Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0006793

Physical Location & Seq

Genomic Coordinates Forward (+)

49917074 .. 49919849

Gene Structure 2776 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG279000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 783 bp

ATGAGTAGCACTAGTGTATTAGTTGCAGGCCTTCCCTGTCATCCAAACCTTAACGCCACTCTTTCTTCTCCAACTCCAACTCCAACTAATACATCAAACGCAAGGGATGGAGACAATTTGGTAATGAAGGTTGATGGGTTTAAGTGGCGTTTGGTTATAGCTTACGACGGCACCCGTTATTCAGGATGGCAATATCAGAGTTCACCACCTACCATACAGCGCTATGTGGAGAAAGCTCTAATGGGAGCAACGAAGCTGGAAAGGAAGGATCTTCATTTGGTTGGTGCAAGTAGGACAGATAAGGGTGTGCATGCTTGGGGTCAGGTTGCACACTTTGTCACACCGTTCAACTATGACAGAATAGAAAGCATTCATGCAGCTCTCAATGGTACTCTTCCAGAGGATATCCGTGTTAGGGAAATTAGTCCTGCTGTGCCTGAATTCCATGCTCGTTTTTCAGCCCAAAGGAAGGTGTATCATTACAGAATATATAATGACACATTCATGGACCCATTTCAGCGTCACAATTCTTACCATAGTGCTCATAAGTTGAACCCTGCTGTTATGAGAGAAGCTGCGAAGTATTTTATTGGAAAGCATGATTTCTCTGCTTTTGTAAATGCATCCCAGAAGGAGCGAGTGCGGGATCCAGTAAAGGATATATTCCGTTTTGATGTTGTCCAAATGGGGGCTCTTTTACAGCTTGAAGTTGAAGGCTCGGGATTCTTATATAGACAAGTCCGGAACATGGTGAGTAATTCATCTCCACCAACTTCATCATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_1

Protein Analysis

260

Amino Acids

29.37

Weight (kDa)

9.47

Isoelectric Point (pI)

36.82

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_1	PF01416	53 - 152	7.7e-09	tRNA pseudouridine synthase
PseudoU_synth_1	PF01416	192 - 252	4.8e-14	tRNA pseudouridine 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: OG0006793)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G06950
fragaria_vesca	FvH4_4g21570 FvH4_4g21570 FvH4_4g21570
malus_domestica	MD13G1140300.v1.1 MD16G1135500.v1.1
prunus_persica	Prupe.1G104700_v2.0.a1 Prupe.1G104700_v2.0.a1 Prupe.1G104700_v2.0.a1 Prupe.1G104700_v2.0.a1
pyrus_communis	pycom13g12200 pycom16g11950
rosa_chinensis	RchiOBHm_Chr4g0427681
rosa_laevigata	RLG00000007217
rosa_multiflora	Rmu_sc0003399.1_g000003 Rmu_sc0016038.1_g000001
rosa_roxburghii	Rroxscaffold_5G00369310
rosa_rugosa	Rorug04G0219100 Rorug04G0219200 Rorug04G0219300 Rorug04G0219400
rosa_samantha	Rh4AG275600 Rh4BG281600 Rh4CG297100 Rh4DG279000
rosa_wichuraiana	Rw4G023920

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	170
AccIII	TCCGGA	1 cut(s)	741
AciI	CCGC	1 cut(s)	643
AclWI	GGATC	3 cut(s)	276, 641, 654
AcsI	RAATTY	1 cut(s)	440
AfaI	GTAC	1 cut(s)	391
AfeI	AGCGCT	1 cut(s)	221
AfiI	CCNNNNNNNGG	4 cut(s)	415, 469, 688, 748
AgsI	TTSAA	4 cut(s)	349, 553, 707, 713
AhlI	ACTAGT	1 cut(s)	11
AluBI	AGCT	6 cut(s)	161, 236, 256, 380, 575, 703
AluI	AGCT	6 cut(s)	161, 236, 256, 380, 575, 703
Alw21I	GWGCWC	1 cut(s)	544
Alw26I	GTCTC	1 cut(s)	105
AlwI	GGATC	3 cut(s)	276, 641, 654
Ama87I	CYCGRG	1 cut(s)	718
Aor13HI	TCCGGA	1 cut(s)	741
Aor51HI	AGCGCT	1 cut(s)	221
AoxI	GGCC	1 cut(s)	28
ApeKI	GCWGC	2 cut(s)	377, 575
ApoI	RAATTY	1 cut(s)	440
Asp700I	GAANNNNTTC	1 cut(s)	369
AspLEI	GCGC	1 cut(s)	222
AspS9I	GGNCC	1 cut(s)	508
AsuHPI	GGTGA	2 cut(s)	195, 763
AvaI	CYCGRG	1 cut(s)	718
AvaII	GGWCC	1 cut(s)	508
BamHI	GGATCC	1 cut(s)	646
BanI	GGYRCC	1 cut(s)	170
BanII	GRGCYC	1 cut(s)	694
Bbv12I	GWGCWC	1 cut(s)	544
BbvI	GCAGC	2 cut(s)	389, 562
BccI	CCATC	3 cut(s)	101, 128, 180
BceAI	ACGGC	1 cut(s)	184
BcoDI	GTCTC	1 cut(s)	105
BcuI	ACTAGT	1 cut(s)	11
BfaI	CTAG	1 cut(s)	12
BfoI	RGCGCY	1 cut(s)	223
BisI	GCNGC	2 cut(s)	378, 576
BlsI	GCNGC	2 cut(s)	379, 577
Bme18I	GGWCC	1 cut(s)	508
BmeT110I	CYCGRG	1 cut(s)	718
BmgT120I	GGNCC	1 cut(s)	508
BmiI	GGNNCC	3 cut(s)	172, 510, 648
BmsI	GCATC	1 cut(s)	632
BsaWI	WCCGGW	1 cut(s)	741
BsaXI	ACNNNNNCTCC	2 cut(s)	64, 94
Bsc4I	CCNNNNNNNGG	4 cut(s)	415, 469, 688, 748
Bse1I	ACTGG	1 cut(s)	650
BseAI	TCCGGA	1 cut(s)	741
BseGI	GGATG	4 cut(s)	40, 112, 191, 623
BseLI	CCNNNNNNNGG	4 cut(s)	415, 469, 688, 748
BseNI	ACTGG	1 cut(s)	650
BseXI	GCAGC	2 cut(s)	389, 562
BshFI	GGCC	1 cut(s)	30
BshNI	GGYRCC	1 cut(s)	170
BsiHKAI	GWGCWC	1 cut(s)	544
BsiHKCI	CYCGRG	1 cut(s)	718
BsiSI	CCGG	1 cut(s)	742
BslI	CCNNNNNNNGG	4 cut(s)	415, 469, 688, 748
BsmAI	GTCTC	1 cut(s)	105
BsmI	GAATGC	1 cut(s)	369
BsnI	GGCC	1 cut(s)	30
BsoBI	CYCGRG	1 cut(s)	718
Bsp1286I	GDGCHC	2 cut(s)	544, 694
Bsp13I	TCCGGA	1 cut(s)	741
Bsp143I	GATC	2 cut(s)	268, 646
BspACI	CCGC	1 cut(s)	643
BspANI	GGCC	1 cut(s)	30
BspEI	TCCGGA	1 cut(s)	741
BspLI	GGNNCC	3 cut(s)	172, 510, 648
BspPI	GGATC	3 cut(s)	276, 641, 654
BspT107I	GGYRCC	1 cut(s)	170
BsrI	ACTGG	1 cut(s)	650
BssMI	GATC	2 cut(s)	268, 646
Bst4CI	ACNGT	1 cut(s)	345
Bst6I	CTCTTC	1 cut(s)	399
BstC8I	GCNNGC	2 cut(s)	28, 312
BstF5I	GGATG	4 cut(s)	40, 112, 191, 623
BstH2I	RGCGCY	1 cut(s)	223
BstHHI	GCGC	1 cut(s)	222
BstKTI	GATC	2 cut(s)	271, 649
BstMAI	GTCTC	1 cut(s)	105
BstMBI	GATC	2 cut(s)	268, 646
BstNSI	RCATGY	1 cut(s)	314
BstV1I	GCAGC	2 cut(s)	389, 562
BstX2I	RGATCY	2 cut(s)	268, 646
BstYI	RGATCY	2 cut(s)	268, 646
BsuRI	GGCC	1 cut(s)	30
BtsCI	GGATG	4 cut(s)	40, 112, 191, 623
Cac8I	GCNNGC	2 cut(s)	28, 312
CfoI	GCGC	1 cut(s)	222
Cfr13I	GGNCC	1 cut(s)	508
CseI	GACGC	1 cut(s)	509
Csp6I	GTAC	1 cut(s)	390
CviAII	CATG	6 cut(s)	311, 374, 446, 505, 599, 748
CviQI	GTAC	1 cut(s)	390
DpnI	GATC	2 cut(s)	270, 648
DpnII	GATC	2 cut(s)	268, 646
Eam1104I	CTCTTC	1 cut(s)	399
EarI	CTCTTC	1 cut(s)	399
Eco147I	AGGCCT	1 cut(s)	30
Eco24I	GRGCYC	1 cut(s)	694
Eco32I	GATATC	1 cut(s)	406
Eco47I	GGWCC	1 cut(s)	508
Eco47III	AGCGCT	1 cut(s)	221
Eco88I	CYCGRG	1 cut(s)	718
EcoRI	GAATTC	1 cut(s)	440
EcoRV	GATATC	1 cut(s)	406
EcoT22I	ATGCAT	1 cut(s)	625
EcoT38I	GRGCYC	1 cut(s)	694
FaeI	CATG	6 cut(s)	314, 377, 449, 508, 602, 751
FatI	CATG	6 cut(s)	310, 373, 445, 504, 598, 747
FauI	CCCGC	1 cut(s)	636
Fnu4HI	GCNGC	2 cut(s)	378, 576
FokI	GGATG	4 cut(s)	27, 119, 198, 610
FriOI	GRGCYC	1 cut(s)	694
Fsp4HI	GCNGC	2 cut(s)	378, 576
FspBI	CTAG	1 cut(s)	12
GlaI	GCGC	1 cut(s)	221
GluI	GCNGC	2 cut(s)	378, 576
HaeII	RGCGCY	1 cut(s)	223
HaeIII	GGCC	1 cut(s)	30
HapII	CCGG	1 cut(s)	742
HgaI	GACGC	1 cut(s)	509
HhaI	GCGC	1 cut(s)	222
Hin1II	CATG	6 cut(s)	314, 377, 449, 508, 602, 751
Hin6I	GCGC	1 cut(s)	220
HinP1I	GCGC	1 cut(s)	220
HinfI	GANTC	1 cut(s)	723
HpaII	CCGG	1 cut(s)	742
HphI	GGTGA	2 cut(s)	195, 763
Hpy166II	GTNNAC	1 cut(s)	203
Hpy188I	TCNGA	1 cut(s)	198
Hpy188III	TCNNGA	4 cut(s)	183, 398, 720, 742
Hpy8I	GTNNAC	1 cut(s)	203
Hpy99I	CGWCG	1 cut(s)	170
HpyAV	CCTTC	6 cut(s)	41, 121, 259, 463, 625, 707
HpyCH4III	ACNGT	1 cut(s)	345
HpyCH4V	TGCA	6 cut(s)	26, 287, 310, 329, 377, 623
Hsp92II	CATG	6 cut(s)	314, 377, 449, 508, 602, 751
HspAI	GCGC	1 cut(s)	220
Kpn2I	TCCGGA	1 cut(s)	741
Kzo9I	GATC	2 cut(s)	268, 646
LmnI	GCTCC	2 cut(s)	245, 634
Lsp1109I	GCAGC	2 cut(s)	389, 562
LweI	GCATC	1 cut(s)	632
MaeI	CTAG	1 cut(s)	12
MaeIII	GTNAC	2 cut(s)	337, 521
MalI	GATC	2 cut(s)	270, 648
MboI	GATC	2 cut(s)	268, 646
MboII	GAAGA	3 cut(s)	57, 263, 386
MflI	RGATCY	2 cut(s)	268, 646
MhlI	GDGCHC	2 cut(s)	544, 694
MluCI	AATT	5 cut(s)	115, 420, 440, 526, 757
MmeI	TCCRAC	3 cut(s)	95, 101, 107
MnlI	CCTC	1 cut(s)	394
Mph1103I	ATGCAT	1 cut(s)	625
MroI	TCCGGA	1 cut(s)	741
MroXI	GAANNNNTTC	1 cut(s)	369
MseI	TTAA	2 cut(s)	51, 141
MslI	CAYNNNNRTG	1 cut(s)	503
MspI	CCGG	1 cut(s)	742
Mva1269I	GAATGC	1 cut(s)	369
NdeII	GATC	2 cut(s)	268, 646
NlaIII	CATG	6 cut(s)	314, 377, 449, 508, 602, 751
NlaIV	GGNNCC	3 cut(s)	172, 510, 648
NmuCI	GTSAC	2 cut(s)	337, 521
NsiI	ATGCAT	1 cut(s)	625
NspI	RCATGY	1 cut(s)	314
PaeI	GCATGC	1 cut(s)	314
PceI	AGGCCT	1 cut(s)	30
PctI	GAATGC	1 cut(s)	369
PdmI	GAANNNNTTC	1 cut(s)	369
PfeI	GAWTC	1 cut(s)	723
PkrI	GCNGC	2 cut(s)	379, 577
PspN4I	GGNNCC	3 cut(s)	172, 510, 648
PspPI	GGNCC	1 cut(s)	508
PsuI	RGATCY	2 cut(s)	268, 646
RsaI	GTAC	1 cut(s)	391
RsaNI	GTAC	1 cut(s)	390
RseI	CAYNNNNRTG	1 cut(s)	503
SaqAI	TTAA	2 cut(s)	51, 141
SatI	GCNGC	2 cut(s)	378, 576
Sau3AI	GATC	2 cut(s)	268, 646
Sau96I	GGNCC	1 cut(s)	508
SduI	GDGCHC	2 cut(s)	544, 694
SfaNI	GCATC	1 cut(s)	632
SinI	GGWCC	1 cut(s)	508
SmiMI	CAYNNNNRTG	1 cut(s)	503
SpeI	ACTAGT	1 cut(s)	11
SphI	GCATGC	1 cut(s)	314
Sse9I	AATT	5 cut(s)	115, 420, 440, 526, 757
SseBI	AGGCCT	1 cut(s)	30
SsiI	CCGC	1 cut(s)	643
SspMI	CTAG	1 cut(s)	12
StuI	AGGCCT	1 cut(s)	30
TaaI	ACNGT	1 cut(s)	345
TasI	AATT	5 cut(s)	115, 420, 440, 526, 757
TfiI	GAWTC	1 cut(s)	723
Tru1I	TTAA	2 cut(s)	51, 141
Tru9I	TTAA	2 cut(s)	51, 141
TseFI	GTSAC	2 cut(s)	337, 521
TseI	GCWGC	2 cut(s)	377, 575
Tsp45I	GTSAC	2 cut(s)	337, 521
TspDTI	ATGAA	6 cut(s)	140, 263, 362, 493, 750, 765
TspGWI	ACGGA	2 cut(s)	398, 656
VpaK11BI	GGWCC	1 cut(s)	508
XapI	RAATTY	1 cut(s)	440
XceI	RCATGY	1 cut(s)	314
XmnI	GAANNNNTTC	1 cut(s)	369
XspI	CTAG	1 cut(s)	12
Zsp2I	ATGCAT	1 cut(s)	625

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