Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0006063

Physical Location & Seq

Genomic Coordinates Reverse (-)

786357 .. 789724

Gene Structure 3368 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00277320.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1077 bp

ATGGAGGACCCGAAAGATGACCCGGCCGTGTTTCTGGATCGCACCTCACGCGCCACCAGAGGGAAGAGGATGACGAAGTTACTGGATGAAGAAATCGAAGAGGACGAGACGTTCTGGAATCAAGAGGCTCTTAAAGATGAGGAAGAAGATGATAACTATGAAGCAGAGCCTGAAGTTGCTGATGTGTTTGATAGCGATTTCGATGAAGATGAGCCTGACCCGGACGAAGGCGCAGAAGACAATGAGGGAGAGGAAAGACGGACGAAGAAGCGGTTGAAATTTCCGGGGAAGCAGCCAAGCAAGATGAAGAAGATAAAAGTGCTTTCGAAGATAGAAGACAGCTCCAAGAATGAAAAGCCGAAATCTTCTTCTAAACCTGAATGGCATCATCATGATGCTCCTGAGGATGGAGAAGGGGAGAGAAGTGTGAGGAAATCTACGAGAACTGCAGTGGTTGTTAGGCAAGCTGAGAGAGAGGCAAATCGTGCTGCTTTGCAAGCAACCATGAGGGTAAGTATAGAAAAAAAGAAGGAGAAAGAGAAGAGGATGAGCCAGGAAGAGATGCTTCTGGAAGCTGCTCAAACAGAAATTATCAACTTGAGGAATTTGGAACGTGTTCTGGCAAGGGAGGAAGAAGTTAAGAAGCGAGCAATTGTGCATAAGGCTGTCTATACTGGTCCACAACTACGTTATTTCTCAAAAGATGGTAACTCATATCTGGAATTCAGCAGAGGGTTATCGTTCCATTCTGATCTCTCTACGACATCTGCTCCCTATCCTGAGAAAGCTGTCTGTGCAGTTACTGGCTTACCTGCCAAGTACCGTGATCCAAAGACAGGGCTACCTTATGCAACAAAGGAAGCTTTTAAAATTATTCGGCAGCGTTTTCTACAAGAAAGTGGTGCGGTTAGGAAAGAGATGGACCTGGGTGATTTGTATGATTCACTTTCCGGAAAAGGTTTTTCAGCAAGGCAGAAGAGATCGGTGGTGTCAAATAAAAGTGAGGTGTCATATCCTCGATACTTTGCACGTTTCCGCAGGGCTCCAGCTCTTGAAAGTGTATCCTCTGAAGAGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006325 GO:0006338 GO:0006996 GO:0008150 GO:0009987 GO:0016043 GO:0034728 GO:0043044 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043486 GO:0043933 GO:0044424 GO:0044464 GO:0051276 GO:0071824 GO:0071840

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

YL1 YL1_C

Protein Analysis

358

Amino Acids

41.08

Weight (kDa)

5.65

Isoelectric Point (pI)

58.55

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
YL1	PF05764	14 - 233	3.5e-40	YL1 nuclear protein
YL1_C	PF08265	264 - 292	3.2e-16	YL1 nuclear protein C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

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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: OG0006063)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G36740 AT2G36740
fragaria_vesca	FvH4_7g33430 FvH4_7g33430 FvH4_7g33430 FvH4_7g33430
malus_domestica	MD07G1075300.v1.1 MD07G1304400.v1.1
prunus_persica	Prupe.2G323000_v2.0.a1
pyrus_communis	pycom07g05940
rosa_chinensis	RchiOBHm_Chr1g0383401
rosa_laevigata	RLG00000026104
rosa_multiflora	Rmu_co8369689.1_g000001 Rmu_sc0007173.1_g000009 Rmu_sc0012471.1_g000026
rosa_roxburghii	Rroxscaffold_4G00277320
rosa_rugosa	Rorug01G0441300 Rorug01G0441400 Rorug01G0441500 Rorug01G0441600
rosa_samantha	Rh1AG467200 Rh1BG424500 Rh1BG424600 Rh1CG437500 Rh1DG457200 Rh1DG457300
rosa_wichuraiana	Rw1G040540

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	820
AccII	CGCG	1 cut(s)	51
AccIII	TCCGGA	1 cut(s)	950
AciI	CCGC	3 cut(s)	271, 905, 1036
AclWI	GGATC	2 cut(s)	45, 821
AcoI	YGGCCR	1 cut(s)	24
AcsI	RAATTY	3 cut(s)	278, 604, 722
AcuI	CTGAAG	1 cut(s)	192
AfaI	GTAC	1 cut(s)	821
AfiI	CCNNNNNNNGG	4 cut(s)	60, 227, 407, 836
AflIII	ACRYGT	1 cut(s)	613
AgsI	TTSAA	2 cut(s)	277, 1055
AjnI	CCWGG	2 cut(s)	552, 924
AloI	GAACNNNNNNTCC	2 cut(s)	95, 127
AluBI	AGCT	6 cut(s)	342, 467, 575, 788, 863, 1049
AluI	AGCT	6 cut(s)	342, 467, 575, 788, 863, 1049
Alw26I	GTCTC	1 cut(s)	101
AlwI	GGATC	2 cut(s)	45, 821
AlwNI	CAGNNNCTG	2 cut(s)	170, 803
Aor13HI	TCCGGA	1 cut(s)	950
AoxI	GGCC	1 cut(s)	24
ApeKI	GCWGC	4 cut(s)	292, 488, 575, 880
ApoI	RAATTY	3 cut(s)	278, 604, 722
Asp700I	GAANNNNTTC	1 cut(s)	615
AspLEI	GCGC	2 cut(s)	53, 233
AspS9I	GGNCC	3 cut(s)	7, 677, 922
AsuC2I	CCSGG	3 cut(s)	23, 221, 285
AsuHPI	GGTGA	1 cut(s)	941
AsuII	TTCGAA	1 cut(s)	326
AvaII	GGWCC	3 cut(s)	7, 677, 922
AxyI	CCTNAGG	1 cut(s)	402
BanII	GRGCYC	1 cut(s)	1045
BbsI	GAAGAC	2 cut(s)	243, 342
BbvI	GCAGC	4 cut(s)	304, 475, 562, 892
BccI	CCATC	3 cut(s)	401, 698, 913
BceAI	ACGGC	1 cut(s)	11
BciT130I	CCWGG	2 cut(s)	554, 926
BciVI	GTATCC	1 cut(s)	1072
BcnI	CCSGG	3 cut(s)	23, 221, 285
BcoDI	GTCTC	1 cut(s)	101
BfmI	CTRYAG	1 cut(s)	447
BfuAI	ACCTGC	1 cut(s)	820
BfuI	GTATCC	1 cut(s)	1072
BisI	GCNGC	4 cut(s)	293, 489, 576, 881
BlsI	GCNGC	4 cut(s)	294, 490, 577, 882
Bme1390I	CCNGG	5 cut(s)	23, 221, 285, 554, 926
Bme18I	GGWCC	3 cut(s)	7, 677, 922
BmgT120I	GGNCC	3 cut(s)	7, 677, 922
BmiI	GGNNCC	2 cut(s)	9, 1044
BmrFI	CCNGG	5 cut(s)	23, 221, 285, 554, 926
BmsI	GCATC	3 cut(s)	385, 394, 552
BpiI	GAAGAC	2 cut(s)	243, 342
BpmI	CTGGAG	1 cut(s)	1029
Bpu14I	TTCGAA	1 cut(s)	326
BpuEI	CTTGAG	1 cut(s)	619
BpuMI	CCSGG	3 cut(s)	23, 221, 285
BsaJI	CCNNGG	2 cut(s)	284, 925
BsaWI	WCCGGW	1 cut(s)	950
BsaXI	ACNNNNNCTCC	2 cut(s)	754, 784
Bsc4I	CCNNNNNNNGG	4 cut(s)	60, 227, 407, 836
Bse1I	ACTGG	3 cut(s)	87, 679, 808
Bse21I	CCTNAGG	1 cut(s)	402
BseAI	TCCGGA	1 cut(s)	950
BseBI	CCWGG	2 cut(s)	554, 926
BseDI	CCNNGG	2 cut(s)	284, 925
BseGI	GGATG	4 cut(s)	75, 91, 412, 552
BseLI	CCNNNNNNNGG	4 cut(s)	60, 227, 407, 836
BseMII	CTCAG	3 cut(s)	393, 459, 771
BseNI	ACTGG	3 cut(s)	87, 679, 808
BseX3I	CGGCCG	1 cut(s)	24
BseXI	GCAGC	4 cut(s)	304, 475, 562, 892
BsgI	GTGCAG	1 cut(s)	816
Bsh1236I	CGCG	1 cut(s)	51
Bsh1285I	CGRYCG	1 cut(s)	27
BshFI	GGCC	1 cut(s)	26
BsiEI	CGRYCG	1 cut(s)	27
BsiSI	CCGG	4 cut(s)	23, 221, 284, 951
BslI	CCNNNNNNNGG	4 cut(s)	60, 227, 407, 836
BsmAI	GTCTC	1 cut(s)	101
BsmBI	CGTCTC	1 cut(s)	101
BsnI	GGCC	1 cut(s)	26
Bsp119I	TTCGAA	1 cut(s)	326
Bsp1286I	GDGCHC	1 cut(s)	1045
Bsp13I	TCCGGA	1 cut(s)	950
Bsp143I	GATC	4 cut(s)	37, 751, 826, 980
BspACI	CCGC	3 cut(s)	271, 905, 1036
BspANI	GGCC	1 cut(s)	26
BspCNI	CTCAG	3 cut(s)	394, 460, 772
BspEI	TCCGGA	1 cut(s)	950
BspFNI	CGCG	1 cut(s)	51
BspHI	TCATGA	1 cut(s)	391
BspLI	GGNNCC	2 cut(s)	9, 1044
BspMAI	CTGCAG	1 cut(s)	451
BspMI	ACCTGC	1 cut(s)	820
BspPI	GGATC	2 cut(s)	45, 821
BspT104I	TTCGAA	1 cut(s)	326
BsrI	ACTGG	3 cut(s)	87, 679, 808
BssECI	CCNNGG	2 cut(s)	284, 925
BssMI	GATC	4 cut(s)	37, 751, 826, 980
Bst2UI	CCWGG	2 cut(s)	554, 926
Bst4CI	ACNGT	1 cut(s)	824
Bst6I	CTCTTC	6 cut(s)	59, 93, 536, 552, 971, 1065
BstAPI	GCANNNNNTGC	1 cut(s)	485
BstBI	TTCGAA	1 cut(s)	326
BstC8I	GCNNGC	3 cut(s)	465, 498, 648
BstDEI	CTNAG	3 cut(s)	402, 468, 780
BstF5I	GGATG	4 cut(s)	75, 91, 412, 552
BstFNI	CGCG	1 cut(s)	51
BstHHI	GCGC	2 cut(s)	53, 233
BstKTI	GATC	4 cut(s)	40, 754, 829, 983
BstMAI	GTCTC	1 cut(s)	101
BstMBI	GATC	4 cut(s)	37, 751, 826, 980
BstMCI	CGRYCG	1 cut(s)	27
BstMWI	GCNNNNNNNGC	4 cut(s)	48, 485, 497, 794
BstNI	CCWGG	2 cut(s)	554, 926
BstSCI	CCNGG	5 cut(s)	21, 219, 283, 552, 924
BstSFI	CTRYAG	1 cut(s)	447
BstUI	CGCG	1 cut(s)	51
BstV1I	GCAGC	4 cut(s)	304, 475, 562, 892
BstV2I	GAAGAC	2 cut(s)	243, 342
BstZI	CGGCCG	1 cut(s)	24
Bsu36I	CCTNAGG	1 cut(s)	402
BsuI	GTATCC	1 cut(s)	1072
BsuRI	GGCC	1 cut(s)	26
BtsCI	GGATG	4 cut(s)	75, 91, 412, 552
BtsI	GCAGTG	1 cut(s)	456
BtsIMutI	CAGTG	1 cut(s)	456
BveI	ACCTGC	1 cut(s)	820
Cac8I	GCNNGC	3 cut(s)	465, 498, 648
CaiI	CAGNNNCTG	2 cut(s)	170, 803
CciI	TCATGA	1 cut(s)	391
CfoI	GCGC	2 cut(s)	53, 233
Cfr13I	GGNCC	3 cut(s)	7, 677, 922
Csp6I	GTAC	1 cut(s)	820
CviAII	CATG	2 cut(s)	392, 505
CviQI	GTAC	1 cut(s)	820
DdeI	CTNAG	3 cut(s)	402, 468, 780
DpnI	GATC	4 cut(s)	39, 753, 828, 982
DpnII	GATC	4 cut(s)	37, 751, 826, 980
DraI	TTTAAA	1 cut(s)	868
EaeI	YGGCCR	1 cut(s)	24
EagI	CGGCCG	1 cut(s)	24
Eam1104I	CTCTTC	6 cut(s)	59, 93, 536, 552, 971, 1065
EarI	CTCTTC	6 cut(s)	59, 93, 536, 552, 971, 1065
EclXI	CGGCCG	1 cut(s)	24
Eco24I	GRGCYC	1 cut(s)	1045
Eco47I	GGWCC	3 cut(s)	7, 677, 922
Eco52I	CGGCCG	1 cut(s)	24
Eco57I	CTGAAG	1 cut(s)	192
Eco81I	CCTNAGG	1 cut(s)	402
EcoO109I	RGGNCCY	1 cut(s)	7
EcoRI	GAATTC	1 cut(s)	722
EcoRII	CCWGG	2 cut(s)	552, 924
EcoT38I	GRGCYC	1 cut(s)	1045
Esp3I	CGTCTC	1 cut(s)	101
FaeI	CATG	2 cut(s)	395, 508
FalI	AAGNNNNNCTT	4 cut(s)	114, 146, 549, 581
FatI	CATG	2 cut(s)	391, 504
Fnu4HI	GCNGC	4 cut(s)	293, 489, 576, 881
FokI	GGATG	4 cut(s)	82, 98, 419, 559
FriOI	GRGCYC	1 cut(s)	1045
Fsp4HI	GCNGC	4 cut(s)	293, 489, 576, 881
GlaI	GCGC	2 cut(s)	52, 232
GluI	GCNGC	4 cut(s)	293, 489, 576, 881
GsuI	CTGGAG	1 cut(s)	1029
HaeIII	GGCC	1 cut(s)	26
HapII	CCGG	4 cut(s)	23, 221, 284, 951
HhaI	GCGC	2 cut(s)	53, 233
Hin1II	CATG	2 cut(s)	395, 508
Hin6I	GCGC	2 cut(s)	51, 231
HinP1I	GCGC	2 cut(s)	51, 231
HindIII	AAGCTT	1 cut(s)	861
HinfI	GANTC	2 cut(s)	118, 941
HpaII	CCGG	4 cut(s)	23, 221, 284, 951
HphI	GGTGA	1 cut(s)	941
Hpy166II	GTNNAC	1 cut(s)	680
Hpy188I	TCNGA	2 cut(s)	751, 1069
Hpy8I	GTNNAC	1 cut(s)	680
HpyAV	CCTTC	3 cut(s)	221, 407, 523
HpyCH4III	ACNGT	1 cut(s)	824
HpyCH4IV	ACGT	4 cut(s)	110, 613, 688, 1030
HpyCH4V	TGCA	6 cut(s)	449, 496, 658, 797, 851, 1028
HpyF10VI	GCNNNNNNNGC	4 cut(s)	48, 485, 497, 794
HpyF3I	CTNAG	3 cut(s)	402, 468, 780
HpySE526I	ACGT	4 cut(s)	110, 613, 688, 1030
Hsp92II	CATG	2 cut(s)	395, 508
HspAI	GCGC	2 cut(s)	51, 231
Kpn2I	TCCGGA	1 cut(s)	950
Kzo9I	GATC	4 cut(s)	37, 751, 826, 980
LmnI	GCTCC	4 cut(s)	347, 403, 775, 1048
Lsp1109I	GCAGC	4 cut(s)	304, 475, 562, 892
LweI	GCATC	3 cut(s)	385, 394, 552
MaeII	ACGT	4 cut(s)	110, 613, 688, 1030
MaeIII	GTNAC	3 cut(s)	78, 707, 799
MalI	GATC	4 cut(s)	39, 753, 828, 982
MboI	GATC	4 cut(s)	37, 751, 826, 980
MfeI	CAATTG	1 cut(s)	651
MhlI	GDGCHC	1 cut(s)	1045
MluCI	AATT	6 cut(s)	278, 588, 604, 651, 722, 870
MroI	TCCGGA	1 cut(s)	950
MroXI	GAANNNNTTC	1 cut(s)	615
MseI	TTAA	3 cut(s)	132, 639, 867
MslI	CAYNNNNRTG	2 cut(s)	390, 393
MspI	CCGG	4 cut(s)	23, 221, 284, 951
MspR9I	CCNGG	5 cut(s)	23, 221, 285, 554, 926
MunI	CAATTG	1 cut(s)	651
MvaI	CCWGG	2 cut(s)	554, 926
MvnI	CGCG	1 cut(s)	51
MwoI	GCNNNNNNNGC	4 cut(s)	48, 485, 497, 794
NciI	CCSGG	3 cut(s)	23, 221, 285
NdeII	GATC	4 cut(s)	37, 751, 826, 980
NlaIII	CATG	2 cut(s)	395, 508
NlaIV	GGNNCC	2 cut(s)	9, 1044
NspV	TTCGAA	1 cut(s)	326
PagI	TCATGA	1 cut(s)	391
PcsI	WCGNNNNNNNCGW	1 cut(s)	102
PdmI	GAANNNNTTC	1 cut(s)	615
PfeI	GAWTC	2 cut(s)	118, 941
PkrI	GCNGC	4 cut(s)	294, 490, 577, 882
PpuMI	RGGWCCY	1 cut(s)	7
Psp5II	RGGWCCY	1 cut(s)	7
Psp6I	CCWGG	2 cut(s)	552, 924
PspGI	CCWGG	2 cut(s)	552, 924
PspN4I	GGNNCC	2 cut(s)	9, 1044
PspPI	GGNCC	3 cut(s)	7, 677, 922
PspPPI	RGGWCCY	1 cut(s)	7
PstI	CTGCAG	1 cut(s)	451
PstNI	CAGNNNCTG	2 cut(s)	170, 803
RsaI	GTAC	1 cut(s)	821
RsaNI	GTAC	1 cut(s)	820
RseI	CAYNNNNRTG	2 cut(s)	390, 393
SaqAI	TTAA	3 cut(s)	132, 639, 867
SatI	GCNGC	4 cut(s)	293, 489, 576, 881
Sau3AI	GATC	4 cut(s)	37, 751, 826, 980
Sau96I	GGNCC	3 cut(s)	7, 677, 922
ScrFI	CCNGG	5 cut(s)	23, 221, 285, 554, 926
SduI	GDGCHC	1 cut(s)	1045
SfaNI	GCATC	3 cut(s)	385, 394, 552
SfcI	CTRYAG	1 cut(s)	447
SfuI	TTCGAA	1 cut(s)	326
SinI	GGWCC	3 cut(s)	7, 677, 922
SmiMI	CAYNNNNRTG	2 cut(s)	390, 393
SmlI	CTYRAG	1 cut(s)	598
SmoI	CTYRAG	1 cut(s)	598
Sse9I	AATT	6 cut(s)	278, 588, 604, 651, 722, 870
SsiI	CCGC	3 cut(s)	271, 905, 1036
StyD4I	CCNGG	5 cut(s)	21, 219, 283, 552, 924
TaaI	ACNGT	1 cut(s)	824
TaiI	ACGT	4 cut(s)	113, 616, 691, 1033
TaqI	TCGA	4 cut(s)	96, 201, 326, 1018
TasI	AATT	6 cut(s)	278, 588, 604, 651, 722, 870
TfiI	GAWTC	2 cut(s)	118, 941
Tru1I	TTAA	3 cut(s)	132, 639, 867
Tru9I	TTAA	3 cut(s)	132, 639, 867
TscAI	CASTG	1 cut(s)	456
TseI	GCWGC	4 cut(s)	292, 488, 575, 880
TspDTI	ATGAA	5 cut(s)	102, 174, 219, 320, 366
TspGWI	ACGGA	1 cut(s)	274
TspRI	CASTG	1 cut(s)	456
VpaK11BI	GGWCC	3 cut(s)	7, 677, 922
XapI	RAATTY	3 cut(s)	278, 604, 722
XmnI	GAANNNNTTC	1 cut(s)	615

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