Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000001

Orthogroup ID

OG0004793

Physical Location & Seq

Genomic Coordinates Forward (+)

24547254 .. 24553156

Gene Structure 5903 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_1G00020210.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1050 bp

ATGTCGGAAAATCTGAAGCACTCACTAGAGAGTTGCTCCCAATCTCCCGAAAGGTCTTCAAAGATTTCGAAAACCAGGGAGGAGCGAGAACCAGAACCGATGAGCCAACCCTCCGGAATTCAACGCTATCTGATCGCAATAGAGTACATTGGTACTCGCTTCTCTGGCTCTCAGCAACAGTCCAATTGCCGCACTGTAGTTGGCGTTCTTGAGGAGGCTTTTCGTAAATTTATTGGGCAGCCGGTGTCAATCTTCTGCTCAAGTCGAACTGATGCAGGAGTCCATGCCTTATCCAATGTTTGTCATGTAGACATTGAGCGCATAAGCAAAAGAAAGCCTGGTGAAGTGTTACCACCTCATGAACCTACAGTGGTCCAAAAAGCTGTAAACCATTTCTTACAGAAGAATGAAGGTGATGTAATGGTGGTGGATGTACAAAAAGTTCCAGCTGATTTTCATGCTAGATTTAAAGCCCAAGAACGCACGTACTTCTATCGCTTGCTATCTGGGCCAGAGCCTTTATCAATCTTCGAAAAAGACCGTGCATGGCATGTACCTGAGGATCTGGATATTTTGGCTATGCAGGAAGCTTGCAAAATTCTGGTTGGACACCATGATTTTAGTTCCTTTAGAGCAGCAGGTTGTCAGGCGAAGTCACCGATCAGAACACTAGATGAGTTGAATGTGTCTGAGGTTATCTCAACTCCAAACTTTCCAACAATTCCAGAGAGGAAAAGCAATTTAGTGCAGGAAGATACTCATTGCACCAACAAATCTGAGACCAACTGCCACCCTAGTTTCAATGGAGGAACTTATCAAGGATTTGGCTTGAGAAAAAAACACAGATGCTTTGTGGTAACAGCTCGAGCACGTGCTTTTCTATACCACCAGGTAAGACTGCTTGTTGGTGTCCTCAAATGTGTTGGAACTGGAGATCTAAAAATACCCGATGTGGAGAGGATCTTGAATGCAAAGACAGTGACTGCTGCTAGCCCCATGGCACCTGCTTGTGGTCTATATCTTGGACATGTGAGATACGATTTGCCATGA

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

349

Amino Acids

39.07

Weight (kDa)

8.58

Isoelectric Point (pI)

48.86

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_1	PF01416	45 - 156	3.3e-08	tRNA pseudouridine synthase
PseudoU_synth_1	PF01416	197 - 347	2.7e-25	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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0004793)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G09800 AT1G09800
fragaria_vesca	FvH4_3g33250
malus_domestica	MD08G1241400.v1.1 MD15G1435400.v1.1
prunus_persica	Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1 Prupe.1G579000_v2.0.a1
pyrus_communis	pycom08g20930 pycom15g38410
rosa_chinensis	RchiOBHm_Chr3g0481081 RchiOBHm_Chr5g0060601
rosa_laevigata	RLG00000035374
rosa_multiflora	Rmu_sc0001650.1_g000001 Rmu_sc0020761.1_g000005
rosa_roxburghii	Rroxscaffold_1G00020210 Rroxscaffold_7G00212020
rosa_rugosa	Rorug05G0331000
rosa_samantha	Rh3AG240400 Rh5AG395500 Rh5BG407800 Rh5CG432300 Rh5DG422700
rosa_wichuraiana	Rw5G037210

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	1012
Acc36I	ACCTGC	2 cut(s)	629, 1012
AccB1I	GGYRCC	1 cut(s)	1000
AccI	GTMKAC	1 cut(s)	309
AccIII	TCCGGA	1 cut(s)	113
AciI	CCGC	1 cut(s)	190
AclWI	GGATC	2 cut(s)	570, 968
AcsI	RAATTY	3 cut(s)	117, 227, 597
AcuI	CTGAAG	1 cut(s)	35
AcvI	CACGTG	1 cut(s)	872
AfaI	GTAC	5 cut(s)	146, 154, 435, 488, 555
AfiI	CCNNNNNNNGG	1 cut(s)	1010
AflIII	ACRYGT	1 cut(s)	1027
AgsI	TTSAA	5 cut(s)	60, 122, 682, 802, 967
AjnI	CCWGG	3 cut(s)	74, 337, 888
AluBI	AGCT	4 cut(s)	383, 449, 590, 863
AluI	AGCT	4 cut(s)	383, 449, 590, 863
Alw21I	GWGCWC	1 cut(s)	871
Alw26I	GTCTC	1 cut(s)	773
AlwI	GGATC	2 cut(s)	570, 968
AlwNI	CAGNNNCTG	1 cut(s)	983
Ama87I	CYCGRG	1 cut(s)	864
Aor13HI	TCCGGA	1 cut(s)	113
AoxI	GGCC	1 cut(s)	509
ApeKI	GCWGC	3 cut(s)	238, 635, 986
ApoI	RAATTY	3 cut(s)	117, 227, 597
AspLEI	GCGC	1 cut(s)	321
AspS9I	GGNCC	2 cut(s)	373, 509
AsuHPI	GGTGA	3 cut(s)	353, 425, 648
AsuII	TTCGAA	2 cut(s)	68, 531
AsuNHI	GCTAGC	1 cut(s)	989
AvaI	CYCGRG	1 cut(s)	864
AvaII	GGWCC	1 cut(s)	373
AxyI	CCTNAGG	1 cut(s)	558
BanI	GGYRCC	1 cut(s)	1000
BbrPI	CACGTG	1 cut(s)	872
BbsI	GAAGAC	1 cut(s)	48
Bbv12I	GWGCWC	1 cut(s)	871
BbvI	GCAGC	3 cut(s)	250, 647, 973
BciT130I	CCWGG	3 cut(s)	76, 339, 890
BcoDI	GTCTC	1 cut(s)	773
BfaI	CTAG	5 cut(s)	26, 462, 671, 795, 990
BfmI	CTRYAG	2 cut(s)	195, 366
BfuAI	ACCTGC	2 cut(s)	629, 1012
BglII	AGATCT	1 cut(s)	934
BisI	GCNGC	4 cut(s)	190, 239, 636, 987
BlsI	GCNGC	4 cut(s)	191, 240, 637, 988
Bme1390I	CCNGG	3 cut(s)	76, 339, 890
Bme18I	GGWCC	1 cut(s)	373
BmeT110I	CYCGRG	1 cut(s)	864
BmgT120I	GGNCC	2 cut(s)	373, 509
BmiI	GGNNCC	1 cut(s)	1002
BmrFI	CCNGG	3 cut(s)	76, 339, 890
BmsI	GCATC	2 cut(s)	262, 836
BmtI	GCTAGC	1 cut(s)	993
BpiI	GAAGAC	1 cut(s)	48
BplI	GAGNNNNNCTC	4 cut(s)	20, 52, 683, 715
BpmI	CTGGAG	1 cut(s)	951
Bpu14I	TTCGAA	2 cut(s)	68, 531
BpuEI	CTTGAG	3 cut(s)	230, 244, 850
BsaAI	YACGTR	2 cut(s)	486, 872
BsaI	GGTCTC	1 cut(s)	773
BsaJI	CCNNGG	2 cut(s)	75, 996
BsaWI	WCCGGW	1 cut(s)	113
Bsc4I	CCNNNNNNNGG	1 cut(s)	1010
Bse118I	RCCGGY	1 cut(s)	241
Bse1I	ACTGG	1 cut(s)	934
Bse21I	CCTNAGG	1 cut(s)	558
Bse3DI	GCAATG	1 cut(s)	760
BseAI	TCCGGA	1 cut(s)	113
BseBI	CCWGG	3 cut(s)	76, 339, 890
BseDI	CCNNGG	2 cut(s)	75, 996
BseGI	GGATG	1 cut(s)	436
BseLI	CCNNNNNNNGG	1 cut(s)	1010
BseMI	GCAATG	1 cut(s)	760
BseMII	CTCAG	4 cut(s)	185, 549, 681, 768
BseNI	ACTGG	1 cut(s)	934
BseRI	GAGGAG	2 cut(s)	95, 227
BseXI	GCAGC	3 cut(s)	250, 647, 973
BsgI	GTGCAG	1 cut(s)	767
BshFI	GGCC	1 cut(s)	511
BshNI	GGYRCC	1 cut(s)	1000
BsiHKAI	GWGCWC	1 cut(s)	871
BsiHKCI	CYCGRG	1 cut(s)	864
BsiSI	CCGG	2 cut(s)	114, 242
BslI	CCNNNNNNNGG	1 cut(s)	1010
BsmAI	GTCTC	1 cut(s)	773
BsmI	GAATGC	1 cut(s)	973
BsnI	GGCC	1 cut(s)	511
Bso31I	GGTCTC	1 cut(s)	773
BsoBI	CYCGRG	1 cut(s)	864
Bsp119I	TTCGAA	2 cut(s)	68, 531
Bsp1286I	GDGCHC	1 cut(s)	871
Bsp13I	TCCGGA	1 cut(s)	113
Bsp1407I	TGTACA	1 cut(s)	433
Bsp143I	GATC	5 cut(s)	132, 562, 660, 934, 960
Bsp19I	CCATGG	1 cut(s)	996
BspACI	CCGC	1 cut(s)	190
BspANI	GGCC	1 cut(s)	511
BspCNI	CTCAG	4 cut(s)	184, 550, 682, 769
BspEI	TCCGGA	1 cut(s)	113
BspHI	TCATGA	1 cut(s)	358
BspLI	GGNNCC	1 cut(s)	1002
BspMI	ACCTGC	2 cut(s)	629, 1012
BspOI	GCTAGC	1 cut(s)	993
BspPI	GGATC	2 cut(s)	570, 968
BspT104I	TTCGAA	2 cut(s)	68, 531
BspT107I	GGYRCC	1 cut(s)	1000
BspTNI	GGTCTC	1 cut(s)	773
BsrDI	GCAATG	1 cut(s)	760
BsrFI	RCCGGY	1 cut(s)	241
BsrGI	TGTACA	1 cut(s)	433
BsrI	ACTGG	1 cut(s)	934
BssAI	RCCGGY	1 cut(s)	241
BssECI	CCNNGG	2 cut(s)	75, 996
BssMI	GATC	5 cut(s)	132, 562, 660, 934, 960
BssT1I	CCWWGG	1 cut(s)	996
Bst2UI	CCWGG	3 cut(s)	76, 339, 890
Bst4CI	ACNGT	5 cut(s)	180, 196, 370, 542, 979
BstAUI	TGTACA	1 cut(s)	433
BstBAI	YACGTR	2 cut(s)	486, 872
BstBI	TTCGAA	2 cut(s)	68, 531
BstC8I	GCNNGC	3 cut(s)	500, 592, 991
BstDEI	CTNAG	4 cut(s)	171, 558, 690, 777
BstDSI	CCRYGG	1 cut(s)	996
BstF5I	GGATG	1 cut(s)	436
BstHHI	GCGC	1 cut(s)	321
BstKTI	GATC	5 cut(s)	135, 565, 663, 937, 963
BstMAI	GTCTC	1 cut(s)	773
BstMBI	GATC	5 cut(s)	132, 562, 660, 934, 960
BstMWI	GCNNNNNNNGC	2 cut(s)	165, 508
BstNI	CCWGG	3 cut(s)	76, 339, 890
BstNSI	RCATGY	2 cut(s)	554, 1031
BstSCI	CCNGG	3 cut(s)	74, 337, 888
BstSFI	CTRYAG	2 cut(s)	195, 366
BstV1I	GCAGC	3 cut(s)	250, 647, 973
BstV2I	GAAGAC	1 cut(s)	48
BstX2I	RGATCY	3 cut(s)	562, 934, 960
BstYI	RGATCY	3 cut(s)	562, 934, 960
Bsu36I	CCTNAGG	1 cut(s)	558
BsuRI	GGCC	1 cut(s)	511
BtgI	CCRYGG	1 cut(s)	996
BtsCI	GGATG	1 cut(s)	436
BtsIMutI	CAGTG	3 cut(s)	192, 375, 984
BveI	ACCTGC	2 cut(s)	629, 1012
Cac8I	GCNNGC	3 cut(s)	500, 592, 991
CaiI	CAGNNNCTG	1 cut(s)	983
CciI	TCATGA	1 cut(s)	358
CfoI	GCGC	1 cut(s)	321
Cfr10I	RCCGGY	1 cut(s)	241
Cfr13I	GGNCC	2 cut(s)	373, 509
CsiI	ACCWGGT	1 cut(s)	888
Csp6I	GTAC	5 cut(s)	145, 153, 434, 487, 554
CviQI	GTAC	5 cut(s)	145, 153, 434, 487, 554
DdeI	CTNAG	4 cut(s)	171, 558, 690, 777
DpnI	GATC	5 cut(s)	134, 564, 662, 936, 962
DpnII	GATC	5 cut(s)	132, 562, 660, 934, 960
DraI	TTTAAA	1 cut(s)	469
Eco130I	CCWWGG	1 cut(s)	996
Eco31I	GGTCTC	1 cut(s)	773
Eco47I	GGWCC	1 cut(s)	373
Eco57I	CTGAAG	1 cut(s)	35
Eco72I	CACGTG	1 cut(s)	872
Eco81I	CCTNAGG	1 cut(s)	558
Eco88I	CYCGRG	1 cut(s)	864
EcoRI	GAATTC	1 cut(s)	117
EcoRII	CCWGG	3 cut(s)	74, 337, 888
EcoT14I	CCWWGG	1 cut(s)	996
ErhI	CCWWGG	1 cut(s)	996
FblI	GTMKAC	1 cut(s)	309
Fnu4HI	GCNGC	4 cut(s)	190, 239, 636, 987
FokI	GGATG	1 cut(s)	443
Fsp4HI	GCNGC	4 cut(s)	190, 239, 636, 987
FspBI	CTAG	5 cut(s)	26, 462, 671, 795, 990
GlaI	GCGC	1 cut(s)	320
GluI	GCNGC	4 cut(s)	190, 239, 636, 987
GsuI	CTGGAG	1 cut(s)	951
HaeIII	GGCC	1 cut(s)	511
HapII	CCGG	2 cut(s)	114, 242
HhaI	GCGC	1 cut(s)	321
Hin6I	GCGC	1 cut(s)	319
HinP1I	GCGC	1 cut(s)	319
HindIII	AAGCTT	1 cut(s)	588
HinfI	GANTC	1 cut(s)	279
HpaII	CCGG	2 cut(s)	114, 242
HphI	GGTGA	3 cut(s)	353, 425, 648
Hpy166II	GTNNAC	2 cut(s)	310, 388
Hpy188I	TCNGA	6 cut(s)	7, 15, 132, 665, 691, 778
Hpy188III	TCNNGA	7 cut(s)	47, 114, 209, 359, 566, 725, 964
Hpy8I	GTNNAC	2 cut(s)	310, 388
HpyAV	CCTTC	1 cut(s)	404
HpyCH4III	ACNGT	5 cut(s)	180, 196, 370, 542, 979
HpyCH4IV	ACGT	2 cut(s)	485, 871
HpyCH4V	TGCA	7 cut(s)	275, 545, 583, 594, 748, 765, 971
HpyF10VI	GCNNNNNNNGC	2 cut(s)	165, 508
HpyF3I	CTNAG	4 cut(s)	171, 558, 690, 777
HpySE526I	ACGT	2 cut(s)	485, 871
HspAI	GCGC	1 cut(s)	319
Kpn2I	TCCGGA	1 cut(s)	113
Kzo9I	GATC	5 cut(s)	132, 562, 660, 934, 960
LmnI	GCTCC	2 cut(s)	41, 82
Lsp1109I	GCAGC	3 cut(s)	250, 647, 973
LweI	GCATC	2 cut(s)	262, 836
MabI	ACCWGGT	1 cut(s)	888
MaeI	CTAG	5 cut(s)	26, 462, 671, 795, 990
MaeII	ACGT	2 cut(s)	485, 871
MaeIII	GTNAC	4 cut(s)	348, 654, 856, 979
MalI	GATC	5 cut(s)	134, 564, 662, 936, 962
MboI	GATC	5 cut(s)	132, 562, 660, 934, 960
MboII	GAAGA	5 cut(s)	48, 244, 415, 520, 764
MfeI	CAATTG	1 cut(s)	184
MflI	RGATCY	3 cut(s)	562, 934, 960
MhlI	GDGCHC	1 cut(s)	871
MluCI	AATT	6 cut(s)	117, 184, 227, 597, 720, 739
MlyI	GAGTC	1 cut(s)	288
MmeI	TCCRAC	3 cut(s)	586, 740, 904
MroI	TCCGGA	1 cut(s)	113
MseI	TTAA	1 cut(s)	468
MspA1I	CMGCKG	1 cut(s)	449
MspI	CCGG	2 cut(s)	114, 242
MspR9I	CCNGG	3 cut(s)	76, 339, 890
MunI	CAATTG	1 cut(s)	184
Mva1269I	GAATGC	1 cut(s)	973
MvaI	CCWGG	3 cut(s)	76, 339, 890
MwoI	GCNNNNNNNGC	2 cut(s)	165, 508
NcoI	CCATGG	1 cut(s)	996
NdeII	GATC	5 cut(s)	132, 562, 660, 934, 960
NheI	GCTAGC	1 cut(s)	989
NlaIV	GGNNCC	1 cut(s)	1002
NmuCI	GTSAC	2 cut(s)	654, 979
NspI	RCATGY	2 cut(s)	554, 1031
NspV	TTCGAA	2 cut(s)	68, 531
PaeR7I	CTCGAG	1 cut(s)	864
PagI	TCATGA	1 cut(s)	358
PaqCI	CACCTGC	1 cut(s)	1012
PciI	ACATGT	1 cut(s)	1027
PctI	GAATGC	1 cut(s)	973
PkrI	GCNGC	4 cut(s)	191, 240, 637, 988
PleI	GAGTC	1 cut(s)	287
PmaCI	CACGTG	1 cut(s)	872
PmlI	CACGTG	1 cut(s)	872
PpsI	GAGTC	1 cut(s)	287
Ppu21I	YACGTR	2 cut(s)	486, 872
PscI	ACATGT	1 cut(s)	1027
Psp6I	CCWGG	3 cut(s)	74, 337, 888
PspCI	CACGTG	1 cut(s)	872
PspGI	CCWGG	3 cut(s)	74, 337, 888
PspN4I	GGNNCC	1 cut(s)	1002
PspPI	GGNCC	2 cut(s)	373, 509
PspXI	VCTCGAGB	1 cut(s)	864
PsrI	GAACNNNNNNTAC	4 cut(s)	189, 221, 426, 458
PstNI	CAGNNNCTG	1 cut(s)	983
PsuI	RGATCY	3 cut(s)	562, 934, 960
PvuII	CAGCTG	1 cut(s)	449
RsaI	GTAC	5 cut(s)	146, 154, 435, 488, 555
RsaNI	GTAC	5 cut(s)	145, 153, 434, 487, 554
SaqAI	TTAA	1 cut(s)	468
SatI	GCNGC	4 cut(s)	190, 239, 636, 987
Sau3AI	GATC	5 cut(s)	132, 562, 660, 934, 960
Sau96I	GGNCC	2 cut(s)	373, 509
SchI	GAGTC	1 cut(s)	288
ScrFI	CCNGG	3 cut(s)	76, 339, 890
SduI	GDGCHC	1 cut(s)	871
SexAI	ACCWGGT	1 cut(s)	888
SfaNI	GCATC	2 cut(s)	262, 836
SfcI	CTRYAG	2 cut(s)	195, 366
Sfr274I	CTCGAG	1 cut(s)	864
SfuI	TTCGAA	2 cut(s)	68, 531
SinI	GGWCC	1 cut(s)	373
SlaI	CTCGAG	1 cut(s)	864
SmlI	CTYRAG	4 cut(s)	209, 259, 829, 864
SmoI	CTYRAG	4 cut(s)	209, 259, 829, 864
Sse9I	AATT	6 cut(s)	117, 184, 227, 597, 720, 739
SsiI	CCGC	1 cut(s)	190
SspMI	CTAG	5 cut(s)	26, 462, 671, 795, 990
StyD4I	CCNGG	3 cut(s)	74, 337, 888
StyI	CCWWGG	1 cut(s)	996
TaaI	ACNGT	5 cut(s)	180, 196, 370, 542, 979
TaiI	ACGT	2 cut(s)	488, 874
TaqI	TCGA	4 cut(s)	68, 265, 531, 865
TasI	AATT	6 cut(s)	117, 184, 227, 597, 720, 739
TatI	WGTACW	2 cut(s)	144, 433
TauI	GCSGC	1 cut(s)	192
Tru1I	TTAA	1 cut(s)	468
Tru9I	TTAA	1 cut(s)	468
TscAI	CASTG	3 cut(s)	199, 375, 984
TseFI	GTSAC	2 cut(s)	654, 979
TseI	GCWGC	3 cut(s)	238, 635, 986
Tsp45I	GTSAC	2 cut(s)	654, 979
TspDTI	ATGAA	3 cut(s)	375, 423, 446
TspRI	CASTG	3 cut(s)	199, 375, 984
VpaK11BI	GGWCC	1 cut(s)	373
XapI	RAATTY	3 cut(s)	117, 227, 597
XceI	RCATGY	2 cut(s)	554, 1031
XhoI	CTCGAG	1 cut(s)	864
XmiI	GTMKAC	1 cut(s)	309
XspI	CTAG	5 cut(s)	26, 462, 671, 795, 990

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