAG	2 cut(s)	106, 293
BseSI	GKGCMC	1 cut(s)	347
BseXI	GCAGC	1 cut(s)	410
BsiSI	CCGG	1 cut(s)	140
BslFI	GGGAC	1 cut(s)	430
BslI	CCNNNNNNNGG	1 cut(s)	340
BsmAI	GTCTC	1 cut(s)	69
BsmFI	GGGAC	1 cut(s)	430
Bsp1286I	GDGCHC	1 cut(s)	347
Bsp143I	GATC	2 cut(s)	87, 285
BspACI	CCGC	2 cut(s)	207, 271
BspCNI	CTCAG	2 cut(s)	105, 292
BspPI	GGATC	2 cut(s)	82, 280
BsrDI	GCAATG	1 cut(s)	28
BssECI	CCNNGG	2 cut(s)	128, 334
BssMI	GATC	2 cut(s)	87, 285
BssT1I	CCWWGG	1 cut(s)	334
Bst2UI	CCWGG	2 cut(s)	204, 225
Bst4CI	ACNGT	2 cut(s)	55, 440
BstAPI	GCANNNNNTGC	1 cut(s)	407
BstC8I	GCNNGC	3 cut(s)	189, 209, 301
BstDEI	CTNAG	3 cut(s)	92, 279, 295
BstDSI	CCRYGG	1 cut(s)	128
BstF5I	GGATG	3 cut(s)	148, 181, 419
BstHHI	GCGC	1 cut(s)	148
BstKTI	GATC	2 cut(s)	90, 288
BstMAI	GTCTC	1 cut(s)	69
BstMBI	GATC	2 cut(s)	87, 285
BstMWI	GCNNNNNNNGC	5 cut(s)	145, 154, 208, 268, 407
BstNI	CCWGG	2 cut(s)	204, 225
BstNSI	RCATGY	1 cut(s)	303
BstSCI	CCNGG	2 cut(s)	202, 223
BstSFI	CTRYAG	1 cut(s)	44
BstSLI	GKGCMC	1 cut(s)	347
BstV1I	GCAGC	1 cut(s)	410
BstX2I	RGATCY	1 cut(s)	285
BstYI	RGATCY	1 cut(s)	285
Bsu36I	CCTNAGG	1 cut(s)	92
BtgI	CCRYGG	1 cut(s)	128
BtgZI	GCGATG	1 cut(s)	314
BtsCI	GGATG	3 cut(s)	148, 181, 419
BtsIMutI	CAGTG	1 cut(s)	445
Cac8I	GCNNGC	3 cut(s)	189, 209, 301
CfoI	GCGC	1 cut(s)	148
CviAII	CATG	4 cut(s)	300, 323, 380, 451
CviJI	RGCY	6 cut(s)	124, 139, 202, 211, 262, 457
CviKI_1	RGCY	6 cut(s)	124, 139, 202, 211, 262, 457
DdeI	CTNAG	3 cut(s)	92, 279, 295
DpnI	GATC	2 cut(s)	89, 287
DpnII	GATC	2 cut(s)	87, 285
Eco130I	CCWWGG	1 cut(s)	334
Eco57I	CTGAAG	1 cut(s)	333
Eco81I	CCTNAGG	1 cut(s)	92
EcoRII	CCWGG	2 cut(s)	202, 223
EcoT14I	CCWWGG	1 cut(s)	334
ErhI	CCWWGG	1 cut(s)	334
FaeI	CATG	4 cut(s)	303, 326, 383, 454
FalI	AAGNNNNNCTT	2 cut(s)	331, 363
FaqI	GGGAC	1 cut(s)	430
FatI	CATG	4 cut(s)	299, 322, 379, 450
FauI	CCCGC	1 cut(s)	200
FblI	GTMKAC	1 cut(s)	43
Fnu4HI	GCNGC	2 cut(s)	272, 399
FokI	GGATG	3 cut(s)	155, 188, 406
Fsp4HI	GCNGC	2 cut(s)	272, 399
FspBI	CTAG	2 cut(s)	335, 362
GlaI	GCGC	1 cut(s)	147
GluI	GCNGC	2 cut(s)	272, 399
GsuI	CTGGAG	2 cut(s)	179, 246
HapII	CCGG	1 cut(s)	140
HhaI	GCGC	1 cut(s)	148
Hin1II	CATG	4 cut(s)	303, 326, 383, 454
Hin6I	GCGC	1 cut(s)	146
HinP1I	GCGC	1 cut(s)	146
HindIII	AAGCTT	1 cut(s)	455
HinfI	GANTC	1 cut(s)	77
HpaII	CCGG	1 cut(s)	140
Hpy166II	GTNNAC	2 cut(s)	44, 104
Hpy188I	TCNGA	1 cut(s)	282
Hpy188III	TCNNGA	1 cut(s)	351
Hpy8I	GTNNAC	2 cut(s)	44, 104
HpyAV	CCTTC	1 cut(s)	333
HpyCH4III	ACNGT	2 cut(s)	55, 440
HpyCH4V	TGCA	2 cut(s)	368, 398
HpyF10VI	GCNNNNNNNGC	5 cut(s)	145, 154, 208, 268, 407
HpyF3I	CTNAG	3 cut(s)	92, 279, 295
Hsp92II	CATG	4 cut(s)	303, 326, 383, 454
HspAI	GCGC	1 cut(s)	146
Kzo9I	GATC	2 cut(s)	87, 285
LmnI	GCTCC	1 cut(s)	267
LpnPI	CCDG	9 cut(s)	79, 143, 153, 189, 210, 216, 237, 251, 336
Lsp1109I	GCAGC	1 cut(s)	410
LweI	GCATC	1 cut(s)	133
MaeI	CTAG	2 cut(s)	335, 362
MaeIII	GTNAC	1 cut(s)	440
MalI	GATC	2 cut(s)	89, 287
MboI	GATC	2 cut(s)	87, 285
MboII	GAAGA	1 cut(s)	295
MfeI	CAATTG	1 cut(s)	107
MflI	RGATCY	1 cut(s)	285
MhlI	GDGCHC	1 cut(s)	347
MluCI	AATT	2 cut(s)	19, 107
MlyI	GAGTC	1 cut(s)	71
MnlI	CCTC	4 cut(s)	101, 154, 166, 221
MslI	CAYNNNNRTG	1 cut(s)	449
MspI	CCGG	1 cut(s)	140
MspR9I	CCNGG	2 cut(s)	204, 225
MunI	CAATTG	1 cut(s)	107
MvaI	CCWGG	2 cut(s)	204, 225
MwoI	GCNNNNNNNGC	5 cut(s)	145, 154, 208, 268, 407
NdeII	GATC	2 cut(s)	87, 285
NlaIII	CATG	4 cut(s)	303, 326, 383, 454
NmuCI	GTSAC	1 cut(s)	440
NspI	RCATGY	1 cut(s)	303
PaeI	GCATGC	1 cut(s)	303
PkrI	GCNGC	2 cut(s)	273, 400
PleI	GAGTC	1 cut(s)	71
PpsI	GAGTC	1 cut(s)	71
Psp6I	CCWGG	2 cut(s)	202, 223
PspGI	CCWGG	2 cut(s)	202, 223
PsuI	RGATCY	1 cut(s)	285
RseI	CAYNNNNRTG	1 cut(s)	449
SatI	GCNGC	2 cut(s)	272, 399
Sau3AI	GATC	2 cut(s)	87, 285
SchI	GAGTC	1 cut(s)	71
ScrFI	CCNGG	2 cut(s)	204, 225
SduI	GDGCHC	1 cut(s)	347
SetI	ASST	6 cut(s)	165, 226, 232, 264, 367, 459
SfaNI	GCATC	1 cut(s)	133
SfcI	CTRYAG	1 cut(s)	44
SmiMI	CAYNNNNRTG	1 cut(s)	449
SphI	GCATGC	1 cut(s)	303
Sse9I	AATT	2 cut(s)	19, 107
SsiI	CCGC	2 cut(s)	207, 271
SspMI	CTAG	2 cut(s)	335, 362
StyD4I	CCNGG	2 cut(s)	202, 223
StyI	CCWWGG	1 cut(s)	334
TaaI	ACNGT	2 cut(s)	55, 440
TaqI	TCGA	1 cut(s)	80
TasI	AATT	2 cut(s)	19, 107
TauI	GCSGC	1 cut(s)	274
TscAI	CASTG	1 cut(s)	445
TseFI	GTSAC	1 cut(s)	440
TseI	GCWGC	1 cut(s)	398
Tsp45I	GTSAC	1 cut(s)	440
TspDTI	ATGAA	3 cut(s)	17, 311, 317
TspGWI	ACGGA	1 cut(s)	117
TspRI	CASTG	1 cut(s)	445
XapI	RAATTY	1 cut(s)	19
XceI	RCATGY	1 cut(s)	303
XmaJI	CCTAGG	1 cut(s)	334
XmiI	GTMKAC	1 cut(s)	43
XspI	CTAG	2 cut(s)	335, 362

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