Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0001594

Physical Location & Seq

Genomic Coordinates Reverse (-)

58870054 .. 58873062

Gene Structure 3009 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000014868

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1041 bp

ATGAAGGTGGGGGCCAAAGACTCGATGAACTTAGGAGATCGAATTTGTCTTCCTATTTCTGTGAAACAGTTCCTTGATGACAAACAAGAAGAGGGACATTGTAGTGAAGAAGAAGTCAAGTTTATTTGTAGTCTTGTGTTGTATAAGGATCCAGCTATTGTTGTCATCAATAAACCCCCTGGATTGCCTGTTCAGGGCGGTATTGGAATCAAAAGGAGTTTAGATGAACTGGCTGCCACTTGTTTAAGTTACGGCTTTTCAGAACCCCCTCGTCTGGTACACAGACTTGACAGAGATTGTAGTGGTATCCTTGTGATGGGACGGACACAAACAAGTGCAACAGTTTTGCATTCCCTCTTCCGTGAGAAAACTTTTGGAGCTTCAGATTATGTTATCGACCATGCTAAAGCCATTCTGCAAAGAAGGTATTGGGCACTCGTCATTGGATCTCCCAGACAACAAAAGGGGTTAATCTCAGTGCCTTTAGGAAAGGTGGTGGTTGACAATGGTAAATCAGATAGGATCACCATTGTGAATAAGGCACAATGTTTGCCATCTCAACATGCAATTACAAAGTTCAAAGTGATTGGATCATCATGTCCTGGTTTCACATGGTTAGAGCTAATTCCACTTACTGGTCGAAAGCACCAGCTGCGTGTACACTGTGCAGAAGTTTTGGGAACACCGATAGTCGGAGACTACAAATATGGATGGCGAACGTATAAGGACTGGAAACCTGTTGCTTGGTCTAAGATTGAATGTCATTCCAATGGGGAGAGTTTGAAGAGAAAAAACATTCATTTTGATCTCAATATGGACAGTGGAAGTATCGCCGAAAAGAATTTGCGCTTACATCTTCATTCTAAGCAAATGATTTTACCTAATGTGTCTCTGGCATTGCAAAATGTGAAACTGCATGCGGAATGTGATCTTTCAGGACTAGAAAGCCTAGAGTTGGTTGCTCCTATGCCTTCATACATGCAAAAAAGTTGGGATATTACAAAATCTGGTTTTGACAGGAGTGATATTACACATTCTTAA

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

347

Amino Acids

38.6

Weight (kDa)

8.98

Isoelectric Point (pI)

43.99

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	53 - 223	1e-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: 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)	635
AciI	CCGC	2 cut(s)	198, 920
AclWI	GGATC	5 cut(s)	143, 156, 454, 530, 598
AcsI	RAATTY	2 cut(s)	42, 841
AcuI	CTGAAG	1 cut(s)	366
AfaI	GTAC	2 cut(s)	279, 660
AfiI	CCNNNNNNNGG	6 cut(s)	194, 274, 316, 635, 692, 955
AgsI	TTSAA	3 cut(s)	580, 758, 784
AjnI	CCWGG	2 cut(s)	178, 601
AleI	CACNNNNGTG	1 cut(s)	530
AloI	GAACNNNNNNTCC	2 cut(s)	174, 206
AluBI	AGCT	4 cut(s)	155, 380, 622, 652
AluI	AGCT	4 cut(s)	155, 380, 622, 652
Alw26I	GTCTC	2 cut(s)	690, 894
AlwI	GGATC	5 cut(s)	143, 156, 454, 530, 598
AoxI	GGCC	1 cut(s)	12
ApeKI	GCWGC	2 cut(s)	233, 652
ApoI	RAATTY	2 cut(s)	42, 841
Asp700I	GAANNNNTTC	1 cut(s)	68
AspLEI	GCGC	1 cut(s)	849
AspS9I	GGNCC	1 cut(s)	12
AsuHPI	GGTGA	1 cut(s)	517
BaeGI	GKGCMC	1 cut(s)	436
BamHI	GGATCC	1 cut(s)	148
BbsI	GAAGAC	1 cut(s)	41
BbvI	GCAGC	2 cut(s)	220, 639
BccI	CCATC	3 cut(s)	310, 562, 705
BceAI	ACGGC	1 cut(s)	268
BciT130I	CCWGG	2 cut(s)	180, 603
BciVI	GTATCC	1 cut(s)	317
BcoDI	GTCTC	2 cut(s)	690, 894
BfaI	CTAG	2 cut(s)	941, 950
BfuI	GTATCC	1 cut(s)	317
BisI	GCNGC	2 cut(s)	234, 653
BlsI	GCNGC	2 cut(s)	235, 654
Bme1390I	CCNGG	2 cut(s)	180, 603
BmgT120I	GGNCC	1 cut(s)	12
BmiI	GGNNCC	2 cut(s)	13, 150
BmrFI	CCNGG	2 cut(s)	180, 603
BpiI	GAAGAC	1 cut(s)	41
BsaJI	CCNNGG	1 cut(s)	178
Bsc4I	CCNNNNNNNGG	6 cut(s)	194, 274, 316, 635, 692, 955
Bse1I	ACTGG	3 cut(s)	234, 640, 734
Bse3DI	GCAATG	1 cut(s)	896
BseBI	CCWGG	2 cut(s)	180, 603
BseDI	CCNNGG	1 cut(s)	178
BseGI	GGATG	1 cut(s)	716
BseLI	CCNNNNNNNGG	6 cut(s)	194, 274, 316, 635, 692, 955
BseMI	GCAATG	1 cut(s)	896
BseMII	CTCAG	1 cut(s)	489
BseNI	ACTGG	3 cut(s)	234, 640, 734
BseSI	GKGCMC	1 cut(s)	436
BseXI	GCAGC	2 cut(s)	220, 639
BsgI	GTGCAG	1 cut(s)	687
BshFI	GGCC	1 cut(s)	14
BslFI	GGGAC	2 cut(s)	108, 333
BslI	CCNNNNNNNGG	6 cut(s)	194, 274, 316, 635, 692, 955
BsmAI	GTCTC	2 cut(s)	690, 894
BsmFI	GGGAC	2 cut(s)	108, 333
BsmI	GAATGC	1 cut(s)	349
BsnI	GGCC	1 cut(s)	14
Bsp1286I	GDGCHC	1 cut(s)	436
Bsp1407I	TGTACA	1 cut(s)	658
Bsp143I	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
BspACI	CCGC	2 cut(s)	198, 920
BspANI	GGCC	1 cut(s)	14
BspCNI	CTCAG	1 cut(s)	488
BspLI	GGNNCC	2 cut(s)	13, 150
BspPI	GGATC	5 cut(s)	143, 156, 454, 530, 598
BsrDI	GCAATG	1 cut(s)	896
BsrGI	TGTACA	1 cut(s)	658
BsrI	ACTGG	3 cut(s)	234, 640, 734
BssECI	CCNNGG	1 cut(s)	178
BssMI	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
Bst2UI	CCWGG	2 cut(s)	180, 603
Bst4CI	ACNGT	4 cut(s)	69, 343, 665, 821
Bst6I	CTCTTC	3 cut(s)	84, 362, 779
BstAPI	GCANNNNNTGC	1 cut(s)	652
BstAUI	TGTACA	1 cut(s)	658
BstC8I	GCNNGC	1 cut(s)	918
BstDEI	CTNAG	4 cut(s)	31, 475, 750, 864
BstF5I	GGATG	1 cut(s)	716
BstHHI	GCGC	1 cut(s)	849
BstKTI	GATC	7 cut(s)	40, 151, 449, 525, 593, 808, 931
BstMAI	GTCTC	2 cut(s)	690, 894
BstMBI	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
BstMWI	GCNNNNNNNGC	1 cut(s)	652
BstNI	CCWGG	2 cut(s)	180, 603
BstNSI	RCATGY	3 cut(s)	566, 920, 982
BstSCI	CCNGG	2 cut(s)	178, 601
BstSLI	GKGCMC	1 cut(s)	436
BstV1I	GCAGC	2 cut(s)	220, 639
BstV2I	GAAGAC	1 cut(s)	41
BstX2I	RGATCY	2 cut(s)	148, 446
BstYI	RGATCY	2 cut(s)	148, 446
BsuI	GTATCC	1 cut(s)	317
BsuRI	GGCC	1 cut(s)	14
BtsCI	GGATG	1 cut(s)	716
BtsIMutI	CAGTG	3 cut(s)	483, 661, 826
Cac8I	GCNNGC	1 cut(s)	918
CfoI	GCGC	1 cut(s)	849
Cfr13I	GGNCC	1 cut(s)	12
Csp6I	GTAC	2 cut(s)	278, 659
CviAII	CATG	6 cut(s)	401, 563, 597, 612, 917, 979
CviJI	RGCY	9 cut(s)	14, 155, 233, 255, 380, 410, 622, 652, 948
CviKI_1	RGCY	9 cut(s)	14, 155, 233, 255, 380, 410, 622, 652, 948
CviQI	GTAC	2 cut(s)	278, 659
DdeI	CTNAG	4 cut(s)	31, 475, 750, 864
DpnI	GATC	7 cut(s)	39, 150, 448, 524, 592, 807, 930
DpnII	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
Eam1104I	CTCTTC	3 cut(s)	84, 362, 779
EarI	CTCTTC	3 cut(s)	84, 362, 779
Eco57I	CTGAAG	1 cut(s)	366
EcoRII	CCWGG	2 cut(s)	178, 601
FaeI	CATG	6 cut(s)	404, 566, 600, 615, 920, 982
FaqI	GGGAC	2 cut(s)	108, 333
FatI	CATG	6 cut(s)	400, 562, 596, 611, 916, 978
Fnu4HI	GCNGC	2 cut(s)	234, 653
FokI	GGATG	1 cut(s)	723
Fsp4HI	GCNGC	2 cut(s)	234, 653
FspBI	CTAG	2 cut(s)	941, 950
GlaI	GCGC	1 cut(s)	848
GluI	GCNGC	2 cut(s)	234, 653
HaeIII	GGCC	1 cut(s)	14
HhaI	GCGC	1 cut(s)	849
Hin1II	CATG	6 cut(s)	404, 566, 600, 615, 920, 982
Hin6I	GCGC	1 cut(s)	847
HinP1I	GCGC	1 cut(s)	847
HincII	GTYRAC	1 cut(s)	502
HindII	GTYRAC	1 cut(s)	502
HinfI	GANTC	2 cut(s)	20, 207
HphI	GGTGA	1 cut(s)	517
Hpy166II	GTNNAC	4 cut(s)	280, 502, 659, 661
Hpy188I	TCNGA	4 cut(s)	262, 385, 517, 695
Hpy188III	TCNNGA	1 cut(s)	936
Hpy8I	GTNNAC	4 cut(s)	280, 502, 659, 661
HpyAV	CCTTC	2 cut(s)	417, 981
HpyCH4III	ACNGT	4 cut(s)	69, 343, 665, 821
HpyCH4IV	ACGT	1 cut(s)	719
HpyCH4V	TGCA	8 cut(s)	338, 349, 418, 566, 668, 901, 916, 982
HpyF10VI	GCNNNNNNNGC	1 cut(s)	652
HpyF3I	CTNAG	4 cut(s)	31, 475, 750, 864
HpySE526I	ACGT	1 cut(s)	719
Hsp92II	CATG	6 cut(s)	404, 566, 600, 615, 920, 982
HspAI	GCGC	1 cut(s)	847
Kzo9I	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
LmnI	GCTCC	2 cut(s)	377, 967
Lsp1109I	GCAGC	2 cut(s)	220, 639
MaeI	CTAG	2 cut(s)	941, 950
MaeII	ACGT	1 cut(s)	719
MaeIII	GTNAC	1 cut(s)	248
MalI	GATC	7 cut(s)	39, 150, 448, 524, 592, 807, 930
MboI	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
MboII	GAAGA	7 cut(s)	41, 101, 119, 122, 349, 796, 848
MflI	RGATCY	2 cut(s)	148, 446
MhlI	GDGCHC	1 cut(s)	436
MluCI	AATT	4 cut(s)	42, 567, 624, 841
MlyI	GAGTC	1 cut(s)	14
MmeI	TCCRAC	1 cut(s)	673
MnlI	CCTC	3 cut(s)	85, 279, 365
MroXI	GAANNNNTTC	1 cut(s)	68
MseI	TTAA	3 cut(s)	245, 470, 1039
MslI	CAYNNNNRTG	3 cut(s)	102, 530, 768
MspA1I	CMGCKG	1 cut(s)	652
MspR9I	CCNGG	2 cut(s)	180, 603
Mva1269I	GAATGC	1 cut(s)	349
MvaI	CCWGG	2 cut(s)	180, 603
MwoI	GCNNNNNNNGC	1 cut(s)	652
NdeII	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
NlaIII	CATG	6 cut(s)	404, 566, 600, 615, 920, 982
NlaIV	GGNNCC	2 cut(s)	13, 150
NspI	RCATGY	3 cut(s)	566, 920, 982
OliI	CACNNNNGTG	1 cut(s)	530
PaeI	GCATGC	1 cut(s)	920
PctI	GAATGC	1 cut(s)	349
PdmI	GAANNNNTTC	1 cut(s)	68
PfeI	GAWTC	1 cut(s)	207
PflMI	CCANNNNNTGG	1 cut(s)	635
PkrI	GCNGC	2 cut(s)	235, 654
PleI	GAGTC	1 cut(s)	14
PpsI	GAGTC	1 cut(s)	14
Psp6I	CCWGG	2 cut(s)	178, 601
PspGI	CCWGG	2 cut(s)	178, 601
PspN4I	GGNNCC	2 cut(s)	13, 150
PspPI	GGNCC	1 cut(s)	12
PsuI	RGATCY	2 cut(s)	148, 446
PvuII	CAGCTG	1 cut(s)	652
RsaI	GTAC	2 cut(s)	279, 660
RsaNI	GTAC	2 cut(s)	278, 659
RseI	CAYNNNNRTG	3 cut(s)	102, 530, 768
SaqAI	TTAA	3 cut(s)	245, 470, 1039
SatI	GCNGC	2 cut(s)	234, 653
Sau3AI	GATC	7 cut(s)	37, 148, 446, 522, 590, 805, 928
Sau96I	GGNCC	1 cut(s)	12
SchI	GAGTC	1 cut(s)	14
ScrFI	CCNGG	2 cut(s)	180, 603
SduI	GDGCHC	1 cut(s)	436
SmiMI	CAYNNNNRTG	3 cut(s)	102, 530, 768
SphI	GCATGC	1 cut(s)	920
Sse9I	AATT	4 cut(s)	42, 567, 624, 841
SsiI	CCGC	2 cut(s)	198, 920
SspMI	CTAG	2 cut(s)	941, 950
StyD4I	CCNGG	2 cut(s)	178, 601
TaaI	ACNGT	4 cut(s)	69, 343, 665, 821
TaiI	ACGT	1 cut(s)	722
TaqI	TCGA	4 cut(s)	23, 40, 396, 640
TasI	AATT	4 cut(s)	42, 567, 624, 841
TatI	WGTACW	1 cut(s)	658
TfiI	GAWTC	1 cut(s)	207
Tru1I	TTAA	3 cut(s)	245, 470, 1039
Tru9I	TTAA	3 cut(s)	245, 470, 1039
TscAI	CASTG	3 cut(s)	483, 668, 826
TseI	GCWGC	2 cut(s)	233, 652
TspDTI	ATGAA	6 cut(s)	17, 41, 240, 788, 848, 963
TspGWI	ACGGA	2 cut(s)	337, 350
TspRI	CASTG	3 cut(s)	483, 668, 826
Van91I	CCANNNNNTGG	1 cut(s)	635
XapI	RAATTY	2 cut(s)	42, 841
XceI	RCATGY	3 cut(s)	566, 920, 982
XmnI	GAANNNNTTC	1 cut(s)	68
XspI	CTAG	2 cut(s)	941, 950

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