Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0002242

Physical Location & Seq

Genomic Coordinates Forward (+)

20711849 .. 20728301

Gene Structure 16453 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG110300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 660 bp

ATGGTGCTGCAATGGAGACAGGGACTTAGTTCAGGTGGACTAATGATTAAGGAGTTGAATGACTTGCTTGATCGTTTGGCATCCGGTGAAAATAGGGCAGAGAAGACTTCAATTCTTTCTACTTTGGTACAGAAGACAAATGCACAAGAAATGAAGTGGATCGTCATGATCATTCTTAAAGATCTGAAATTGGGAATTAGTGAAAAGAGCATCTTCCATGAATTTCATCCGGATGCTGAAGACTTGTTTAACGTTACCTGTGACTTGAAATTGGTTTGTGAAAAGCTGAGGGACAGAAGTCAACGACATAAACGACAGGACATTGAAGTTGGAAAAACTGTGCGCCCGCAGCTAGCTATGAGAGTTGGTGATGCAACTGGTGCATGGAAAAAGTTTCATGGAAAGGAAGTTGTTGTTGAGTGTAAATTCGACGGCGATCGCATCCAAATTCATAAGAATGGAACTGAAGTACATTACTTCTCAAGTTGTGCTGTATCCTTTTTGTCTCTTGCCTCGGTCAATAGAATGTTGCAAATCAAGCACGTTGAAGAAATGGATGTCAACATGGTTTCCCTTGGTCAGACTATCTTGGATGGAATCAAGAGTGTGGATGCATTCAACTACATAATGGATGAGGTTGAGGTTGCCATGGAGATGTGA

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

219

Amino Acids

24.93

Weight (kDa)

6.18

Isoelectric Point (pI)

32.62

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_ligase_A_N	PF04675	9 - 76	3.4e-15	DNA ligase N terminus
DNA_ligase_A_M	PF01068	116 - 169	2.1e-08	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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Publication-ready

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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)
AccIII	TCCGGA	1 cut(s)	229
AciI	CCGC	1 cut(s)	347
AclI	AACGTT	1 cut(s)	252
AclWI	GGATC	1 cut(s)	167
AcsI	RAATTY	3 cut(s)	221, 425, 447
AcuI	CTGAAG	2 cut(s)	258, 486
AfaI	GTAC	2 cut(s)	129, 471
AgsI	TTSAA	6 cut(s)	58, 111, 268, 326, 548, 619
AluBI	AGCT	3 cut(s)	286, 352, 356
AluI	AGCT	3 cut(s)	286, 352, 356
Alw26I	GTCTC	2 cut(s)	10, 510
AlwI	GGATC	1 cut(s)	167
Aor13HI	TCCGGA	1 cut(s)	229
ApeKI	GCWGC	2 cut(s)	7, 349
ApoI	RAATTY	3 cut(s)	221, 425, 447
AsiSI	GCGATCGC	1 cut(s)	439
AspLEI	GCGC	1 cut(s)	345
AsuHPI	GGTGA	2 cut(s)	98, 380
AsuNHI	GCTAGC	1 cut(s)	352
BbsI	GAAGAC	3 cut(s)	110, 140, 246
BbvCI	CCTCAGC	1 cut(s)	287
BbvI	GCAGC	1 cut(s)	361
BccI	CCATC	1 cut(s)	587
BceAI	ACGGC	1 cut(s)	448
BciVI	GTATCC	1 cut(s)	505
BclI	TGATCA	1 cut(s)	168
BcoDI	GTCTC	2 cut(s)	10, 510
BfaI	CTAG	1 cut(s)	353
BfuI	GTATCC	1 cut(s)	505
BglII	AGATCT	1 cut(s)	181
BisI	GCNGC	2 cut(s)	8, 350
BlsI	GCNGC	2 cut(s)	9, 351
BmsI	GCATC	6 cut(s)	89, 219, 223, 361, 450, 601
BmtI	GCTAGC	1 cut(s)	356
BoxI	GACNNNNGTC	1 cut(s)	297
BpiI	GAAGAC	3 cut(s)	110, 140, 246
Bpu10I	CCTNAGC	1 cut(s)	287
BpuEI	CTTGAG	1 cut(s)	466
BsaJI	CCNNGG	3 cut(s)	513, 574, 648
BsaWI	WCCGGW	2 cut(s)	83, 229
Bse1I	ACTGG	1 cut(s)	382
Bse3DI	GCAATG	1 cut(s)	17
BseAI	TCCGGA	1 cut(s)	229
BseDI	CCNNGG	3 cut(s)	513, 574, 648
BseGI	GGATG	8 cut(s)	80, 226, 238, 441, 562, 598, 616, 637
BseMI	GCAATG	1 cut(s)	17
BseMII	CTCAG	1 cut(s)	278
BseNI	ACTGG	1 cut(s)	382
BseXI	GCAGC	1 cut(s)	361
Bsh1285I	CGRYCG	1 cut(s)	439
BsiEI	CGRYCG	1 cut(s)	439
BsiSI	CCGG	2 cut(s)	84, 230
BslFI	GGGAC	2 cut(s)	36, 305
BsmAI	GTCTC	2 cut(s)	10, 510
BsmFI	GGGAC	2 cut(s)	36, 305
BsmI	GAATGC	1 cut(s)	614
Bsp13I	TCCGGA	1 cut(s)	229
Bsp143I	GATC	5 cut(s)	70, 159, 168, 181, 436
Bsp19I	CCATGG	1 cut(s)	648
BspACI	CCGC	1 cut(s)	347
BspCNI	CTCAG	1 cut(s)	279
BspEI	TCCGGA	1 cut(s)	229
BspHI	TCATGA	1 cut(s)	165
BspOI	GCTAGC	1 cut(s)	356
BspPI	GGATC	1 cut(s)	167
BsrDI	GCAATG	1 cut(s)	17
BsrI	ACTGG	1 cut(s)	382
BssECI	CCNNGG	3 cut(s)	513, 574, 648
BssMI	GATC	5 cut(s)	70, 159, 168, 181, 436
BssT1I	CCWWGG	2 cut(s)	574, 648
Bst4CI	ACNGT	1 cut(s)	340
BstAPI	GCANNNNNTGC	1 cut(s)	380
BstC8I	GCNNGC	2 cut(s)	347, 354
BstDEI	CTNAG	2 cut(s)	26, 287
BstDSI	CCRYGG	1 cut(s)	648
BstF5I	GGATG	8 cut(s)	80, 226, 238, 441, 562, 598, 616, 637
BstHHI	GCGC	1 cut(s)	345
BstKTI	GATC	5 cut(s)	73, 162, 171, 184, 439
BstMAI	GTCTC	2 cut(s)	10, 510
BstMBI	GATC	5 cut(s)	70, 159, 168, 181, 436
BstMCI	CGRYCG	1 cut(s)	439
BstMWI	GCNNNNNNNGC	3 cut(s)	349, 380, 538
BstPAI	GACNNNNGTC	1 cut(s)	297
BstV1I	GCAGC	1 cut(s)	361
BstV2I	GAAGAC	3 cut(s)	110, 140, 246
BstX2I	RGATCY	1 cut(s)	181
BstYI	RGATCY	1 cut(s)	181
BsuI	GTATCC	1 cut(s)	505
BtgI	CCRYGG	1 cut(s)	648
BtsCI	GGATG	8 cut(s)	80, 226, 238, 441, 562, 598, 616, 637
Cac8I	GCNNGC	2 cut(s)	347, 354
CciI	TCATGA	1 cut(s)	165
CfoI	GCGC	1 cut(s)	345
Csp6I	GTAC	2 cut(s)	128, 470
CviAII	CATG	6 cut(s)	166, 218, 384, 398, 565, 649
CviJI	RGCY	3 cut(s)	286, 352, 356
CviKI_1	RGCY	3 cut(s)	286, 352, 356
CviQI	GTAC	2 cut(s)	128, 470
DdeI	CTNAG	2 cut(s)	26, 287
DpnI	GATC	5 cut(s)	72, 161, 170, 183, 438
DpnII	GATC	5 cut(s)	70, 159, 168, 181, 436
Eco130I	CCWWGG	2 cut(s)	574, 648
Eco57I	CTGAAG	2 cut(s)	258, 486
EcoT14I	CCWWGG	2 cut(s)	574, 648
EcoT22I	ATGCAT	1 cut(s)	616
ErhI	CCWWGG	2 cut(s)	574, 648
FaeI	CATG	6 cut(s)	169, 221, 387, 401, 568, 652
FalI	AAGNNNNNCTT	2 cut(s)	197, 229
FaqI	GGGAC	2 cut(s)	36, 305
FatI	CATG	6 cut(s)	165, 217, 383, 397, 564, 648
FauI	CCCGC	1 cut(s)	354
FbaI	TGATCA	1 cut(s)	168
Fnu4HI	GCNGC	2 cut(s)	8, 350
FokI	GGATG	8 cut(s)	67, 213, 245, 428, 569, 605, 623, 644
Fsp4HI	GCNGC	2 cut(s)	8, 350
FspBI	CTAG	1 cut(s)	353
GlaI	GCGC	1 cut(s)	344
GluI	GCNGC	2 cut(s)	8, 350
HapII	CCGG	2 cut(s)	84, 230
HhaI	GCGC	1 cut(s)	345
Hin1II	CATG	6 cut(s)	169, 221, 387, 401, 568, 652
Hin6I	GCGC	1 cut(s)	343
HinP1I	GCGC	1 cut(s)	343
HincII	GTYRAC	2 cut(s)	302, 562
HindII	GTYRAC	2 cut(s)	302, 562
HinfI	GANTC	1 cut(s)	597
HpaII	CCGG	2 cut(s)	84, 230
HphI	GGTGA	2 cut(s)	98, 380
Hpy166II	GTNNAC	3 cut(s)	38, 302, 562
Hpy188I	TCNGA	2 cut(s)	186, 582
Hpy188III	TCNNGA	3 cut(s)	166, 230, 601
Hpy8I	GTNNAC	3 cut(s)	38, 302, 562
Hpy99I	CGWCG	1 cut(s)	434
HpyCH4III	ACNGT	1 cut(s)	340
HpyCH4IV	ACGT	2 cut(s)	252, 543
HpyCH4V	TGCA	6 cut(s)	10, 143, 374, 383, 532, 614
HpyF10VI	GCNNNNNNNGC	3 cut(s)	349, 380, 538
HpyF3I	CTNAG	2 cut(s)	26, 287
HpySE526I	ACGT	2 cut(s)	252, 543
Hsp92II	CATG	6 cut(s)	169, 221, 387, 401, 568, 652
HspAI	GCGC	1 cut(s)	343
Kpn2I	TCCGGA	1 cut(s)	229
Ksp22I	TGATCA	1 cut(s)	168
Kzo9I	GATC	5 cut(s)	70, 159, 168, 181, 436
LpnPI	CCDG	7 cut(s)	5, 18, 97, 243, 271, 302, 363
Lsp1109I	GCAGC	1 cut(s)	361
LweI	GCATC	6 cut(s)	89, 219, 223, 361, 450, 601
MaeI	CTAG	1 cut(s)	353
MaeII	ACGT	2 cut(s)	252, 543
MaeIII	GTNAC	2 cut(s)	253, 260
MalI	GATC	5 cut(s)	72, 161, 170, 183, 438
MboI	GATC	5 cut(s)	70, 159, 168, 181, 436
MboII	GAAGA	5 cut(s)	115, 145, 205, 251, 560
MflI	RGATCY	1 cut(s)	181
MluCI	AATT	7 cut(s)	111, 188, 195, 221, 269, 425, 447
MmeI	TCCRAC	1 cut(s)	310
MnlI	CCTC	4 cut(s)	282, 523, 628, 634
Mph1103I	ATGCAT	1 cut(s)	616
MroI	TCCGGA	1 cut(s)	229
MseI	TTAA	3 cut(s)	48, 177, 249
MslI	CAYNNNNRTG	3 cut(s)	231, 456, 653
MspI	CCGG	2 cut(s)	84, 230
Mva1269I	GAATGC	1 cut(s)	614
MwoI	GCNNNNNNNGC	3 cut(s)	349, 380, 538
NcoI	CCATGG	1 cut(s)	648
NdeII	GATC	5 cut(s)	70, 159, 168, 181, 436
NheI	GCTAGC	1 cut(s)	352
NlaIII	CATG	6 cut(s)	169, 221, 387, 401, 568, 652
NmuCI	GTSAC	1 cut(s)	260
NsiI	ATGCAT	1 cut(s)	616
PagI	TCATGA	1 cut(s)	165
PcsI	WCGNNNNNNNCGW	1 cut(s)	310
PctI	GAATGC	1 cut(s)	614
PfeI	GAWTC	1 cut(s)	597
PkrI	GCNGC	2 cut(s)	9, 351
Ple19I	CGATCG	1 cut(s)	439
PshAI	GACNNNNGTC	1 cut(s)	297
Psp1406I	AACGTT	1 cut(s)	252
PsuI	RGATCY	1 cut(s)	181
PvuI	CGATCG	1 cut(s)	439
RgaI	GCGATCGC	1 cut(s)	439
RsaI	GTAC	2 cut(s)	129, 471
RsaNI	GTAC	2 cut(s)	128, 470
RseI	CAYNNNNRTG	3 cut(s)	231, 456, 653
SaqAI	TTAA	3 cut(s)	48, 177, 249
SatI	GCNGC	2 cut(s)	8, 350
Sau3AI	GATC	5 cut(s)	70, 159, 168, 181, 436
SetI	ASST	9 cut(s)	37, 255, 260, 288, 354, 358, 546, 639, 645
SfaAI	GCGATCGC	1 cut(s)	439
SfaNI	GCATC	6 cut(s)	89, 219, 223, 361, 450, 601
SgfI	GCGATCGC	1 cut(s)	439
SmiMI	CAYNNNNRTG	3 cut(s)	231, 456, 653
SmlI	CTYRAG	1 cut(s)	481
SmoI	CTYRAG	1 cut(s)	481
Sse9I	AATT	7 cut(s)	111, 188, 195, 221, 269, 425, 447
SsiI	CCGC	1 cut(s)	347
SspMI	CTAG	1 cut(s)	353
StyI	CCWWGG	2 cut(s)	574, 648
TaaI	ACNGT	1 cut(s)	340
TaiI	ACGT	2 cut(s)	255, 546
TaqI	TCGA	1 cut(s)	429
TaqII	GACCGA	1 cut(s)	505
TasI	AATT	7 cut(s)	111, 188, 195, 221, 269, 425, 447
TatI	WGTACW	1 cut(s)	469
TfiI	GAWTC	1 cut(s)	597
Tru1I	TTAA	3 cut(s)	48, 177, 249
Tru9I	TTAA	3 cut(s)	48, 177, 249
TseFI	GTSAC	1 cut(s)	260
TseI	GCWGC	2 cut(s)	7, 349
Tsp45I	GTSAC	1 cut(s)	260
TspDTI	ATGAA	5 cut(s)	167, 215, 234, 386, 440
XapI	RAATTY	3 cut(s)	221, 425, 447
XspI	CTAG	1 cut(s)	353
Zsp2I	ATGCAT	1 cut(s)	616

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