Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0001594

Physical Location & Seq

Genomic Coordinates Reverse (-)

58627222 .. 58630046

Gene Structure 2825 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000014859

Sequence Viewer

CDS Protein Promoter (2k)

Length: 999 bp

ATGAACTTAGGAGATCGAATTTGTCTTCCTATTTCTGTGAAAGAGTTCCCTGATGATAGACAAGAAGAGGGACATTGTAGTGAAGAAGAAGTCAAGTTTATTCGTAGTCTTGTGTTGTATAAGGATCCAGCTATTGTTGTCATCAATAAACCCCCTGGATTGCCTGTTCAGGGTGGTATTGGAATCAAAAGGAGTTTAGATGAACTGGCTGCCACTTGTTTAAGTTATGGCTTTTCAGAAACCCCTCGTCTGGTACACAGACTTGACAGAGATTGTAGTGGCATCCTTGTGATGGGACGGACACAAACAAGTGCAACAGTTTTGCATTCCCTCTTCCGTGAGAAAACTTTTGGAGCTTCAGATGATGTTATCGACCATGCTAAAGCCATTCTGCAAAGAAGGTATTGGGCACTCGTGATTGGATCTCCCAGACAACAAGAGGGGTTAATCTCCGTGCCTTTAGGAAAGGTGGTGGTAGACAATGGTAAATCAGATAGGATCACCATTGTGAATAAGGCACAATGTTTGCCATCTCAACATGCACTTACAAAGTACAAGGTGATTGGATCATCATGTCCTGGTTTCACATGGTTAGAGCTAATTCCACTTACTGGTCGAAAGCACCAGCTGCGTGTACACTGTGCAGAAGTTTTGGGAACACCAATAGTCGGAGACTACAAATATGGATGGCAAACGCATAAGGACTGGAAACCTGTTGCTTGGTCTAAGATTGAAAGCCATTCCAATGAGGGGCTTTCAAAGAGAAAAAAAATTCCTTTTGATCTCAATATGGACTGTGGAAGTATCGCCGAAAAGAATTTGCGCTTACATCTTCATTCTAAGCAAATGGTTTTGCCTAATGTGTCTCTGGCTTTGCAAAATGTGAAACTGCATGCGGAGTGTGATCTTTCAGGACTAGAAAGCCTAGAATTGGTTGCTCCTATGCCTTCATACATGCAAAAAAGTTGGGAAATGACAAATTCTGGTTTTGACGGGTGA

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

333

Amino Acids

37.0

Weight (kDa)

8.49

Isoelectric Point (pI)

42.23

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	45 - 215	9.5e-23	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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Tree File

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Publication-ready

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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)
AccB7I	CCANNNNNTGG	1 cut(s)	611
AccI	GTMKAC	1 cut(s)	477
AciI	CCGC	1 cut(s)	896
AclWI	GGATC	5 cut(s)	119, 132, 430, 506, 574
AcsI	RAATTY	4 cut(s)	18, 771, 817, 979
AcuI	CTGAAG	1 cut(s)	342
AfaI	GTAC	3 cut(s)	255, 554, 636
AfiI	CCNNNNNNNGG	7 cut(s)	170, 250, 292, 611, 668, 750, 931
AgsI	TTSAA	2 cut(s)	734, 759
AjnI	CCWGG	2 cut(s)	154, 577
AleI	CACNNNNGTG	1 cut(s)	506
AloI	GAACNNNNNNTCC	2 cut(s)	150, 182
AluBI	AGCT	4 cut(s)	131, 356, 598, 628
AluI	AGCT	4 cut(s)	131, 356, 598, 628
Alw26I	GTCTC	2 cut(s)	666, 870
AlwI	GGATC	5 cut(s)	119, 132, 430, 506, 574
ApeKI	GCWGC	2 cut(s)	209, 628
ApoI	RAATTY	4 cut(s)	18, 771, 817, 979
Asp700I	GAANNNNTTC	1 cut(s)	44
AspLEI	GCGC	1 cut(s)	825
AsuHPI	GGTGA	2 cut(s)	493, 571
BaeGI	GKGCMC	1 cut(s)	412
BamHI	GGATCC	1 cut(s)	124
BauI	CACGAG	1 cut(s)	413
BbsI	GAAGAC	1 cut(s)	17
BbvI	GCAGC	2 cut(s)	196, 615
BccI	CCATC	3 cut(s)	286, 538, 681
BciT130I	CCWGG	2 cut(s)	156, 579
BcoDI	GTCTC	2 cut(s)	666, 870
BfaI	CTAG	2 cut(s)	917, 926
BisI	GCNGC	2 cut(s)	210, 629
BlsI	GCNGC	2 cut(s)	211, 630
Bme1390I	CCNGG	2 cut(s)	156, 579
BmiI	GGNNCC	1 cut(s)	126
BmrFI	CCNGG	2 cut(s)	156, 579
BmsI	GCATC	1 cut(s)	291
BpiI	GAAGAC	1 cut(s)	17
BsaJI	CCNNGG	1 cut(s)	154
Bsc4I	CCNNNNNNNGG	7 cut(s)	170, 250, 292, 611, 668, 750, 931
Bse1I	ACTGG	3 cut(s)	210, 616, 710
BseBI	CCWGG	2 cut(s)	156, 579
BseDI	CCNNGG	1 cut(s)	154
BseGI	GGATG	2 cut(s)	282, 692
BseLI	CCNNNNNNNGG	7 cut(s)	170, 250, 292, 611, 668, 750, 931
BseNI	ACTGG	3 cut(s)	210, 616, 710
BseSI	GKGCMC	1 cut(s)	412
BseXI	GCAGC	2 cut(s)	196, 615
BsgI	GTGCAG	1 cut(s)	663
BslFI	GGGAC	2 cut(s)	84, 309
BslI	CCNNNNNNNGG	7 cut(s)	170, 250, 292, 611, 668, 750, 931
BsmAI	GTCTC	2 cut(s)	666, 870
BsmFI	GGGAC	2 cut(s)	84, 309
BsmI	GAATGC	1 cut(s)	325
Bsp1286I	GDGCHC	1 cut(s)	412
Bsp1407I	TGTACA	1 cut(s)	634
Bsp143I	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
BspACI	CCGC	1 cut(s)	896
BspLI	GGNNCC	1 cut(s)	126
BspPI	GGATC	5 cut(s)	119, 132, 430, 506, 574
BsrGI	TGTACA	1 cut(s)	634
BsrI	ACTGG	3 cut(s)	210, 616, 710
BssECI	CCNNGG	1 cut(s)	154
BssMI	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
BssSI	CACGAG	1 cut(s)	413
Bst2BI	CACGAG	1 cut(s)	413
Bst2UI	CCWGG	2 cut(s)	156, 579
Bst4CI	ACNGT	3 cut(s)	319, 641, 797
Bst6I	CTCTTC	2 cut(s)	60, 338
BstAPI	GCANNNNNTGC	1 cut(s)	628
BstAUI	TGTACA	1 cut(s)	634
BstC8I	GCNNGC	1 cut(s)	894
BstDEI	CTNAG	3 cut(s)	7, 726, 840
BstF5I	GGATG	2 cut(s)	282, 692
BstHHI	GCGC	1 cut(s)	825
BstKTI	GATC	7 cut(s)	16, 127, 425, 501, 569, 784, 907
BstMAI	GTCTC	2 cut(s)	666, 870
BstMBI	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
BstMWI	GCNNNNNNNGC	1 cut(s)	628
BstNI	CCWGG	2 cut(s)	156, 579
BstNSI	RCATGY	3 cut(s)	542, 896, 958
BstSCI	CCNGG	2 cut(s)	154, 577
BstSLI	GKGCMC	1 cut(s)	412
BstV1I	GCAGC	2 cut(s)	196, 615
BstV2I	GAAGAC	1 cut(s)	17
BstX2I	RGATCY	2 cut(s)	124, 422
BstYI	RGATCY	2 cut(s)	124, 422
BtsCI	GGATG	2 cut(s)	282, 692
BtsIMutI	CAGTG	1 cut(s)	637
Cac8I	GCNNGC	1 cut(s)	894
CfoI	GCGC	1 cut(s)	825
Csp6I	GTAC	3 cut(s)	254, 553, 635
CviAII	CATG	6 cut(s)	377, 539, 573, 588, 893, 955
CviQI	GTAC	3 cut(s)	254, 553, 635
DdeI	CTNAG	3 cut(s)	7, 726, 840
DpnI	GATC	7 cut(s)	15, 126, 424, 500, 568, 783, 906
DpnII	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
Eam1104I	CTCTTC	2 cut(s)	60, 338
EarI	CTCTTC	2 cut(s)	60, 338
Eco57I	CTGAAG	1 cut(s)	342
EcoRII	CCWGG	2 cut(s)	154, 577
FaeI	CATG	6 cut(s)	380, 542, 576, 591, 896, 958
FaqI	GGGAC	2 cut(s)	84, 309
FatI	CATG	6 cut(s)	376, 538, 572, 587, 892, 954
FblI	GTMKAC	1 cut(s)	477
Fnu4HI	GCNGC	2 cut(s)	210, 629
FokI	GGATG	2 cut(s)	269, 699
Fsp4HI	GCNGC	2 cut(s)	210, 629
FspBI	CTAG	2 cut(s)	917, 926
GlaI	GCGC	1 cut(s)	824
GluI	GCNGC	2 cut(s)	210, 629
HhaI	GCGC	1 cut(s)	825
Hin1II	CATG	6 cut(s)	380, 542, 576, 591, 896, 958
Hin6I	GCGC	1 cut(s)	823
HinP1I	GCGC	1 cut(s)	823
HinfI	GANTC	1 cut(s)	183
HphI	GGTGA	2 cut(s)	493, 571
Hpy166II	GTNNAC	4 cut(s)	256, 478, 635, 637
Hpy188I	TCNGA	4 cut(s)	238, 361, 493, 671
Hpy188III	TCNNGA	2 cut(s)	415, 912
Hpy8I	GTNNAC	4 cut(s)	256, 478, 635, 637
HpyAV	CCTTC	2 cut(s)	393, 957
HpyCH4III	ACNGT	3 cut(s)	319, 641, 797
HpyCH4V	TGCA	8 cut(s)	314, 325, 394, 542, 644, 877, 892, 958
HpyF10VI	GCNNNNNNNGC	1 cut(s)	628
HpyF3I	CTNAG	3 cut(s)	7, 726, 840
Hsp92II	CATG	6 cut(s)	380, 542, 576, 591, 896, 958
HspAI	GCGC	1 cut(s)	823
Kzo9I	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
LmnI	GCTCC	2 cut(s)	353, 943
Lsp1109I	GCAGC	2 cut(s)	196, 615
LweI	GCATC	1 cut(s)	291
MaeI	CTAG	2 cut(s)	917, 926
MalI	GATC	7 cut(s)	15, 126, 424, 500, 568, 783, 906
MboI	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
MboII	GAAGA	6 cut(s)	17, 77, 95, 98, 325, 824
MflI	RGATCY	2 cut(s)	124, 422
MhlI	GDGCHC	1 cut(s)	412
MluCI	AATT	6 cut(s)	18, 600, 771, 817, 929, 979
MmeI	TCCRAC	1 cut(s)	649
MnlI	CCTC	5 cut(s)	61, 255, 341, 433, 742
MroXI	GAANNNNTTC	1 cut(s)	44
MseI	TTAA	2 cut(s)	221, 446
MslI	CAYNNNNRTG	4 cut(s)	78, 287, 506, 744
MspA1I	CMGCKG	1 cut(s)	628
MspR9I	CCNGG	2 cut(s)	156, 579
Mva1269I	GAATGC	1 cut(s)	325
MvaI	CCWGG	2 cut(s)	156, 579
MwoI	GCNNNNNNNGC	1 cut(s)	628
NdeII	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
NlaIII	CATG	6 cut(s)	380, 542, 576, 591, 896, 958
NlaIV	GGNNCC	1 cut(s)	126
NspI	RCATGY	3 cut(s)	542, 896, 958
OliI	CACNNNNGTG	1 cut(s)	506
PaeI	GCATGC	1 cut(s)	896
PctI	GAATGC	1 cut(s)	325
PdmI	GAANNNNTTC	1 cut(s)	44
PfeI	GAWTC	1 cut(s)	183
PflMI	CCANNNNNTGG	1 cut(s)	611
PkrI	GCNGC	2 cut(s)	211, 630
Psp6I	CCWGG	2 cut(s)	154, 577
PspGI	CCWGG	2 cut(s)	154, 577
PspN4I	GGNNCC	1 cut(s)	126
PsuI	RGATCY	2 cut(s)	124, 422
PvuII	CAGCTG	1 cut(s)	628
RsaI	GTAC	3 cut(s)	255, 554, 636
RsaNI	GTAC	3 cut(s)	254, 553, 635
RseI	CAYNNNNRTG	4 cut(s)	78, 287, 506, 744
SaqAI	TTAA	2 cut(s)	221, 446
SatI	GCNGC	2 cut(s)	210, 629
Sau3AI	GATC	7 cut(s)	13, 124, 422, 498, 566, 781, 904
ScrFI	CCNGG	2 cut(s)	156, 579
SduI	GDGCHC	1 cut(s)	412
SetI	ASST	8 cut(s)	133, 358, 404, 471, 561, 600, 630, 715
SfaNI	GCATC	1 cut(s)	291
SmiMI	CAYNNNNRTG	4 cut(s)	78, 287, 506, 744
SphI	GCATGC	1 cut(s)	896
Sse9I	AATT	6 cut(s)	18, 600, 771, 817, 929, 979
SsiI	CCGC	1 cut(s)	896
SspMI	CTAG	2 cut(s)	917, 926
StyD4I	CCNGG	2 cut(s)	154, 577
TaaI	ACNGT	3 cut(s)	319, 641, 797
TaqI	TCGA	3 cut(s)	16, 372, 616
TasI	AATT	6 cut(s)	18, 600, 771, 817, 929, 979
TatI	WGTACW	2 cut(s)	552, 634
TfiI	GAWTC	1 cut(s)	183
Tru1I	TTAA	2 cut(s)	221, 446
Tru9I	TTAA	2 cut(s)	221, 446
TscAI	CASTG	1 cut(s)	644
TseI	GCWGC	2 cut(s)	209, 628
TspDTI	ATGAA	4 cut(s)	17, 216, 824, 939
TspGWI	ACGGA	3 cut(s)	313, 326, 442
TspRI	CASTG	1 cut(s)	644
Van91I	CCANNNNNTGG	1 cut(s)	611
XapI	RAATTY	4 cut(s)	18, 771, 817, 979
XceI	RCATGY	3 cut(s)	542, 896, 958
XmiI	GTMKAC	1 cut(s)	477
XmnI	GAANNNNTTC	1 cut(s)	44
XspI	CTAG	2 cut(s)	917, 926

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