Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0007476

Physical Location & Seq

Genomic Coordinates Forward (+)

68050983 .. 68051834

Gene Structure 852 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG420700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 663 bp

ATGGCCAGCAGCAACAACCAGAGCTCCTCAAGCTCCCATGGTAAAACCCTTTACAAAATTCCTTGTTGGGTCACACCGGATAAGAAGGAGTTTCACAATAGAACAATGGAGTTCCTTACGTGGTACCGGAAGTCTAACCGCACCTTGCCTTCCCCCTCCAATAAATGCATGAAGGTCAAAGATATGTCTCGCGAAGAAGTATTGGAGAAAATTAGGGAGGAGAAGAAACGTATTGAAGATGATTGTTCCTTTGAGTTGGTTGATCAATCGGCCTCCAACAAAATGTTCGATGGCGGTGCCCAACGTTTAGTTCTAAAAGACGGTTGCACTCGTACCAGCCTCAATGTCATTGCAGGAGATAGAGGCTTTGTCATAGGTCCTTTTACTTTCAATCTAGTCGGAAGATCGGTCGATTGTAACAGTGAATTTGGTCCAGATAATAAGGTCAGGGTTGGACAAGTCGTTCCGCCTTGTATAAGTTCTGTTAGTGATATGAAGAACAATGGTGCAAAGTACGTGTTAGGAGTGGAAAGTGTTTCTGCTTATCAAAGATTGACGGGGGACAACTTTCATAATGATTATAAGTGTATAATCATGACCGGAAAGGGAATGTCTGATCTAGCACGTAGAGAATTCGCAAAGTATATAATGGACACGTTCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000228 GO:0000280 GO:0000706 GO:0000729 GO:0003674 GO:0003676 GO:0003677 GO:0003824 GO:0003916 GO:0003918 GO:0004518 GO:0004519 GO:0004520 GO:0004536 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0006139 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0007127 GO:0007131 GO:0008094 GO:0008134 GO:0008150 GO:0008152 GO:0009987 GO:0016043 GO:0016462 GO:0016787 GO:0016788 GO:0016817 GO:0016818 GO:0016853 GO:0016887 GO:0016889 GO:0016894 GO:0017111 GO:0022402 GO:0022414 GO:0030957 GO:0031974 GO:0031981 GO:0033554 GO:0034641 GO:0035825 GO:0042138 GO:0042623 GO:0042802 GO:0042803 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0046983 GO:0048285 GO:0050896 GO:0051321 GO:0051716 GO:0061505 GO:0061982 GO:0070013 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0097159 GO:0140013 GO:0140097 GO:1901360 GO:1901363 GO:1903046

KEGG Pathways

Metabolic & Signaling

ko04113 map04113

Pfam Domains

Protein Families

TP6A_N

Protein Analysis

220

Amino Acids

24.82

Weight (kDa)

8.91

Isoelectric Point (pI)

43.62

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TOP6A-Spo11_Toprim	PF21180	172 - 218	4.9e-09	Topoisomerase 6 subunit A/Spo11, Toprim 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: OG0007476)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_1g02062 FvH4_7g23893
rosa_chinensis	RchiOBHm_Chr3g0447681 RchiOBHm_Chr5g0062071
rosa_laevigata	RLG00000015854 RLG00000025979 RLG00000035529
rosa_multiflora	Rmu_sc0002296.1_g000012 Rmu_sc0006064.1_g000010 Rmu_sc0017669.1_g000013
rosa_roxburghii	Rroxscaffold_2G00153710
rosa_rugosa	Rorug01G0475300 Rorug05G0345800
rosa_samantha	Rh2BG027000 Rh2BG028800 Rh3AG004200 Rh3BG003800 Rh3CG004200 Rh3DG004100 Rh5AG407400 Rh5BG420600 Rh5BG420700 Rh5CG444600 Rh5CG444800 Rh5DG435800

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	582
Acc65I	GGTACC	1 cut(s)	123
AccB1I	GGYRCC	2 cut(s)	123, 296
AccII	CGCG	1 cut(s)	192
AciI	CCGC	3 cut(s)	139, 294, 467
AclI	AACGTT	1 cut(s)	304
AcoI	YGGCCR	1 cut(s)	3
AcsI	RAATTY	3 cut(s)	57, 425, 632
AfaI	GTAC	3 cut(s)	125, 334, 515
AflIII	ACRYGT	2 cut(s)	516, 654
AgsI	TTSAA	2 cut(s)	236, 391
AjuI	GAANNNNNNNTTGG	4 cut(s)	269, 294, 301, 326
AloI	GAACNNNNNNTCC	2 cut(s)	447, 479
AluBI	AGCT	2 cut(s)	24, 33
AluI	AGCT	2 cut(s)	24, 33
Alw21I	GWGCWC	1 cut(s)	26
Alw26I	GTCTC	1 cut(s)	192
AoxI	GGCC	2 cut(s)	3, 270
ApeKI	GCWGC	1 cut(s)	9
ApoI	RAATTY	3 cut(s)	57, 425, 632
Asp718I	GGTACC	1 cut(s)	123
AspS9I	GGNCC	2 cut(s)	377, 431
AvaII	GGWCC	2 cut(s)	377, 431
BaeGI	GKGCMC	1 cut(s)	301
BalI	TGGCCA	1 cut(s)	5
BanI	GGYRCC	2 cut(s)	123, 296
BanII	GRGCYC	1 cut(s)	26
Bbv12I	GWGCWC	1 cut(s)	26
BbvI	GCAGC	1 cut(s)	21
BccI	CCATC	1 cut(s)	284
BcgI	CGANNNNNNTGC	2 cut(s)	278, 312
BclI	TGATCA	1 cut(s)	262
BcoDI	GTCTC	1 cut(s)	192
BfaI	CTAG	3 cut(s)	395, 620, 661
BisI	GCNGC	1 cut(s)	10
BlsI	GCNGC	1 cut(s)	11
Bme18I	GGWCC	2 cut(s)	377, 431
BmgT120I	GGNCC	2 cut(s)	377, 431
BmiI	GGNNCC	2 cut(s)	125, 298
BpuEI	CTTGAG	1 cut(s)	13
BsaAI	YACGTR	3 cut(s)	120, 517, 626
BsaJI	CCNNGG	1 cut(s)	37
BsaWI	WCCGGW	3 cut(s)	76, 126, 599
BsaXI	ACNNNNNCTCC	2 cut(s)	8, 38
Bse3DI	GCAATG	1 cut(s)	348
BseDI	CCNNGG	1 cut(s)	37
BseMI	GCAATG	1 cut(s)	348
BseRI	GAGGAG	2 cut(s)	16, 233
BseSI	GKGCMC	1 cut(s)	301
BseXI	GCAGC	1 cut(s)	21
Bsh1236I	CGCG	1 cut(s)	192
Bsh1285I	CGRYCG	1 cut(s)	411
BshFI	GGCC	2 cut(s)	5, 272
BshNI	GGYRCC	2 cut(s)	123, 296
BsiEI	CGRYCG	1 cut(s)	411
BsiHKAI	GWGCWC	1 cut(s)	26
BsiSI	CCGG	3 cut(s)	77, 127, 600
BslFI	GGGAC	1 cut(s)	575
BsmAI	GTCTC	1 cut(s)	192
BsmFI	GGGAC	1 cut(s)	575
BsnI	GGCC	2 cut(s)	5, 272
Bsp1286I	GDGCHC	2 cut(s)	26, 301
Bsp143I	GATC	3 cut(s)	262, 404, 616
Bsp19I	CCATGG	1 cut(s)	37
Bsp68I	TCGCGA	1 cut(s)	192
BspACI	CCGC	3 cut(s)	139, 294, 467
BspANI	GGCC	2 cut(s)	5, 272
BspFNI	CGCG	1 cut(s)	192
BspHI	TCATGA	1 cut(s)	594
BspLI	GGNNCC	2 cut(s)	125, 298
BspT107I	GGYRCC	2 cut(s)	123, 296
BsrDI	GCAATG	1 cut(s)	348
BssECI	CCNNGG	1 cut(s)	37
BssMI	GATC	3 cut(s)	262, 404, 616
BssT1I	CCWWGG	1 cut(s)	37
Bst4CI	ACNGT	2 cut(s)	323, 422
BstBAI	YACGTR	3 cut(s)	120, 517, 626
BstC8I	GCNNGC	1 cut(s)	7
BstDSI	CCRYGG	1 cut(s)	37
BstFNI	CGCG	1 cut(s)	192
BstKTI	GATC	3 cut(s)	265, 407, 619
BstMAI	GTCTC	1 cut(s)	192
BstMBI	GATC	3 cut(s)	262, 404, 616
BstMCI	CGRYCG	1 cut(s)	411
BstMWI	GCNNNNNNNGC	1 cut(s)	30
BstSLI	GKGCMC	1 cut(s)	301
BstUI	CGCG	1 cut(s)	192
BstV1I	GCAGC	1 cut(s)	21
BsuRI	GGCC	2 cut(s)	5, 272
BtgI	CCRYGG	1 cut(s)	37
BtsIMutI	CAGTG	1 cut(s)	427
BtuMI	TCGCGA	1 cut(s)	192
Cac8I	GCNNGC	1 cut(s)	7
CciI	TCATGA	1 cut(s)	594
Cfr13I	GGNCC	2 cut(s)	377, 431
Csp6I	GTAC	3 cut(s)	124, 333, 514
CviAII	CATG	3 cut(s)	38, 169, 595
CviJI	RGCY	6 cut(s)	5, 24, 33, 272, 339, 366
CviKI_1	RGCY	6 cut(s)	5, 24, 33, 272, 339, 366
CviQI	GTAC	3 cut(s)	124, 333, 514
DpnI	GATC	3 cut(s)	264, 406, 618
DpnII	GATC	3 cut(s)	262, 404, 616
EaeI	YGGCCR	1 cut(s)	3
EciI	GGCGGA	1 cut(s)	456
Ecl136II	GAGCTC	1 cut(s)	24
Eco130I	CCWWGG	1 cut(s)	37
Eco24I	GRGCYC	1 cut(s)	26
Eco47I	GGWCC	2 cut(s)	377, 431
Eco53kI	GAGCTC	1 cut(s)	24
EcoICRI	GAGCTC	1 cut(s)	24
EcoO109I	RGGNCCY	1 cut(s)	377
EcoRI	GAATTC	1 cut(s)	632
EcoT14I	CCWWGG	1 cut(s)	37
EcoT22I	ATGCAT	1 cut(s)	170
EcoT38I	GRGCYC	1 cut(s)	26
ErhI	CCWWGG	1 cut(s)	37
FaeI	CATG	3 cut(s)	41, 172, 598
FaqI	GGGAC	1 cut(s)	575
FatI	CATG	3 cut(s)	37, 168, 594
FbaI	TGATCA	1 cut(s)	262
Fnu4HI	GCNGC	1 cut(s)	10
FriOI	GRGCYC	1 cut(s)	26
Fsp4HI	GCNGC	1 cut(s)	10
FspBI	CTAG	3 cut(s)	395, 620, 661
GluI	GCNGC	1 cut(s)	10
HaeIII	GGCC	2 cut(s)	5, 272
HapII	CCGG	3 cut(s)	77, 127, 600
Hin1II	CATG	3 cut(s)	41, 172, 598
HpaII	CCGG	3 cut(s)	77, 127, 600
Hpy188I	TCNGA	2 cut(s)	401, 616
Hpy188III	TCNNGA	3 cut(s)	191, 434, 595
HpyAV	CCTTC	3 cut(s)	79, 159, 166
HpyCH4III	ACNGT	2 cut(s)	323, 422
HpyCH4IV	ACGT	6 cut(s)	119, 229, 304, 516, 625, 656
HpyCH4V	TGCA	4 cut(s)	168, 327, 353, 509
HpyF10VI	GCNNNNNNNGC	1 cut(s)	30
HpySE526I	ACGT	6 cut(s)	119, 229, 304, 516, 625, 656
Hsp92II	CATG	3 cut(s)	41, 172, 598
KpnI	GGTACC	1 cut(s)	127
Ksp22I	TGATCA	1 cut(s)	262
Kzo9I	GATC	3 cut(s)	262, 404, 616
LmnI	GCTCC	2 cut(s)	29, 38
LpnPI	CCDG	9 cut(s)	19, 32, 90, 140, 339, 349, 433, 447, 613
Lsp1109I	GCAGC	1 cut(s)	21
MaeI	CTAG	3 cut(s)	395, 620, 661
MaeII	ACGT	6 cut(s)	119, 229, 304, 516, 625, 656
MaeIII	GTNAC	2 cut(s)	70, 416
MalI	GATC	3 cut(s)	264, 406, 618
MboI	GATC	3 cut(s)	262, 404, 616
MboII	GAAGA	5 cut(s)	206, 235, 248, 414, 508
MhlI	GDGCHC	2 cut(s)	26, 301
MlsI	TGGCCA	1 cut(s)	5
MluCI	AATT	4 cut(s)	57, 210, 425, 632
MluNI	TGGCCA	1 cut(s)	5
MmeI	TCCRAC	3 cut(s)	300, 379, 433
MnlI	CCTC	6 cut(s)	37, 166, 211, 283, 350, 356
Mox20I	TGGCCA	1 cut(s)	5
Mph1103I	ATGCAT	1 cut(s)	170
MscI	TGGCCA	1 cut(s)	5
Msp20I	TGGCCA	1 cut(s)	5
MspI	CCGG	3 cut(s)	77, 127, 600
MvnI	CGCG	1 cut(s)	192
MwoI	GCNNNNNNNGC	1 cut(s)	30
NcoI	CCATGG	1 cut(s)	37
NdeII	GATC	3 cut(s)	262, 404, 616
NlaIII	CATG	3 cut(s)	41, 172, 598
NlaIV	GGNNCC	2 cut(s)	125, 298
NmuCI	GTSAC	1 cut(s)	70
NruI	TCGCGA	1 cut(s)	192
NsiI	ATGCAT	1 cut(s)	170
PagI	TCATGA	1 cut(s)	594
PkrI	GCNGC	1 cut(s)	11
Ppu21I	YACGTR	3 cut(s)	120, 517, 626
PpuMI	RGGWCCY	1 cut(s)	377
PsiI	TTATAA	1 cut(s)	582
Psp124BI	GAGCTC	1 cut(s)	26
Psp1406I	AACGTT	1 cut(s)	304
Psp5II	RGGWCCY	1 cut(s)	377
PspN4I	GGNNCC	2 cut(s)	125, 298
PspPI	GGNCC	2 cut(s)	377, 431
PspPPI	RGGWCCY	1 cut(s)	377
RruI	TCGCGA	1 cut(s)	192
RsaI	GTAC	3 cut(s)	125, 334, 515
RsaNI	GTAC	3 cut(s)	124, 333, 514
SacI	GAGCTC	1 cut(s)	26
SatI	GCNGC	1 cut(s)	10
Sau3AI	GATC	3 cut(s)	262, 404, 616
Sau96I	GGNCC	2 cut(s)	377, 431
SduI	GDGCHC	2 cut(s)	26, 301
SinI	GGWCC	2 cut(s)	377, 431
SmlI	CTYRAG	1 cut(s)	28
SmoI	CTYRAG	1 cut(s)	28
Sse9I	AATT	4 cut(s)	57, 210, 425, 632
SsiI	CCGC	3 cut(s)	139, 294, 467
SspMI	CTAG	3 cut(s)	395, 620, 661
SstI	GAGCTC	1 cut(s)	26
StyI	CCWWGG	1 cut(s)	37
TaaI	ACNGT	2 cut(s)	323, 422
TaiI	ACGT	6 cut(s)	122, 232, 307, 519, 628, 659
TaqI	TCGA	2 cut(s)	288, 411
TaqII	GACCGA	1 cut(s)	397
TasI	AATT	4 cut(s)	57, 210, 425, 632
TscAI	CASTG	1 cut(s)	427
TseFI	GTSAC	1 cut(s)	70
TseI	GCWGC	1 cut(s)	9
Tsp45I	GTSAC	1 cut(s)	70
TspDTI	ATGAA	3 cut(s)	185, 509, 560
TspRI	CASTG	1 cut(s)	427
VpaK11BI	GGWCC	2 cut(s)	377, 431
XapI	RAATTY	3 cut(s)	57, 425, 632
XspI	CTAG	3 cut(s)	395, 620, 661
Zsp2I	ATGCAT	1 cut(s)	170

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