Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4B

Orthogroup ID

OG0006852

Physical Location & Seq

Genomic Coordinates Reverse (-)

40259170 .. 40259658

Gene Structure 489 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4BG236700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 489 bp

ATGGATGATTTGTTGAACAAGGAAGAGTTGAAGGAGAAAACAGAAGAAGATAAGCTTGCTGTTCACTGGAATGCAAACAAGGAAGTTGCTATTTTTCTAAATCATCGGAGAGAAGTGTCAGATTTTGAAGAGAAACAAGCTTGGGAGCTCAGCATACAAATCTTTGAACTAGAGGCGCAAAAATCAAAATTGGAGATTCAAAAAACTCATCCAAGTAATGAGTATAATGCCTCTAACGCTGGAAAACTCGAGTTAAACATTGAAATAGAGAAGATAATGAAGAAGATTCATGAGCTGAGTCTACAAGAGCATACCAAAGCCTGTAGTCAAACTTATCGATTAGAAACATCCAAAGAGAATTACCTTGATCCCAGGATTACTGTTGCATGGTGTCTACGACATCGGATTTCAGTTTCTAAGATTTTTGACTTGCGTCTCCGAAACAAATTCATGTGGGCAATGAATGTGGAGTCTGATTTTAGATATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0003674 GO:0003824 GO:0003916 GO:0003917 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005694 GO:0005730 GO:0006139 GO:0006259 GO:0006260 GO:0006265 GO:0006325 GO:0006338 GO:0006725 GO:0006807 GO:0006996 GO:0007059 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0016020 GO:0016043 GO:0016853 GO:0031298 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0034645 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0046483 GO:0051276 GO:0070013 GO:0071103 GO:0071704 GO:0071840 GO:0090304 GO:0140097 GO:1901360 GO:1901576

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Topo_C_assoc Topoisom_I Topoisom_I_N

Protein Analysis

162

Amino Acids

19.4

Weight (kDa)

6.1

Isoelectric Point (pI)

46.88

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Topoisom_I	PF01028	2 - 65	1.4e-06	Eukaryotic DNA topoisomerase I, catalytic core
Topo_C_assoc	PF14370	94 - 161	7.1e-23	C-terminal topoisomerase 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: OG0006852)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G26701
rosa_chinensis	RchiOBHm_Chr1g0370531 RchiOBHm_Chr4g0420291 RchiOBHm_Chr4g0421651 RchiOBHm_Chr4g0421661
rosa_laevigata	RLG00000007661 RLG00000027031
rosa_multiflora	Rmu_sc0022275.1_g000007 Rmu_sc0026595.1_g000002
rosa_roxburghii	Rroxscaffold_5G00362880 Rroxscaffold_5G00362920
rosa_rugosa	Rorug01G0357400 Rorug04G0161800 Rorug04G0174200
rosa_samantha	Rh1AG366300 Rh1BG328900 Rh1BG329600 Rh1BG329800 Rh1CG342300 Rh1CG342400 Rh1CG343500 Rh1CG343700 Rh4BG236700 Rh4BG236800 Rh4CG248500 Rh4CG248600

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	2 cut(s)	301, 394
AclWI	GGATC	1 cut(s)	362
AcsI	RAATTY	1 cut(s)	446
AgsI	TTSAA	6 cut(s)	16, 31, 128, 167, 200, 263
AjnI	CCWGG	1 cut(s)	371
AluBI	AGCT	4 cut(s)	55, 140, 148, 295
AluI	AGCT	4 cut(s)	55, 140, 148, 295
Alw21I	GWGCWC	1 cut(s)	150
Alw26I	GTCTC	1 cut(s)	440
AlwI	GGATC	1 cut(s)	362
Ama87I	CYCGRG	1 cut(s)	248
ApoI	RAATTY	1 cut(s)	446
AspLEI	GCGC	1 cut(s)	178
AvaI	CYCGRG	1 cut(s)	248
BanII	GRGCYC	1 cut(s)	150
Bbv12I	GWGCWC	1 cut(s)	150
BciT130I	CCWGG	1 cut(s)	373
BcoDI	GTCTC	1 cut(s)	440
BfaI	CTAG	1 cut(s)	170
BfmI	CTRYAG	1 cut(s)	322
BlpI	GCTNAGC	1 cut(s)	149
Bme1390I	CCNGG	1 cut(s)	373
BmeT110I	CYCGRG	1 cut(s)	248
BmrFI	CCNGG	1 cut(s)	373
BoxI	GACNNNNGTC	1 cut(s)	432
Bpu1102I	GCTNAGC	1 cut(s)	149
Bsa29I	ATCGAT	1 cut(s)	337
BsaJI	CCNNGG	1 cut(s)	371
Bse1I	ACTGG	1 cut(s)	71
Bse3DI	GCAATG	1 cut(s)	465
BseBI	CCWGG	1 cut(s)	373
BseCI	ATCGAT	1 cut(s)	337
BseDI	CCNNGG	1 cut(s)	371
BseGI	GGATG	3 cut(s)	10, 208, 347
BseMI	GCAATG	1 cut(s)	465
BseMII	CTCAG	2 cut(s)	163, 287
BseNI	ACTGG	1 cut(s)	71
BshVI	ATCGAT	1 cut(s)	337
BsiHKAI	GWGCWC	1 cut(s)	150
BsiHKCI	CYCGRG	1 cut(s)	248
BsmAI	GTCTC	1 cut(s)	440
BsmBI	CGTCTC	1 cut(s)	440
BsmI	GAATGC	1 cut(s)	76
BsoBI	CYCGRG	1 cut(s)	248
Bsp1286I	GDGCHC	1 cut(s)	150
Bsp143I	GATC	1 cut(s)	367
Bsp1720I	GCTNAGC	1 cut(s)	149
BspCNI	CTCAG	2 cut(s)	162, 288
BspDI	ATCGAT	1 cut(s)	337
BspHI	TCATGA	1 cut(s)	289
BspPI	GGATC	1 cut(s)	362
BsrDI	GCAATG	1 cut(s)	465
BsrI	ACTGG	1 cut(s)	71
BssECI	CCNNGG	1 cut(s)	371
BssMI	GATC	1 cut(s)	367
Bst2UI	CCWGG	1 cut(s)	373
Bst4CI	ACNGT	1 cut(s)	382
Bst6I	CTCTTC	2 cut(s)	18, 123
BstC8I	GCNNGC	1 cut(s)	57
BstDEI	CTNAG	3 cut(s)	149, 296, 417
BstF5I	GGATG	3 cut(s)	10, 208, 347
BstHHI	GCGC	1 cut(s)	178
BstKTI	GATC	1 cut(s)	370
BstMAI	GTCTC	1 cut(s)	440
BstMBI	GATC	1 cut(s)	367
BstMWI	GCNNNNNNNGC	1 cut(s)	236
BstNI	CCWGG	1 cut(s)	373
BstPAI	GACNNNNGTC	1 cut(s)	432
BstSCI	CCNGG	1 cut(s)	371
BstSFI	CTRYAG	1 cut(s)	322
Bsu15I	ATCGAT	1 cut(s)	337
BsuTUI	ATCGAT	1 cut(s)	337
BtsCI	GGATG	3 cut(s)	10, 208, 347
BtsIMutI	CAGTG	1 cut(s)	64
Cac8I	GCNNGC	1 cut(s)	57
CciI	TCATGA	1 cut(s)	289
CfoI	GCGC	1 cut(s)	178
ClaI	ATCGAT	1 cut(s)	337
CseI	GACGC	1 cut(s)	422
CspCI	CAANNNNNGTGG	2 cut(s)	447, 482
CviAII	CATG	3 cut(s)	290, 387, 451
CviJI	RGCY	5 cut(s)	55, 140, 148, 295, 320
CviKI_1	RGCY	5 cut(s)	55, 140, 148, 295, 320
DdeI	CTNAG	3 cut(s)	149, 296, 417
DpnI	GATC	1 cut(s)	369
DpnII	GATC	1 cut(s)	367
Eam1104I	CTCTTC	2 cut(s)	18, 123
EarI	CTCTTC	2 cut(s)	18, 123
Ecl136II	GAGCTC	1 cut(s)	148
Eco24I	GRGCYC	1 cut(s)	150
Eco53kI	GAGCTC	1 cut(s)	148
Eco88I	CYCGRG	1 cut(s)	248
EcoICRI	GAGCTC	1 cut(s)	148
EcoRII	CCWGG	1 cut(s)	371
EcoT38I	GRGCYC	1 cut(s)	150
Esp3I	CGTCTC	1 cut(s)	440
FaeI	CATG	3 cut(s)	293, 390, 454
FaiI	YATR	6 cut(s)	155, 225, 291, 312, 388, 452
FalI	AAGNNNNNCTT	2 cut(s)	39, 71
FatI	CATG	3 cut(s)	289, 386, 450
FblI	GTMKAC	2 cut(s)	301, 394
FokI	GGATG	3 cut(s)	17, 195, 334
FriOI	GRGCYC	1 cut(s)	150
FspBI	CTAG	1 cut(s)	170
GlaI	GCGC	1 cut(s)	177
HgaI	GACGC	1 cut(s)	422
HhaI	GCGC	1 cut(s)	178
Hin1II	CATG	3 cut(s)	293, 390, 454
Hin6I	GCGC	1 cut(s)	176
HinP1I	GCGC	1 cut(s)	176
HindIII	AAGCTT	2 cut(s)	53, 138
HinfI	GANTC	4 cut(s)	196, 286, 298, 470
Hpy166II	GTNNAC	3 cut(s)	64, 302, 395
Hpy188I	TCNGA	5 cut(s)	108, 121, 405, 440, 475
Hpy188III	TCNNGA	1 cut(s)	290
Hpy8I	GTNNAC	3 cut(s)	64, 302, 395
HpyAV	CCTTC	1 cut(s)	25
HpyCH4III	ACNGT	1 cut(s)	382
HpyCH4V	TGCA	2 cut(s)	74, 386
HpyF10VI	GCNNNNNNNGC	1 cut(s)	236
HpyF3I	CTNAG	3 cut(s)	149, 296, 417
Hsp92II	CATG	3 cut(s)	293, 390, 454
HspAI	GCGC	1 cut(s)	176
Kzo9I	GATC	1 cut(s)	367
LmnI	GCTCC	1 cut(s)	145
LpnPI	CCDG	5 cut(s)	52, 225, 334, 358, 385
MaeI	CTAG	1 cut(s)	170
MalI	GATC	1 cut(s)	369
MboI	GATC	1 cut(s)	367
MboII	GAAGA	7 cut(s)	35, 56, 59, 140, 283, 292, 295
MhlI	GDGCHC	1 cut(s)	150
MluCI	AATT	3 cut(s)	188, 358, 446
MlyI	GAGTC	2 cut(s)	307, 479
MnlI	CCTC	2 cut(s)	166, 241
MseI	TTAA	1 cut(s)	254
MslI	CAYNNNNRTG	1 cut(s)	69
MspR9I	CCNGG	1 cut(s)	373
Mva1269I	GAATGC	1 cut(s)	76
MvaI	CCWGG	1 cut(s)	373
MwoI	GCNNNNNNNGC	1 cut(s)	236
NdeII	GATC	1 cut(s)	367
NlaIII	CATG	3 cut(s)	293, 390, 454
PaeR7I	CTCGAG	1 cut(s)	248
PagI	TCATGA	1 cut(s)	289
PctI	GAATGC	1 cut(s)	76
PfeI	GAWTC	2 cut(s)	196, 286
PleI	GAGTC	2 cut(s)	306, 478
PpsI	GAGTC	2 cut(s)	306, 478
PshAI	GACNNNNGTC	1 cut(s)	432
Psp124BI	GAGCTC	1 cut(s)	150
Psp6I	CCWGG	1 cut(s)	371
PspGI	CCWGG	1 cut(s)	371
PspXI	VCTCGAGB	1 cut(s)	248
RseI	CAYNNNNRTG	1 cut(s)	69
SacI	GAGCTC	1 cut(s)	150
SaqAI	TTAA	1 cut(s)	254
Sau3AI	GATC	1 cut(s)	367
SchI	GAGTC	2 cut(s)	307, 479
ScrFI	CCNGG	1 cut(s)	373
SduI	GDGCHC	1 cut(s)	150
SetI	ASST	5 cut(s)	57, 142, 150, 297, 366
SfcI	CTRYAG	1 cut(s)	322
Sfr274I	CTCGAG	1 cut(s)	248
SlaI	CTCGAG	1 cut(s)	248
SmiMI	CAYNNNNRTG	1 cut(s)	69
SmlI	CTYRAG	1 cut(s)	248
SmoI	CTYRAG	1 cut(s)	248
Sse9I	AATT	3 cut(s)	188, 358, 446
SspMI	CTAG	1 cut(s)	170
SstI	GAGCTC	1 cut(s)	150
StyD4I	CCNGG	1 cut(s)	371
TaaI	ACNGT	1 cut(s)	382
TaqI	TCGA	2 cut(s)	249, 337
TasI	AATT	3 cut(s)	188, 358, 446
TfiI	GAWTC	2 cut(s)	196, 286
Tru1I	TTAA	1 cut(s)	254
Tru9I	TTAA	1 cut(s)	254
TscAI	CASTG	1 cut(s)	71
TspDTI	ATGAA	4 cut(s)	278, 293, 439, 476
TspRI	CASTG	1 cut(s)	71
XapI	RAATTY	1 cut(s)	446
XhoI	CTCGAG	1 cut(s)	248
XmiI	GTMKAC	2 cut(s)	301, 394
XspI	CTAG	1 cut(s)	170

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