Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0001033

Physical Location & Seq

Genomic Coordinates Forward (+)

35217980 .. 35219719

Gene Structure 1740 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG170700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 555 bp

ATGATCTGTGGTAGTACCAGCCATGTGGAGAGGACGAAAATTCTAGAAGCCTTCAAAACAAGTCAGGACATAAATACTGTTTTCTTGTCTAAGGTGGGTGATAATTCCATAGACATTCCTGAGGCAAATGTGATTATTCAGATTTCATCACATGCTGGTTCAAGACGTCAAGAAGCACAGCGTCTTGGTCGTATTTTAAGAGCTAAGGGTAGACCTCAGGATCGGATAGCAGGAGGAAAAGAGGAGTACAATGCATTTTTTTATTCCCTCGTGTCTACGGATACTCAGGAAATGTACTTTTCAACTAAACGGCAGCAGTTTTTGATCGATCAAGGTTATAGTTTTAAGGTTATTACAAGCTTACCTCCTCCTGAATCAGGAGCTGATTTGAGCTATCATCGTGTTGAAGACCAACTGGCACTGCTCTCAAAGGTGTTGAGTGCTGGTGATGATAAAGTTGGCTTAGAGCCACATGAAGATGATGCAGATGAGATTTCCCTTCAGAAAGCACGTCGTTCAAAGAGACATCATTTGTTTAAACAACGCCGTGGCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0008150 GO:0009314 GO:0009411 GO:0009416 GO:0009628 GO:0010224 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0050896

KEGG Pathways

Metabolic & Signaling

ko03022 ko03420 map03022 map03420

Pfam Domains

Protein Families

ERCC3_RAD25_C Helicase_C_3 ResIII

Protein Analysis

184

Amino Acids

20.76

Weight (kDa)

8.65

Isoelectric Point (pI)

49.42

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
ERCC3_RAD25_C	PF16203	1 - 162	8.2e-69	ERCC3/RAD25/XPB C-terminal helicase
Helicase_C	PF00271	3 - 69	4.3e-10	Helicase conserved C-terminal 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: OG0001033)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G41360 AT5G41360 AT5G41370
fragaria_vesca	FvH4_5g02840 FvH4_5g02840 FvH4_5g02840 FvH4_5g02840 FvH4_5g02840 FvH4_5g19420 FvH4_5g19430 FvH4_7g08220 FvH4_7g08220
malus_domestica	MD06G1087900.v1.1
prunus_persica	Prupe.5G104000_v2.0.a1
pyrus_communis	pycom06g08400
rosa_chinensis	RchiOBHm_Chr1g0341611 RchiOBHm_Chr1g0341621 RchiOBHm_Chr1g0341861 RchiOBHm_Chr7g0197061 RchiOBHm_Chr7g0203931
rosa_laevigata	RLG00000003497 RLG00000003962 RLG00000029105 RLG00000029132
rosa_multiflora	Rmu_co8328521.1_g000001 Rmu_co8329503.1_g000001 Rmu_sc0002302.1_g000034 Rmu_sc0002322.1_g000070 Rmu_sc0003411.1_g000004 Rmu_sc0013871.1_g000001 Rmu_sc0032022.1_g000001
rosa_roxburghii	Rroxscaffold_3G00258690 Rroxscaffold_4G00312270 Rroxscaffold_4G00312590
rosa_rugosa	Rorug01G0154800.1 Rorug07G0037400 Rorug07G0079500
rosa_samantha	Rh1AG168500 Rh1AG170500 Rh1BG136800 Rh1BG138300 Rh1BG138400 Rh1CG156100 Rh1CG158700 Rh1DG170300 Rh1DG170600 Rh1DG170700 Rh7AG162300 Rh7AG209400 Rh7AG209500 Rh7BG164400 Rh7BG208200 Rh7BG208300 Rh7CG170500 Rh7CG221900 Rh7DG163800 Rh7DG216500
rosa_wichuraiana	Rw1G014160 Rw1G014180 Rw7G014170 Rw7G018250

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	169
AccI	GTMKAC	2 cut(s)	211, 275
AclWI	GGATC	1 cut(s)	228
AcsI	RAATTY	1 cut(s)	39
AcuI	CTGAAG	1 cut(s)	485
AcyI	GRCGYC	1 cut(s)	166
AfaI	GTAC	3 cut(s)	16, 248, 296
AfiI	CCNNNNNNNGG	1 cut(s)	377
AgsI	TTSAA	5 cut(s)	55, 162, 303, 407, 519
AjiI	CACGTC	1 cut(s)	512
AluBI	AGCT	4 cut(s)	203, 360, 383, 393
AluI	AGCT	4 cut(s)	203, 360, 383, 393
Alw26I	GTCTC	1 cut(s)	517
AlwI	GGATC	1 cut(s)	228
AlwNI	CAGNNNCTG	1 cut(s)	383
ApeKI	GCWGC	1 cut(s)	313
ApoI	RAATTY	1 cut(s)	39
AsuHPI	GGTGA	2 cut(s)	110, 458
AxyI	CCTNAGG	2 cut(s)	120, 216
BauI	CACGAG	1 cut(s)	269
BbsI	GAAGAC	1 cut(s)	414
BbvI	GCAGC	1 cut(s)	325
BceAI	ACGGC	2 cut(s)	326, 531
BciVI	GTATCC	1 cut(s)	274
BcoDI	GTCTC	1 cut(s)	517
BfaI	CTAG	1 cut(s)	44
BfuI	GTATCC	1 cut(s)	274
BisI	GCNGC	1 cut(s)	314
BlsI	GCNGC	1 cut(s)	315
BmgBI	CACGTC	1 cut(s)	512
BmsI	GCATC	1 cut(s)	472
BpiI	GAAGAC	1 cut(s)	414
Bpu10I	CCTNAGC	1 cut(s)	204
Bsa29I	ATCGAT	1 cut(s)	327
BsaHI	GRCGYC	1 cut(s)	166
BsaJI	CCNNGG	1 cut(s)	547
Bsc4I	CCNNNNNNNGG	1 cut(s)	377
Bse1I	ACTGG	1 cut(s)	420
Bse21I	CCTNAGG	2 cut(s)	120, 216
BseCI	ATCGAT	1 cut(s)	327
BseDI	CCNNGG	1 cut(s)	547
BseLI	CCNNNNNNNGG	1 cut(s)	377
BseMII	CTCAG	3 cut(s)	111, 230, 299
BseNI	ACTGG	1 cut(s)	420
BseRI	GAGGAG	2 cut(s)	257, 357
BseXI	GCAGC	1 cut(s)	325
BshVI	ATCGAT	1 cut(s)	327
BslI	CCNNNNNNNGG	1 cut(s)	377
BsmAI	GTCTC	1 cut(s)	517
Bsp143I	GATC	4 cut(s)	3, 220, 324, 328
BspCNI	CTCAG	3 cut(s)	112, 229, 298
BspDI	ATCGAT	1 cut(s)	327
BspPI	GGATC	1 cut(s)	228
BsrI	ACTGG	1 cut(s)	420
BssECI	CCNNGG	1 cut(s)	547
BssMI	GATC	4 cut(s)	3, 220, 324, 328
BssNI	GRCGYC	1 cut(s)	166
BssSI	CACGAG	1 cut(s)	269
Bst2BI	CACGAG	1 cut(s)	269
Bst4CI	ACNGT	1 cut(s)	79
BstACI	GRCGYC	1 cut(s)	166
BstDEI	CTNAG	6 cut(s)	90, 120, 204, 216, 285, 463
BstDSI	CCRYGG	1 cut(s)	547
BstENI	CCTNNNNNAGG	1 cut(s)	375
BstKTI	GATC	4 cut(s)	6, 223, 327, 331
BstMAI	GTCTC	1 cut(s)	517
BstMBI	GATC	4 cut(s)	3, 220, 324, 328
BstNSI	RCATGY	1 cut(s)	155
BstV1I	GCAGC	1 cut(s)	325
BstV2I	GAAGAC	1 cut(s)	414
BstXI	CCANNNNNNTGG	1 cut(s)	25
Bsu15I	ATCGAT	1 cut(s)	327
Bsu36I	CCTNAGG	2 cut(s)	120, 216
BsuI	GTATCC	1 cut(s)	274
BsuTUI	ATCGAT	1 cut(s)	327
BtgI	CCRYGG	1 cut(s)	547
BtrI	CACGTC	1 cut(s)	512
BtsI	GCAGTG	1 cut(s)	419
BtsIMutI	CAGTG	1 cut(s)	419
CaiI	CAGNNNCTG	1 cut(s)	383
ClaI	ATCGAT	1 cut(s)	327
CseI	GACGC	1 cut(s)	170
Csp6I	GTAC	3 cut(s)	15, 247, 295
CviAII	CATG	3 cut(s)	23, 152, 473
CviJI	RGCY	9 cut(s)	21, 50, 203, 360, 383, 393, 462, 469, 552
CviKI_1	RGCY	9 cut(s)	21, 50, 203, 360, 383, 393, 462, 469, 552
CviQI	GTAC	3 cut(s)	15, 247, 295
DdeI	CTNAG	6 cut(s)	90, 120, 204, 216, 285, 463
DpnI	GATC	4 cut(s)	5, 222, 326, 330
DpnII	GATC	4 cut(s)	3, 220, 324, 328
DraI	TTTAAA	1 cut(s)	538
Eco57I	CTGAAG	1 cut(s)	485
Eco81I	CCTNAGG	2 cut(s)	120, 216
EcoNI	CCTNNNNNAGG	1 cut(s)	375
EcoT22I	ATGCAT	1 cut(s)	256
FaeI	CATG	3 cut(s)	26, 155, 476
FaiI	YATR	6 cut(s)	24, 71, 110, 153, 339, 474
FatI	CATG	3 cut(s)	22, 151, 472
FblI	GTMKAC	2 cut(s)	211, 275
Fnu4HI	GCNGC	1 cut(s)	314
Fsp4HI	GCNGC	1 cut(s)	314
FspBI	CTAG	1 cut(s)	44
GluI	GCNGC	1 cut(s)	314
HgaI	GACGC	1 cut(s)	170
Hin1I	GRCGYC	1 cut(s)	166
Hin1II	CATG	3 cut(s)	26, 155, 476
HindIII	AAGCTT	1 cut(s)	358
HinfI	GANTC	1 cut(s)	374
HphI	GGTGA	2 cut(s)	110, 458
Hpy166II	GTNNAC	2 cut(s)	212, 276
Hpy188I	TCNGA	3 cut(s)	141, 225, 504
Hpy188III	TCNNGA	9 cut(s)	44, 65, 119, 162, 170, 218, 287, 371, 378
Hpy8I	GTNNAC	2 cut(s)	212, 276
Hpy99I	CGWCG	1 cut(s)	516
HpyAV	CCTTC	2 cut(s)	61, 509
HpyCH4III	ACNGT	1 cut(s)	79
HpyCH4IV	ACGT	2 cut(s)	166, 511
HpyCH4V	TGCA	2 cut(s)	254, 485
HpyF3I	CTNAG	6 cut(s)	90, 120, 204, 216, 285, 463
HpySE526I	ACGT	2 cut(s)	166, 511
Hsp92I	GRCGYC	1 cut(s)	166
Hsp92II	CATG	3 cut(s)	26, 155, 476
Kzo9I	GATC	4 cut(s)	3, 220, 324, 328
LmnI	GCTCC	1 cut(s)	380
Lsp1109I	GCAGC	1 cut(s)	325
LweI	GCATC	1 cut(s)	472
MaeI	CTAG	1 cut(s)	44
MaeII	ACGT	2 cut(s)	166, 511
MalI	GATC	4 cut(s)	5, 222, 326, 330
MboI	GATC	4 cut(s)	3, 220, 324, 328
MboII	GAAGA	2 cut(s)	419, 488
MluCI	AATT	2 cut(s)	39, 103
MnlI	CCTC	8 cut(s)	24, 115, 225, 227, 235, 278, 375, 378
Mph1103I	ATGCAT	1 cut(s)	256
MseI	TTAA	3 cut(s)	197, 345, 537
MslI	CAYNNNNRTG	1 cut(s)	477
MssI	GTTTAAAC	1 cut(s)	538
NdeII	GATC	4 cut(s)	3, 220, 324, 328
NlaIII	CATG	3 cut(s)	26, 155, 476
NsiI	ATGCAT	1 cut(s)	256
NspI	RCATGY	1 cut(s)	155
PfeI	GAWTC	1 cut(s)	374
PkrI	GCNGC	1 cut(s)	315
PmeI	GTTTAAAC	1 cut(s)	538
PstNI	CAGNNNCTG	1 cut(s)	383
RsaI	GTAC	3 cut(s)	16, 248, 296
RsaNI	GTAC	3 cut(s)	15, 247, 295
RseI	CAYNNNNRTG	1 cut(s)	477
SaqAI	TTAA	3 cut(s)	197, 345, 537
SatI	GCNGC	1 cut(s)	314
Sau3AI	GATC	4 cut(s)	3, 220, 324, 328
SfaNI	GCATC	1 cut(s)	472
SmiMI	CAYNNNNRTG	1 cut(s)	477
Sse9I	AATT	2 cut(s)	39, 103
SspMI	CTAG	1 cut(s)	44
TaaI	ACNGT	1 cut(s)	79
TaiI	ACGT	2 cut(s)	169, 514
TaqI	TCGA	1 cut(s)	327
TasI	AATT	2 cut(s)	39, 103
TatI	WGTACW	2 cut(s)	246, 294
TfiI	GAWTC	1 cut(s)	374
Tru1I	TTAA	3 cut(s)	197, 345, 537
Tru9I	TTAA	3 cut(s)	197, 345, 537
TscAI	CASTG	1 cut(s)	426
TseI	GCWGC	1 cut(s)	313
TspDTI	ATGAA	2 cut(s)	135, 489
TspGWI	ACGGA	1 cut(s)	293
TspRI	CASTG	1 cut(s)	426
XagI	CCTNNNNNAGG	1 cut(s)	375
XapI	RAATTY	1 cut(s)	39
XbaI	TCTAGA	1 cut(s)	43
XceI	RCATGY	1 cut(s)	155
XmiI	GTMKAC	2 cut(s)	211, 275
XspI	CTAG	1 cut(s)	44
ZraI	GACGTC	1 cut(s)	167
Zsp2I	ATGCAT	1 cut(s)	256

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