Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0001833

Physical Location & Seq

Genomic Coordinates Forward (+)

9519794 .. 9522229

Gene Structure 2436 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000011451

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1023 bp

ATGGAGGAAGGTGCAAGAGTATATGTGCCCGTGTCGATTGCGGATAGTAAGGTTTCAAGGAGATTCGACTGCATACCGAGTGAGACATTGTACCCAAATGCGGATGAGATTGACTACTTGCAAAGGCTTGTCAAGTACAAGGACTCTGCTATAATAGTGCTGAACAAGCCCCCAAAATTACCCGTTAAGGGTAATGTGCCAGTCCATAACAGCATGGATGCACTGGCAGCAGCAGCGTTATCTTATGATTATGATGAAGGTCCTAAATTGGTTCATCGGCTTGATAGAGAGAGCAGTGGCCTCCTTTTAATGGGAAGAACAAAAGAAAGCGTATCTCTTCTGCAGTCATTATACACTGACATCAACAGTGGGAAATCATCGTGCAGGGCTTGGAATGATGCATGTAGAGCAAAATGTCAGAGGTACTGGGCATTGGTTATAGGGTCACCCAAGGAAAAGGAAGGCTTAATTTGTGCTCCTCTTACAAAGGTGTATCTTGACGATGGAAAGACAGAGAGGATCATCTTGGCTCATCAATCAGGATTAGAAGCTTCCCAACCGGCTCTAACTCAATATCGGGTGCTTGGTCCTACGATAAATGGATGCTCATGGATTGAATTACAACCACTCACTAGCCGAAAGCATCAGCTCCGTGTTCATTGTGCTGAAGCTCTAGGCACACCAATTGTGGGTGACTATAAGTATGGGTGGTTTGTTCACCGGAGATGGAAACAAATGCCTCAAGTCGATATTGAGCCTGCAACTGGGCTACAATACAAGTTGCGGAGGCCAGCGGGTCTGGATGTACAGAAGGGAAGTGTTCTATCAAAAGTCCCTCTTTTACATCTACATTGTAGAGAGCTCGCACTCCCCAATATTGCTAAGTTCCTTGTTTTATTGGATCAGAAGTTAGACAACCGGCACCCTGTAGATAGTTCGAAGCCAGATGTCCTTCGGTTTGTGGCATCAATGCCAACCCACATGAAACTTAGTTGGAATCTCATGACATCTTATTTGGTGTAG

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

341

Amino Acids

38.21

Weight (kDa)

9.12

Isoelectric Point (pI)

49.83

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	51 - 222	6.8e-22	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)

Image

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: OG0001833)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G78910 AT1G78910
fragaria_vesca	FvH4_5g04730 FvH4_5g04730 FvH4_5g04730 FvH4_5g04730
malus_domestica	MD06G1108500.v1.1
prunus_persica	Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1 Prupe.5G121100_v2.0.a1
pyrus_communis	pycom06g10190
rosa_chinensis	RchiOBHm_Chr1g0363621 RchiOBHm_Chr6g0299231 RchiOBHm_Chr7g0194671
rosa_laevigata	RLG00000004184 RLG00000011451
rosa_multiflora	Rmu_sc0000548.1_g000009 Rmu_sc0015513.1_g000002
rosa_roxburghii	Rroxscaffold_3G00261180 Rroxscaffold_3G00261210 Rroxscaffold_7G00168890
rosa_rugosa	Rorug01G0308200 Rorug01G0308200 Rorug06G0286400 Rorug07G0016600 Rorug07G0016700
rosa_samantha	Rh1AG317100 Rh6CG412300 Rh6DG399000 Rh7BG144500 Rh7CG148400 Rh7DG145800
rosa_wichuraiana	Rw1G028120 Rw6G034810 Rw7G012340

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	921
AciI	CCGC	4 cut(s)	41, 101, 784, 794
AclWI	GGATC	2 cut(s)	527, 909
AcuI	CTGAAG	1 cut(s)	687
AfaI	GTAC	4 cut(s)	92, 137, 425, 807
AfiI	CCNNNNNNNGG	5 cut(s)	100, 188, 310, 689, 764
AgsI	TTSAA	2 cut(s)	57, 617
AluBI	AGCT	4 cut(s)	551, 649, 671, 862
AluI	AGCT	4 cut(s)	551, 649, 671, 862
Alw21I	GWGCWC	2 cut(s)	478, 864
Alw26I	GTCTC	1 cut(s)	77
AlwI	GGATC	2 cut(s)	527, 909
AoxI	GGCC	2 cut(s)	298, 788
ApeKI	GCWGC	3 cut(s)	227, 230, 233
ArsI	GACNNNNNNTTYG	1 cut(s)	997
AspS9I	GGNCC	2 cut(s)	260, 587
AsuHPI	GGTGA	3 cut(s)	438, 704, 710
AsuII	TTCGAA	1 cut(s)	938
AvaII	GGWCC	2 cut(s)	260, 587
BaeGI	GKGCMC	1 cut(s)	30
BanI	GGYRCC	1 cut(s)	921
BanII	GRGCYC	1 cut(s)	864
Bbv12I	GWGCWC	2 cut(s)	478, 864
BbvI	GCAGC	3 cut(s)	239, 242, 245
BccI	CCATC	2 cut(s)	497, 720
BcoDI	GTCTC	1 cut(s)	77
BfaI	CTAG	2 cut(s)	633, 674
BfmI	CTRYAG	2 cut(s)	341, 927
BisI	GCNGC	3 cut(s)	228, 231, 234
BlsI	GCNGC	3 cut(s)	229, 232, 235
Bme18I	GGWCC	2 cut(s)	260, 587
BmgT120I	GGNCC	2 cut(s)	260, 587
BmiI	GGNNCC	1 cut(s)	923
BmrI	ACTGGG	2 cut(s)	436, 774
BmsI	GCATC	5 cut(s)	208, 388, 593, 652, 974
BmuI	ACTGGG	2 cut(s)	436, 774
Bpu14I	TTCGAA	1 cut(s)	938
BpuEI	CTTGAG	1 cut(s)	726
BsaJI	CCNNGG	1 cut(s)	450
BsaWI	WCCGGW	1 cut(s)	720
Bsc4I	CCNNNNNNNGG	5 cut(s)	100, 188, 310, 689, 764
Bse118I	RCCGGY	2 cut(s)	559, 918
Bse1I	ACTGG	4 cut(s)	200, 228, 431, 769
BseDI	CCNNGG	1 cut(s)	450
BseGI	GGATG	4 cut(s)	109, 223, 608, 808
BseLI	CCNNNNNNNGG	5 cut(s)	100, 188, 310, 689, 764
BseNI	ACTGG	4 cut(s)	200, 228, 431, 769
BseRI	GAGGAG	1 cut(s)	468
BseSI	GKGCMC	1 cut(s)	30
BseXI	GCAGC	3 cut(s)	239, 242, 245
BsgI	GTGCAG	1 cut(s)	403
BshFI	GGCC	2 cut(s)	300, 790
BshNI	GGYRCC	1 cut(s)	921
BsiHKAI	GWGCWC	2 cut(s)	478, 864
BsiSI	CCGG	3 cut(s)	560, 721, 919
BslFI	GGGAC	1 cut(s)	818
BslI	CCNNNNNNNGG	5 cut(s)	100, 188, 310, 689, 764
BsmAI	GTCTC	1 cut(s)	77
BsmFI	GGGAC	1 cut(s)	818
BsnI	GGCC	2 cut(s)	300, 790
Bsp119I	TTCGAA	1 cut(s)	938
Bsp1286I	GDGCHC	3 cut(s)	30, 478, 864
Bsp1407I	TGTACA	1 cut(s)	805
Bsp143I	GATC	2 cut(s)	519, 901
BspACI	CCGC	4 cut(s)	41, 101, 784, 794
BspANI	GGCC	2 cut(s)	300, 790
BspHI	TCATGA	1 cut(s)	1002
BspLI	GGNNCC	1 cut(s)	923
BspMAI	CTGCAG	1 cut(s)	345
BspPI	GGATC	2 cut(s)	527, 909
BspT104I	TTCGAA	1 cut(s)	938
BspT107I	GGYRCC	1 cut(s)	921
BsrFI	RCCGGY	2 cut(s)	559, 918
BsrGI	TGTACA	1 cut(s)	805
BsrI	ACTGG	4 cut(s)	200, 228, 431, 769
BssAI	RCCGGY	2 cut(s)	559, 918
BssECI	CCNNGG	1 cut(s)	450
BssMI	GATC	2 cut(s)	519, 901
BssT1I	CCWWGG	1 cut(s)	450
Bst4CI	ACNGT	1 cut(s)	368
Bst6I	CTCTTC	1 cut(s)	342
BstAUI	TGTACA	1 cut(s)	805
BstBI	TTCGAA	1 cut(s)	938
BstC8I	GCNNGC	3 cut(s)	759, 792, 864
BstDEI	CTNAG	2 cut(s)	882, 989
BstEII	GGTNACC	1 cut(s)	444
BstF5I	GGATG	4 cut(s)	109, 223, 608, 808
BstKTI	GATC	2 cut(s)	522, 904
BstMAI	GTCTC	1 cut(s)	77
BstMBI	GATC	2 cut(s)	519, 901
BstMWI	GCNNNNNNNGC	4 cut(s)	166, 227, 233, 407
BstNSI	RCATGY	1 cut(s)	405
BstPI	GGTNACC	1 cut(s)	444
BstSFI	CTRYAG	2 cut(s)	341, 927
BstSLI	GKGCMC	1 cut(s)	30
BstV1I	GCAGC	3 cut(s)	239, 242, 245
BsuRI	GGCC	2 cut(s)	300, 790
BtsCI	GGATG	4 cut(s)	109, 223, 608, 808
BtsI	GCAGTG	1 cut(s)	301
BtsIMutI	CAGTG	4 cut(s)	221, 301, 354, 373
Cac8I	GCNNGC	3 cut(s)	759, 792, 864
CciI	TCATGA	1 cut(s)	1002
Cfr10I	RCCGGY	2 cut(s)	559, 918
Cfr13I	GGNCC	2 cut(s)	260, 587
Csp6I	GTAC	4 cut(s)	91, 136, 424, 806
CviAII	CATG	5 cut(s)	214, 402, 609, 982, 1003
CviQI	GTAC	4 cut(s)	91, 136, 424, 806
DdeI	CTNAG	2 cut(s)	882, 989
DpnI	GATC	2 cut(s)	521, 903
DpnII	GATC	2 cut(s)	519, 901
Eam1104I	CTCTTC	1 cut(s)	342
EarI	CTCTTC	1 cut(s)	342
Ecl136II	GAGCTC	1 cut(s)	862
Eco130I	CCWWGG	1 cut(s)	450
Eco24I	GRGCYC	1 cut(s)	864
Eco47I	GGWCC	2 cut(s)	260, 587
Eco53kI	GAGCTC	1 cut(s)	862
Eco57I	CTGAAG	1 cut(s)	687
Eco91I	GGTNACC	1 cut(s)	444
EcoICRI	GAGCTC	1 cut(s)	862
EcoO109I	RGGNCCY	1 cut(s)	260
EcoO65I	GGTNACC	1 cut(s)	444
EcoT14I	CCWWGG	1 cut(s)	450
EcoT22I	ATGCAT	1 cut(s)	403
EcoT38I	GRGCYC	1 cut(s)	864
ErhI	CCWWGG	1 cut(s)	450
FaeI	CATG	5 cut(s)	217, 405, 612, 985, 1006
FalI	AAGNNNNNCTT	4 cut(s)	449, 481, 822, 854
FaqI	GGGAC	1 cut(s)	818
FatI	CATG	5 cut(s)	213, 401, 608, 981, 1002
FauI	CCCGC	1 cut(s)	787
Fnu4HI	GCNGC	3 cut(s)	228, 231, 234
FokI	GGATG	4 cut(s)	116, 230, 615, 815
FriOI	GRGCYC	1 cut(s)	864
Fsp4HI	GCNGC	3 cut(s)	228, 231, 234
FspBI	CTAG	2 cut(s)	633, 674
GluI	GCNGC	3 cut(s)	228, 231, 234
HaeIII	GGCC	2 cut(s)	300, 790
HapII	CCGG	3 cut(s)	560, 721, 919
Hin1II	CATG	5 cut(s)	217, 405, 612, 985, 1006
HindIII	AAGCTT	1 cut(s)	549
HinfI	GANTC	3 cut(s)	63, 143, 997
HpaII	CCGG	3 cut(s)	560, 721, 919
HphI	GGTGA	3 cut(s)	438, 704, 710
Hpy166II	GTNNAC	1 cut(s)	718
Hpy188I	TCNGA	2 cut(s)	420, 906
Hpy188III	TCNNGA	4 cut(s)	497, 540, 800, 1003
Hpy8I	GTNNAC	1 cut(s)	718
HpyAV	CCTTC	4 cut(s)	251, 455, 805, 962
HpyCH4III	ACNGT	1 cut(s)	368
HpyCH4V	TGCA	8 cut(s)	14, 72, 121, 221, 343, 384, 401, 761
HpyF10VI	GCNNNNNNNGC	4 cut(s)	166, 227, 233, 407
HpyF3I	CTNAG	2 cut(s)	882, 989
Hsp92II	CATG	5 cut(s)	217, 405, 612, 985, 1006
Kzo9I	GATC	2 cut(s)	519, 901
LmnI	GCTCC	2 cut(s)	481, 654
Lsp1109I	GCAGC	3 cut(s)	239, 242, 245
LweI	GCATC	5 cut(s)	208, 388, 593, 652, 974
MaeI	CTAG	2 cut(s)	633, 674
MaeIII	GTNAC	2 cut(s)	444, 692
MalI	GATC	2 cut(s)	521, 903
MboI	GATC	2 cut(s)	519, 901
MboII	GAAGA	2 cut(s)	327, 329
MfeI	CAATTG	1 cut(s)	684
MhlI	GDGCHC	3 cut(s)	30, 478, 864
MluCI	AATT	5 cut(s)	176, 266, 468, 617, 684
MlyI	GAGTC	1 cut(s)	137
MmeI	TCCRAC	1 cut(s)	974
MnlI	CCTC	7 cut(s)	311, 414, 489, 510, 750, 780, 846
Mph1103I	ATGCAT	1 cut(s)	403
MseI	TTAA	3 cut(s)	186, 308, 467
MspA1I	CMGCKG	1 cut(s)	794
MspI	CCGG	3 cut(s)	560, 721, 919
MunI	CAATTG	1 cut(s)	684
MwoI	GCNNNNNNNGC	4 cut(s)	166, 227, 233, 407
NdeII	GATC	2 cut(s)	519, 901
NlaIII	CATG	5 cut(s)	217, 405, 612, 985, 1006
NlaIV	GGNNCC	1 cut(s)	923
NmuCI	GTSAC	2 cut(s)	444, 692
NsiI	ATGCAT	1 cut(s)	403
NspI	RCATGY	1 cut(s)	405
NspV	TTCGAA	1 cut(s)	938
PagI	TCATGA	1 cut(s)	1002
PfeI	GAWTC	2 cut(s)	63, 997
PkrI	GCNGC	3 cut(s)	229, 232, 235
PleI	GAGTC	1 cut(s)	137
PpsI	GAGTC	1 cut(s)	137
PpuMI	RGGWCCY	1 cut(s)	260
Psp124BI	GAGCTC	1 cut(s)	864
Psp5II	RGGWCCY	1 cut(s)	260
PspEI	GGTNACC	1 cut(s)	444
PspN4I	GGNNCC	1 cut(s)	923
PspPI	GGNCC	2 cut(s)	260, 587
PspPPI	RGGWCCY	1 cut(s)	260
PstI	CTGCAG	1 cut(s)	345
RsaI	GTAC	4 cut(s)	92, 137, 425, 807
RsaNI	GTAC	4 cut(s)	91, 136, 424, 806
SacI	GAGCTC	1 cut(s)	864
SaqAI	TTAA	3 cut(s)	186, 308, 467
SatI	GCNGC	3 cut(s)	228, 231, 234
Sau3AI	GATC	2 cut(s)	519, 901
Sau96I	GGNCC	2 cut(s)	260, 587
SchI	GAGTC	1 cut(s)	137
SduI	GDGCHC	3 cut(s)	30, 478, 864
SetI	ASST	9 cut(s)	13, 54, 262, 425, 492, 553, 651, 673, 864
SfaNI	GCATC	5 cut(s)	208, 388, 593, 652, 974
SfcI	CTRYAG	2 cut(s)	341, 927
SfuI	TTCGAA	1 cut(s)	938
SinI	GGWCC	2 cut(s)	260, 587
SmlI	CTYRAG	1 cut(s)	741
SmoI	CTYRAG	1 cut(s)	741
Sse9I	AATT	5 cut(s)	176, 266, 468, 617, 684
SsiI	CCGC	4 cut(s)	41, 101, 784, 794
SspI	AATATT	1 cut(s)	877
SspMI	CTAG	2 cut(s)	633, 674
SstI	GAGCTC	1 cut(s)	864
StyI	CCWWGG	1 cut(s)	450
TaaI	ACNGT	1 cut(s)	368
TaqI	TCGA	4 cut(s)	35, 66, 747, 938
TasI	AATT	5 cut(s)	176, 266, 468, 617, 684
TatI	WGTACW	2 cut(s)	135, 805
TfiI	GAWTC	2 cut(s)	63, 997
Tru1I	TTAA	3 cut(s)	186, 308, 467
Tru9I	TTAA	3 cut(s)	186, 308, 467
TscAI	CASTG	4 cut(s)	228, 301, 361, 373
TseFI	GTSAC	2 cut(s)	444, 692
TseI	GCWGC	3 cut(s)	227, 230, 233
Tsp45I	GTSAC	2 cut(s)	444, 692
TspDTI	ATGAA	4 cut(s)	263, 270, 647, 998
TspGWI	ACGGA	1 cut(s)	641
TspRI	CASTG	4 cut(s)	228, 301, 361, 373
VpaK11BI	GGWCC	2 cut(s)	260, 587
XceI	RCATGY	1 cut(s)	405
XspI	CTAG	2 cut(s)	633, 674
Zsp2I	ATGCAT	1 cut(s)	403

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