Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0004698

Physical Location & Seq

Genomic Coordinates Reverse (-)

39161688 .. 39163659

Gene Structure 1972 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG345100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 464 bp

ATGAACATCTGCTTTGGAAATTTACAGCATTGCTTTGTTGGTCTACATATAACAGTTGATGGAGAAGTTATTAGAGACTCGAATACGATCCTCAGGGTTGGTTCACAATTGTATGAGGATGATGATATGATTGCTTTGAATAAGCCAGGCAGGCTACAAGTTTTACCTGGAGGTCTTTTCCAGCAACGGACAGTTCTAACACAACTCCTATGGCGGCAAACTCAAAAGATCCATCACTTAGCATGCCAAAAATCACATCTTGTTCCTGTTCATCGCCTAGGAAGGGGCACTTCAGGAATACTGCTATGTGCAAAGATAAATCATGCCAAAAAGCAACTTGCAGCATATTTTGCTGATGGGACATCCCATATTGGAGATGACAGGAAAATCTCAAAGATATACAGGGCCCTAGGGACTGGGATACTTTGTGAGGAGGAGGTAATACTATCTCATGAGACTCTGAA

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

17.19

Weight (kDa)

8.66

Isoelectric Point (pI)

37.48

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	43 - 139	1.5e-09	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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Publication-ready

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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	1 cut(s)	214
AclWI	GGATC	2 cut(s)	82, 223
AcsI	RAATTY	1 cut(s)	19
AcuI	CTGAAG	1 cut(s)	276
AfiI	CCNNNNNNNGG	1 cut(s)	283
AgsI	TTSAA	1 cut(s)	139
AjnI	CCWGG	2 cut(s)	145, 166
Alw26I	GTCTC	2 cut(s)	69, 449
AlwI	GGATC	2 cut(s)	82, 223
AoxI	GGCC	1 cut(s)	405
ApaI	GGGCCC	1 cut(s)	409
ApeKI	GCWGC	1 cut(s)	341
ApoI	RAATTY	1 cut(s)	19
AspA2I	CCTAGG	2 cut(s)	277, 409
AspS9I	GGNCC	2 cut(s)	405, 406
AvrII	CCTAGG	2 cut(s)	277, 409
AxyI	CCTNAGG	1 cut(s)	92
BaeGI	GKGCMC	2 cut(s)	290, 409
BanII	GRGCYC	1 cut(s)	409
BbvI	GCAGC	1 cut(s)	353
BccI	CCATC	3 cut(s)	53, 240, 350
BciT130I	CCWGG	2 cut(s)	147, 168
BciVI	GTATCC	1 cut(s)	414
BcoDI	GTCTC	2 cut(s)	69, 449
BfaI	CTAG	2 cut(s)	278, 410
BfuI	GTATCC	1 cut(s)	414
BglI	GCCNNNNNGGC	1 cut(s)	151
BisI	GCNGC	2 cut(s)	215, 342
BlnI	CCTAGG	2 cut(s)	277, 409
BlsI	GCNGC	2 cut(s)	216, 343
Bme1390I	CCNGG	2 cut(s)	147, 168
BmgT120I	GGNCC	2 cut(s)	405, 406
BmiI	GGNNCC	1 cut(s)	407
BmrFI	CCNGG	2 cut(s)	147, 168
BmrI	ACTGGG	1 cut(s)	426
BmuI	ACTGGG	1 cut(s)	426
BpmI	CTGGAG	1 cut(s)	189
BsaJI	CCNNGG	2 cut(s)	277, 409
Bsc4I	CCNNNNNNNGG	1 cut(s)	283
Bse1I	ACTGG	1 cut(s)	421
Bse21I	CCTNAGG	1 cut(s)	92
Bse3DI	GCAATG	1 cut(s)	28
BseBI	CCWGG	2 cut(s)	147, 168
BseDI	CCNNGG	2 cut(s)	277, 409
BseGI	GGATG	2 cut(s)	124, 362
BseLI	CCNNNNNNNGG	1 cut(s)	283
BseMI	GCAATG	1 cut(s)	28
BseMII	CTCAG	1 cut(s)	106
BseNI	ACTGG	1 cut(s)	421
BseRI	GAGGAG	2 cut(s)	446, 449
BseSI	GKGCMC	2 cut(s)	290, 409
BseXI	GCAGC	1 cut(s)	353
BshFI	GGCC	1 cut(s)	407
BslFI	GGGAC	2 cut(s)	373, 427
BslI	CCNNNNNNNGG	1 cut(s)	283
BsmAI	GTCTC	2 cut(s)	69, 449
BsmFI	GGGAC	2 cut(s)	373, 427
BsnI	GGCC	1 cut(s)	407
Bsp120I	GGGCCC	1 cut(s)	405
Bsp1286I	GDGCHC	2 cut(s)	290, 409
Bsp143I	GATC	2 cut(s)	87, 228
BspACI	CCGC	1 cut(s)	214
BspANI	GGCC	1 cut(s)	407
BspCNI	CTCAG	1 cut(s)	105
BspHI	TCATGA	1 cut(s)	451
BspLI	GGNNCC	1 cut(s)	407
BspPI	GGATC	2 cut(s)	82, 223
BsrDI	GCAATG	1 cut(s)	28
BsrI	ACTGG	1 cut(s)	421
BssECI	CCNNGG	2 cut(s)	277, 409
BssMI	GATC	2 cut(s)	87, 228
BssT1I	CCWWGG	2 cut(s)	277, 409
Bst2UI	CCWGG	2 cut(s)	147, 168
Bst4CI	ACNGT	2 cut(s)	55, 193
BstAPI	GCANNNNNTGC	1 cut(s)	350
BstC8I	GCNNGC	2 cut(s)	152, 244
BstDEI	CTNAG	2 cut(s)	92, 238
BstF5I	GGATG	2 cut(s)	124, 362
BstKTI	GATC	2 cut(s)	90, 231
BstMAI	GTCTC	2 cut(s)	69, 449
BstMBI	GATC	2 cut(s)	87, 228
BstMWI	GCNNNNNNNGC	2 cut(s)	151, 350
BstNI	CCWGG	2 cut(s)	147, 168
BstNSI	RCATGY	1 cut(s)	246
BstSCI	CCNGG	2 cut(s)	145, 166
BstSLI	GKGCMC	2 cut(s)	290, 409
BstV1I	GCAGC	1 cut(s)	353
BstX2I	RGATCY	1 cut(s)	228
BstYI	RGATCY	1 cut(s)	228
Bsu36I	CCTNAGG	1 cut(s)	92
BsuI	GTATCC	1 cut(s)	414
BsuRI	GGCC	1 cut(s)	407
BtgZI	GCGATG	1 cut(s)	257
BtsCI	GGATG	2 cut(s)	124, 362
Cac8I	GCNNGC	2 cut(s)	152, 244
CciI	TCATGA	1 cut(s)	451
Cfr13I	GGNCC	2 cut(s)	405, 406
CviAII	CATG	3 cut(s)	243, 323, 452
CviJI	RGCY	3 cut(s)	145, 154, 407
CviKI_1	RGCY	3 cut(s)	145, 154, 407
DdeI	CTNAG	2 cut(s)	92, 238
DpnI	GATC	2 cut(s)	89, 230
DpnII	GATC	2 cut(s)	87, 228
Eco130I	CCWWGG	2 cut(s)	277, 409
Eco24I	GRGCYC	1 cut(s)	409
Eco57I	CTGAAG	1 cut(s)	276
Eco81I	CCTNAGG	1 cut(s)	92
EcoO109I	RGGNCCY	2 cut(s)	405, 406
EcoRII	CCWGG	2 cut(s)	145, 166
EcoT14I	CCWWGG	2 cut(s)	277, 409
EcoT38I	GRGCYC	1 cut(s)	409
ErhI	CCWWGG	2 cut(s)	277, 409
FaeI	CATG	3 cut(s)	246, 326, 455
FalI	AAGNNNNNCTT	2 cut(s)	274, 306
FaqI	GGGAC	2 cut(s)	373, 427
FatI	CATG	3 cut(s)	242, 322, 451
FblI	GTMKAC	1 cut(s)	43
Fnu4HI	GCNGC	2 cut(s)	215, 342
FokI	GGATG	2 cut(s)	131, 349
FriOI	GRGCYC	1 cut(s)	409
Fsp4HI	GCNGC	2 cut(s)	215, 342
FspBI	CTAG	2 cut(s)	278, 410
GluI	GCNGC	2 cut(s)	215, 342
GsuI	CTGGAG	1 cut(s)	189
HaeIII	GGCC	1 cut(s)	407
Hin1II	CATG	3 cut(s)	246, 326, 455
HinfI	GANTC	2 cut(s)	77, 457
Hpy166II	GTNNAC	2 cut(s)	44, 104
Hpy188I	TCNGA	1 cut(s)	462
Hpy188III	TCNNGA	2 cut(s)	294, 452
Hpy8I	GTNNAC	2 cut(s)	44, 104
HpyAV	CCTTC	1 cut(s)	276
HpyCH4III	ACNGT	2 cut(s)	55, 193
HpyCH4V	TGCA	2 cut(s)	311, 341
HpyF10VI	GCNNNNNNNGC	2 cut(s)	151, 350
HpyF3I	CTNAG	2 cut(s)	92, 238
Hsp92II	CATG	3 cut(s)	246, 326, 455
Kzo9I	GATC	2 cut(s)	87, 228
Lsp1109I	GCAGC	1 cut(s)	353
MaeI	CTAG	2 cut(s)	278, 410
MalI	GATC	2 cut(s)	89, 230
MboI	GATC	2 cut(s)	87, 228
MfeI	CAATTG	1 cut(s)	107
MflI	RGATCY	1 cut(s)	228
MhlI	GDGCHC	2 cut(s)	290, 409
MluCI	AATT	2 cut(s)	19, 107
MlyI	GAGTC	2 cut(s)	71, 451
MnlI	CCTC	6 cut(s)	101, 109, 164, 424, 427, 430
MspR9I	CCNGG	2 cut(s)	147, 168
MunI	CAATTG	1 cut(s)	107
MvaI	CCWGG	2 cut(s)	147, 168
MwoI	GCNNNNNNNGC	2 cut(s)	151, 350
NdeII	GATC	2 cut(s)	87, 228
NlaIII	CATG	3 cut(s)	246, 326, 455
NlaIV	GGNNCC	1 cut(s)	407
NspI	RCATGY	1 cut(s)	246
PaeI	GCATGC	1 cut(s)	246
PagI	TCATGA	1 cut(s)	451
PkrI	GCNGC	2 cut(s)	216, 343
PleI	GAGTC	2 cut(s)	71, 451
PpsI	GAGTC	2 cut(s)	71, 451
Psp6I	CCWGG	2 cut(s)	145, 166
PspGI	CCWGG	2 cut(s)	145, 166
PspN4I	GGNNCC	1 cut(s)	407
PspOMI	GGGCCC	1 cut(s)	405
PspPI	GGNCC	2 cut(s)	405, 406
PsuI	RGATCY	1 cut(s)	228
SatI	GCNGC	2 cut(s)	215, 342
Sau3AI	GATC	2 cut(s)	87, 228
Sau96I	GGNCC	2 cut(s)	405, 406
SchI	GAGTC	2 cut(s)	71, 451
ScrFI	CCNGG	2 cut(s)	147, 168
SduI	GDGCHC	2 cut(s)	290, 409
SetI	ASST	3 cut(s)	169, 175, 441
SphI	GCATGC	1 cut(s)	246
Sse9I	AATT	2 cut(s)	19, 107
SsiI	CCGC	1 cut(s)	214
SspMI	CTAG	2 cut(s)	278, 410
StyD4I	CCNGG	2 cut(s)	145, 166
StyI	CCWWGG	2 cut(s)	277, 409
TaaI	ACNGT	2 cut(s)	55, 193
TaqI	TCGA	1 cut(s)	80
TasI	AATT	2 cut(s)	19, 107
TauI	GCSGC	1 cut(s)	217
TseI	GCWGC	1 cut(s)	341
TspDTI	ATGAA	2 cut(s)	17, 260
TspGWI	ACGGA	1 cut(s)	202
XapI	RAATTY	1 cut(s)	19
XceI	RCATGY	1 cut(s)	246
XmaJI	CCTAGG	2 cut(s)	277, 409
XmiI	GTMKAC	1 cut(s)	43
XspI	CTAG	2 cut(s)	278, 410

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