Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6B

Orthogroup ID

OG0001594

Physical Location & Seq

Genomic Coordinates Forward (+)

10253986 .. 10255626

Gene Structure 1641 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6BG065900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 462 bp

ATGGATCAAGGTGTTCAAGCACTTAAAAGGTTCCCTGATGATAAACAAGAAGAGGGACATTGTAGTGAAGAAGAAGTCAAGTTTATTTGTAGTCTCGTGTTGTATAAGGATCCAGCTATTGTTGTCATCAATAAACCCCCTGGATTGCTTGTTCAGGGCGGTATTGGAATCAAAAGGAGTTTAGATGAACTGGCTGCCACTTGTTTAAGTTACGGCTTTTCAGAACCCCCTCGTCTGGTACACAGACTTGACAGAGATTGTAGTGGTATCCTTGTGATGGGACGGCCACAAATAAGTGCAACAGTTTTGCATTCCCTCTTCCGTGAGAAAACTTTTGGAGCTGCAGATGATGTTATCGACCATGCTAAAGCCATTCTGCAAAGAAGGTATTGGGCATTCGTCATTGGATCTCCCAGACAACAAGAGGGGTTAATCTCAGTACGTGCCTTTAGGAAAGGTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001522 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0006139 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:0016853 GO:0016866 GO:0031119 GO:0034470 GO:0034641 GO:0034660 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_2

Protein Analysis

153

Amino Acids

17.03

Weight (kDa)

8.38

Isoelectric Point (pI)

46.14

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	40 - 135	3.5e-10	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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Orthologous Genes (Group: OG0001594)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G19440 AT3G19440
fragaria_vesca	FvH4_2g05120 FvH4_2g05120 FvH4_2g05120 FvH4_2g05120
malus_domestica	MD10G1097600.v1.1
prunus_persica	Prupe.8G135400_v2.0.a1 Prupe.8G135400_v2.0.a1 Prupe.8G135400_v2.0.a1
pyrus_communis	pycom01g14220 pycom10g08370
rosa_chinensis	RchiOBHm_Chr4g0415551 RchiOBHm_Chr6g0255041
rosa_laevigata	RLG00000003460 RLG00000014859 RLG00000014868 RLG00000018864 RLG00000024043 RLG00000027684
rosa_multiflora	Rmu_ssc0000011.1_g000078
rosa_roxburghii	Rroxscaffold_2G00121110 Rroxscaffold_6G00396470 Rroxscaffold_6G00402590 Rroxscaffold_7G00210260
rosa_rugosa	Rorug03G0278700 Rorug03G0278800 Rorug03G0278900 Rorug05G0556400 Rorug05G0556500
rosa_samantha	Rh1AG091300 Rh1AG167900 Rh1DG094800 Rh2BG117700 Rh2BG330200 Rh2DG118600 Rh3BG349000 Rh4CG206700 Rh5BG449900 Rh6AG035800 Rh6AG073700 Rh6BG065900 Rh6BG066100 Rh6BG131700 Rh7AG357100 Rh7CG374500
rosa_wichuraiana	Rw2G034900 Rw6G006400 Rw6G006410 Rw6G026380

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	159
AclWI	GGATC	4 cut(s)	12, 104, 117, 415
AcoI	YGGCCR	1 cut(s)	284
AfaI	GTAC	2 cut(s)	240, 441
AfiI	CCNNNNNNNGG	2 cut(s)	235, 277
AgsI	TTSAA	1 cut(s)	17
AjnI	CCWGG	1 cut(s)	139
AloI	GAACNNNNNNTCC	2 cut(s)	135, 167
AluBI	AGCT	2 cut(s)	116, 341
AluI	AGCT	2 cut(s)	116, 341
Alw26I	GTCTC	1 cut(s)	98
AlwI	GGATC	4 cut(s)	12, 104, 117, 415
AoxI	GGCC	1 cut(s)	284
ApeKI	GCWGC	2 cut(s)	194, 341
BamHI	GGATCC	1 cut(s)	109
BauI	CACGAG	1 cut(s)	95
BbvI	GCAGC	2 cut(s)	181, 328
BccI	CCATC	1 cut(s)	271
BceAI	ACGGC	2 cut(s)	229, 299
BciT130I	CCWGG	1 cut(s)	141
BciVI	GTATCC	1 cut(s)	278
BcoDI	GTCTC	1 cut(s)	98
BfmI	CTRYAG	1 cut(s)	342
BfuI	GTATCC	1 cut(s)	278
BisI	GCNGC	2 cut(s)	195, 342
BlsI	GCNGC	2 cut(s)	196, 343
Bme1390I	CCNGG	1 cut(s)	141
BmiI	GGNNCC	2 cut(s)	32, 111
BmrFI	CCNGG	1 cut(s)	141
BsaAI	YACGTR	1 cut(s)	443
BsaJI	CCNNGG	1 cut(s)	139
Bsc4I	CCNNNNNNNGG	2 cut(s)	235, 277
Bse1I	ACTGG	1 cut(s)	195
BseBI	CCWGG	1 cut(s)	141
BseDI	CCNNGG	1 cut(s)	139
BseLI	CCNNNNNNNGG	2 cut(s)	235, 277
BseMII	CTCAG	1 cut(s)	450
BseNI	ACTGG	1 cut(s)	195
BseXI	GCAGC	2 cut(s)	181, 328
BshFI	GGCC	1 cut(s)	286
BslFI	GGGAC	2 cut(s)	69, 294
BslI	CCNNNNNNNGG	2 cut(s)	235, 277
BsmAI	GTCTC	1 cut(s)	98
BsmFI	GGGAC	2 cut(s)	69, 294
BsmI	GAATGC	2 cut(s)	310, 395
BsnI	GGCC	1 cut(s)	286
Bsp143I	GATC	3 cut(s)	4, 109, 407
BspACI	CCGC	1 cut(s)	159
BspANI	GGCC	1 cut(s)	286
BspCNI	CTCAG	1 cut(s)	449
BspLI	GGNNCC	2 cut(s)	32, 111
BspMAI	CTGCAG	1 cut(s)	346
BspPI	GGATC	4 cut(s)	12, 104, 117, 415
BsrI	ACTGG	1 cut(s)	195
BssECI	CCNNGG	1 cut(s)	139
BssMI	GATC	3 cut(s)	4, 109, 407
BssSI	CACGAG	1 cut(s)	95
Bst2BI	CACGAG	1 cut(s)	95
Bst2UI	CCWGG	1 cut(s)	141
Bst4CI	ACNGT	1 cut(s)	304
Bst6I	CTCTTC	2 cut(s)	45, 323
BstBAI	YACGTR	1 cut(s)	443
BstDEI	CTNAG	1 cut(s)	436
BstKTI	GATC	3 cut(s)	7, 112, 410
BstMAI	GTCTC	1 cut(s)	98
BstMBI	GATC	3 cut(s)	4, 109, 407
BstNI	CCWGG	1 cut(s)	141
BstSCI	CCNGG	1 cut(s)	139
BstSFI	CTRYAG	1 cut(s)	342
BstV1I	GCAGC	2 cut(s)	181, 328
BstX2I	RGATCY	2 cut(s)	109, 407
BstYI	RGATCY	2 cut(s)	109, 407
BsuI	GTATCC	1 cut(s)	278
BsuRI	GGCC	1 cut(s)	286
Csp6I	GTAC	2 cut(s)	239, 440
CviAII	CATG	1 cut(s)	362
CviJI	RGCY	6 cut(s)	116, 194, 216, 286, 341, 371
CviKI_1	RGCY	6 cut(s)	116, 194, 216, 286, 341, 371
CviQI	GTAC	2 cut(s)	239, 440
DdeI	CTNAG	1 cut(s)	436
DpnI	GATC	3 cut(s)	6, 111, 409
DpnII	GATC	3 cut(s)	4, 109, 407
EaeI	YGGCCR	1 cut(s)	284
Eam1104I	CTCTTC	2 cut(s)	45, 323
EarI	CTCTTC	2 cut(s)	45, 323
EcoRII	CCWGG	1 cut(s)	139
FaeI	CATG	1 cut(s)	365
FaiI	YATR	2 cut(s)	105, 363
FaqI	GGGAC	2 cut(s)	69, 294
FatI	CATG	1 cut(s)	361
Fnu4HI	GCNGC	2 cut(s)	195, 342
Fsp4HI	GCNGC	2 cut(s)	195, 342
GluI	GCNGC	2 cut(s)	195, 342
HaeIII	GGCC	1 cut(s)	286
Hin1II	CATG	1 cut(s)	365
HinfI	GANTC	1 cut(s)	168
Hpy166II	GTNNAC	1 cut(s)	241
Hpy188I	TCNGA	1 cut(s)	223
Hpy8I	GTNNAC	1 cut(s)	241
HpyAV	CCTTC	1 cut(s)	378
HpyCH4III	ACNGT	1 cut(s)	304
HpyCH4IV	ACGT	1 cut(s)	442
HpyCH4V	TGCA	4 cut(s)	299, 310, 344, 379
HpyF3I	CTNAG	1 cut(s)	436
HpySE526I	ACGT	1 cut(s)	442
Hsp92II	CATG	1 cut(s)	365
Kzo9I	GATC	3 cut(s)	4, 109, 407
LmnI	GCTCC	1 cut(s)	338
LpnPI	CCDG	8 cut(s)	48, 126, 126, 140, 153, 176, 221, 427
Lsp1109I	GCAGC	2 cut(s)	181, 328
MaeII	ACGT	1 cut(s)	442
MaeIII	GTNAC	1 cut(s)	209
MalI	GATC	3 cut(s)	6, 111, 409
MboI	GATC	3 cut(s)	4, 109, 407
MboII	GAAGA	4 cut(s)	62, 80, 83, 310
MflI	RGATCY	2 cut(s)	109, 407
MnlI	CCTC	4 cut(s)	46, 240, 326, 418
MseI	TTAA	3 cut(s)	24, 206, 431
MslI	CAYNNNNRTG	1 cut(s)	63
MspR9I	CCNGG	1 cut(s)	141
Mva1269I	GAATGC	2 cut(s)	310, 395
MvaI	CCWGG	1 cut(s)	141
NdeII	GATC	3 cut(s)	4, 109, 407
NlaIII	CATG	1 cut(s)	365
NlaIV	GGNNCC	2 cut(s)	32, 111
PctI	GAATGC	2 cut(s)	310, 395
PfeI	GAWTC	1 cut(s)	168
PkrI	GCNGC	2 cut(s)	196, 343
Ppu21I	YACGTR	1 cut(s)	443
Psp6I	CCWGG	1 cut(s)	139
PspGI	CCWGG	1 cut(s)	139
PspN4I	GGNNCC	2 cut(s)	32, 111
PstI	CTGCAG	1 cut(s)	346
PsuI	RGATCY	2 cut(s)	109, 407
RsaI	GTAC	2 cut(s)	240, 441
RsaNI	GTAC	2 cut(s)	239, 440
RseI	CAYNNNNRTG	1 cut(s)	63
SaqAI	TTAA	3 cut(s)	24, 206, 431
SatI	GCNGC	2 cut(s)	195, 342
Sau3AI	GATC	3 cut(s)	4, 109, 407
ScrFI	CCNGG	1 cut(s)	141
SetI	ASST	7 cut(s)	13, 32, 118, 343, 389, 445, 460
SfcI	CTRYAG	1 cut(s)	342
SmiMI	CAYNNNNRTG	1 cut(s)	63
SsiI	CCGC	1 cut(s)	159
StyD4I	CCNGG	1 cut(s)	139
TaaI	ACNGT	1 cut(s)	304
TaiI	ACGT	1 cut(s)	445
TaqI	TCGA	1 cut(s)	357
TfiI	GAWTC	1 cut(s)	168
Tru1I	TTAA	3 cut(s)	24, 206, 431
Tru9I	TTAA	3 cut(s)	24, 206, 431
TseI	GCWGC	2 cut(s)	194, 341
TspDTI	ATGAA	1 cut(s)	201
TspGWI	ACGGA	1 cut(s)	311

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