Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0002242

Physical Location & Seq

Genomic Coordinates Reverse (-)

43708923 .. 43717239

Gene Structure 8317 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG357600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 285 bp

ATGGTCTTAAGGAGTCGGTGCTCGCCACCTGCCTCATCGACACTCTCGGCATGTCCTGAGACTCCGACGTCGCCTCTTGGTGCAAGGGCGGTGCCAAGACCGGTGCCAAAGCAGGACATTGAAGTTGGAAAAGCTGTGCGCCCGCAGCTAGCTATGAGAGTCGGTGATGCAACTGGTGCATGGAAAAAGTTTCATGGAAAAGAAGTTGTTGTTGAGTGTAAATTCGACGGCAATCGGATCCAAATTCATAAGAATGGAAACGAAGTACATTACTTCTCAAGGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000726 GO:0003674 GO:0003824 GO:0003909 GO:0003910 GO:0005575 GO:0005576 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0005911 GO:0006139 GO:0006259 GO:0006266 GO:0006281 GO:0006289 GO:0006297 GO:0006302 GO:0006303 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009314 GO:0009506 GO:0009628 GO:0009987 GO:0010165 GO:0010212 GO:0016874 GO:0016886 GO:0030054 GO:0032807 GO:0032991 GO:0033554 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0048046 GO:0050896 GO:0051103 GO:0051716 GO:0055044 GO:0071704 GO:0090304 GO:0140097 GO:1901360

KEGG Pathways

Metabolic & Signaling

ko03450 map03450

Pfam Domains

Protein Families

BRCT_2 DNA_ligase_A_C DNA_ligase_A_M DNA_ligase_A_N DNA_ligase_IV

Protein Analysis

94

Amino Acids

10.3

Weight (kDa)

9.85

Isoelectric Point (pI)

68.37

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_ligase_A_M	PF01068	48 - 94	4.3e-10	ATP dependent DNA ligase domain

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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Orthologous Genes (Group: OG0002242)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G57160 AT5G57160
fragaria_vesca	FvH4_4g07160
malus_domestica	MD16G1247900.v1.1
prunus_persica	Prupe.1G074600_v2.0.a1 Prupe.1G074600_v2.0.a1
pyrus_communis	pycom12g16110 pycom12g16210 pycom16g20800
rosa_chinensis	RchiOBHm_Chr0c22g0500591 RchiOBHm_Chr4g0399311 RchiOBHm_Chr5g0052491 RchiOBHm_Chr7g0206661
rosa_laevigata	RLG00000009274 RLG00000012027 RLG00000013478 RLG00000013735 RLG00000034678
rosa_multiflora	Rmu_co8101330.1_g000001 Rmu_co8329359.1_g000001 Rmu_sc0000924.1_g000031 Rmu_sc0003135.1_g000008
rosa_roxburghii	Rroxscaffold_4G00283390 Rroxscaffold_4G00329320 Rroxscaffold_5G00344240
rosa_rugosa	Rorug04G0016500
rosa_samantha	Rh2AG218900 Rh2BG192100 Rh2BG230700 Rh2CG361900 Rh2DG225100 Rh3BG254200 Rh3DG357600 Rh4AG094200 Rh4AG102100 Rh4BG091600 Rh4CG102400 Rh4CG110300 Rh4DG086300 Rh7DG237100 Rh7DG335000 Rh7DG335200
rosa_wichuraiana	Rw4G007730

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	37
AasI	GACNNNNNNGTC	1 cut(s)	67
AatII	GACGTC	1 cut(s)	71
Acc36I	ACCTGC	1 cut(s)	37
AccB1I	GGYRCC	2 cut(s)	91, 103
AciI	CCGC	2 cut(s)	89, 143
AclWI	GGATC	2 cut(s)	232, 245
AcsI	RAATTY	2 cut(s)	221, 243
AcyI	GRCGYC	1 cut(s)	68
AfaI	GTAC	1 cut(s)	267
AflII	CTTAAG	1 cut(s)	7
AgeI	ACCGGT	1 cut(s)	100
AgsI	TTSAA	1 cut(s)	122
AluBI	AGCT	3 cut(s)	134, 148, 152
AluI	AGCT	3 cut(s)	134, 148, 152
Alw21I	GWGCWC	1 cut(s)	23
Alw26I	GTCTC	1 cut(s)	53
AlwI	GGATC	2 cut(s)	232, 245
ApeKI	GCWGC	1 cut(s)	145
ApoI	RAATTY	2 cut(s)	221, 243
AsiGI	ACCGGT	1 cut(s)	100
AspLEI	GCGC	1 cut(s)	141
AsuHPI	GGTGA	1 cut(s)	176
AsuNHI	GCTAGC	1 cut(s)	148
BamHI	GGATCC	1 cut(s)	237
BanI	GGYRCC	2 cut(s)	91, 103
Bbv12I	GWGCWC	1 cut(s)	23
BbvI	GCAGC	1 cut(s)	157
BceAI	ACGGC	1 cut(s)	244
BcoDI	GTCTC	1 cut(s)	53
BfaI	CTAG	1 cut(s)	149
BfrI	CTTAAG	1 cut(s)	7
BfuAI	ACCTGC	1 cut(s)	37
BisI	GCNGC	1 cut(s)	146
BlsI	GCNGC	1 cut(s)	147
BmiI	GGNNCC	3 cut(s)	93, 105, 239
BmsI	GCATC	1 cut(s)	157
BmtI	GCTAGC	1 cut(s)	152
BpuEI	CTTGAG	1 cut(s)	262
BsaHI	GRCGYC	1 cut(s)	68
BsaWI	WCCGGW	1 cut(s)	100
Bse118I	RCCGGY	1 cut(s)	100
Bse1I	ACTGG	1 cut(s)	178
BseMII	CTCAG	1 cut(s)	48
BseNI	ACTGG	1 cut(s)	178
BseXI	GCAGC	1 cut(s)	157
BshNI	GGYRCC	2 cut(s)	91, 103
BshTI	ACCGGT	1 cut(s)	100
BsiHKAI	GWGCWC	1 cut(s)	23
BsiSI	CCGG	1 cut(s)	101
BsmAI	GTCTC	1 cut(s)	53
Bsp1286I	GDGCHC	1 cut(s)	23
Bsp143I	GATC	1 cut(s)	237
BspACI	CCGC	2 cut(s)	89, 143
BspCNI	CTCAG	1 cut(s)	49
BspLI	GGNNCC	3 cut(s)	93, 105, 239
BspMI	ACCTGC	1 cut(s)	37
BspOI	GCTAGC	1 cut(s)	152
BspPI	GGATC	2 cut(s)	232, 245
BspT107I	GGYRCC	2 cut(s)	91, 103
BspTI	CTTAAG	1 cut(s)	7
BsrFI	RCCGGY	1 cut(s)	100
BsrI	ACTGG	1 cut(s)	178
BssAI	RCCGGY	1 cut(s)	100
BssMI	GATC	1 cut(s)	237
BssNI	GRCGYC	1 cut(s)	68
BstACI	GRCGYC	1 cut(s)	68
BstAFI	CTTAAG	1 cut(s)	7
BstAPI	GCANNNNNTGC	1 cut(s)	176
BstC8I	GCNNGC	3 cut(s)	23, 143, 150
BstDEI	CTNAG	1 cut(s)	57
BstHHI	GCGC	1 cut(s)	141
BstKTI	GATC	1 cut(s)	240
BstMAI	GTCTC	1 cut(s)	53
BstMBI	GATC	1 cut(s)	237
BstMWI	GCNNNNNNNGC	2 cut(s)	145, 176
BstNSI	RCATGY	1 cut(s)	54
BstV1I	GCAGC	1 cut(s)	157
BstX2I	RGATCY	1 cut(s)	237
BstYI	RGATCY	1 cut(s)	237
BveI	ACCTGC	1 cut(s)	37
Cac8I	GCNNGC	3 cut(s)	23, 143, 150
CfoI	GCGC	1 cut(s)	141
Cfr10I	RCCGGY	1 cut(s)	100
Csp6I	GTAC	1 cut(s)	266
CspAI	ACCGGT	1 cut(s)	100
CviAII	CATG	3 cut(s)	51, 180, 194
CviJI	RGCY	3 cut(s)	134, 148, 152
CviKI_1	RGCY	3 cut(s)	134, 148, 152
CviQI	GTAC	1 cut(s)	266
DdeI	CTNAG	1 cut(s)	57
DpnI	GATC	1 cut(s)	239
DpnII	GATC	1 cut(s)	237
DrdI	GACNNNNNNGTC	1 cut(s)	67
DseDI	GACNNNNNNGTC	1 cut(s)	67
FaeI	CATG	3 cut(s)	54, 183, 197
FaiI	YATR	5 cut(s)	52, 155, 181, 195, 249
FatI	CATG	3 cut(s)	50, 179, 193
FauI	CCCGC	1 cut(s)	150
Fnu4HI	GCNGC	1 cut(s)	146
Fsp4HI	GCNGC	1 cut(s)	146
FspBI	CTAG	1 cut(s)	149
GlaI	GCGC	1 cut(s)	140
GluI	GCNGC	1 cut(s)	146
HapII	CCGG	1 cut(s)	101
HhaI	GCGC	1 cut(s)	141
Hin1I	GRCGYC	1 cut(s)	68
Hin1II	CATG	3 cut(s)	54, 183, 197
Hin6I	GCGC	1 cut(s)	139
HinP1I	GCGC	1 cut(s)	139
HinfI	GANTC	3 cut(s)	13, 61, 159
HpaII	CCGG	1 cut(s)	101
HphI	GGTGA	1 cut(s)	176
Hpy188I	TCNGA	2 cut(s)	66, 237
Hpy188III	TCNNGA	1 cut(s)	56
Hpy99I	CGWCG	3 cut(s)	70, 73, 230
HpyCH4IV	ACGT	1 cut(s)	68
HpyCH4V	TGCA	3 cut(s)	83, 170, 179
HpyF10VI	GCNNNNNNNGC	2 cut(s)	145, 176
HpyF3I	CTNAG	1 cut(s)	57
HpySE526I	ACGT	1 cut(s)	68
Hsp92I	GRCGYC	1 cut(s)	68
Hsp92II	CATG	3 cut(s)	54, 183, 197
HspAI	GCGC	1 cut(s)	139
Kzo9I	GATC	1 cut(s)	237
LpnPI	CCDG	5 cut(s)	42, 69, 98, 114, 159
Lsp1109I	GCAGC	1 cut(s)	157
LweI	GCATC	1 cut(s)	157
MaeI	CTAG	1 cut(s)	149
MaeII	ACGT	1 cut(s)	68
MalI	GATC	1 cut(s)	239
MboI	GATC	1 cut(s)	237
MflI	RGATCY	1 cut(s)	237
MhlI	GDGCHC	1 cut(s)	23
MluCI	AATT	2 cut(s)	221, 243
MlyI	GAGTC	3 cut(s)	22, 55, 168
MmeI	TCCRAC	2 cut(s)	89, 106
MnlI	CCTC	2 cut(s)	43, 84
MseI	TTAA	1 cut(s)	8
MslI	CAYNNNNRTG	1 cut(s)	252
MspCI	CTTAAG	1 cut(s)	7
MspI	CCGG	1 cut(s)	101
MwoI	GCNNNNNNNGC	2 cut(s)	145, 176
NdeII	GATC	1 cut(s)	237
NheI	GCTAGC	1 cut(s)	148
NlaIII	CATG	3 cut(s)	54, 183, 197
NlaIV	GGNNCC	3 cut(s)	93, 105, 239
NmeAIII	GCCGAG	1 cut(s)	26
NspI	RCATGY	1 cut(s)	54
PaqCI	CACCTGC	1 cut(s)	37
PinAI	ACCGGT	1 cut(s)	100
PkrI	GCNGC	1 cut(s)	147
PleI	GAGTC	3 cut(s)	21, 55, 167
PpsI	GAGTC	3 cut(s)	21, 55, 167
PspN4I	GGNNCC	3 cut(s)	93, 105, 239
PsuI	RGATCY	1 cut(s)	237
RsaI	GTAC	1 cut(s)	267
RsaNI	GTAC	1 cut(s)	266
RseI	CAYNNNNRTG	1 cut(s)	252
SaqAI	TTAA	1 cut(s)	8
SatI	GCNGC	1 cut(s)	146
Sau3AI	GATC	1 cut(s)	237
SchI	GAGTC	3 cut(s)	22, 55, 168
SduI	GDGCHC	1 cut(s)	23
SetI	ASST	6 cut(s)	31, 71, 136, 150, 154, 284
SfaNI	GCATC	1 cut(s)	157
SmiMI	CAYNNNNRTG	1 cut(s)	252
SmlI	CTYRAG	2 cut(s)	7, 277
SmoI	CTYRAG	2 cut(s)	7, 277
Sse9I	AATT	2 cut(s)	221, 243
SsiI	CCGC	2 cut(s)	89, 143
SspMI	CTAG	1 cut(s)	149
TaiI	ACGT	1 cut(s)	71
TaqI	TCGA	2 cut(s)	38, 225
TasI	AATT	2 cut(s)	221, 243
TatI	WGTACW	1 cut(s)	265
Tru1I	TTAA	1 cut(s)	8
Tru9I	TTAA	1 cut(s)	8
TseI	GCWGC	1 cut(s)	145
TspDTI	ATGAA	2 cut(s)	182, 236
Vha464I	CTTAAG	1 cut(s)	7
XapI	RAATTY	2 cut(s)	221, 243
XceI	RCATGY	1 cut(s)	54
XspI	CTAG	1 cut(s)	149
ZraI	GACGTC	1 cut(s)	69

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