Basic Information

Type: gene

Biological Identity

Species

rosa_chinensis

Chromosome

Orthogroup ID

OG0009688

Physical Location & Seq

Genomic Coordinates Forward (+)

12445247 .. 12446882

Gene Structure 1636 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

PRQ29813

Sequence Viewer

CDS Protein Promoter (2k)

Length: 990 bp

ATGGTGGAGTCATCAACTCTCAATGCCATGGCTTCTATTAATTTCCAGAATGATTGGATTGTGGACTCCGGCTGTGGCCATCATTTGACAGGTGATGAATCAAAGTTCTCCAAGTTACAACCACACATTGGCAATGAAGCTATGGTGACAGCAGATAATACAGTTCACAAGGTTGAGAATGAAGGCACGGTAGTCATTAACGATGGAGGTAACGATTCTATCACCTTAAATAATGTTTTCCATGTTCCTGGCATGAAGAAGAATTTATTTTCAGTTCCAAATGCTGTGGATGCTGGTTCTAGTGTCTTGTTTGGGCCACATGATGTTAAATTTCTCCTAAATATTAAATTTATAAAGGCAGATGTTATGCATACTGGTAGGAGGGTAAAAGATACATTTGTGTTGTCTACCTCTTCATCTTATATTGATAAAGTGAGCTGCAATGAGAATGCATCCTTGTGGCATGCTAGATTGGGGCATGTGAACTTTGATAAGTTGAAAGTCATGGTTCGGAAGAATTTGGTGAAAGGTCTACCAAGCTTGACAACCTTTCCTAGCAAAGAAGTGTGTGAAGGGTGCCAATTCGGTAAGTCTCATCGTCTTCCATTCGGAATTTCTCAATCAAGAAGCAAGGCTCCCTTGGAATGCATTCATGGTGATTTATTTGGTCCTACTAGAACTCCTTCATTTTCTGGTCTTCGATATATGTTGATTCTTGTTGATGATTTTTCAAGATTTACATGGGTCTATTGTATTAAGCAAAAATCAGATGCTTTCTCAAAGTTTCAAGAGTTCAAAGAGATTGTTGAAGGTGTTCTTGGTTTGAAAATTAAGCGGCTGCGAACCGACAATGGGGGAGAGTTCATCTCTGATGAATTTTTTTTCTTTTTGTCATCGGTTTGGGATAAGAAGAGAGTTGTCTTGTGCAGAAACCCCCCAGCAAAATGGCATCGCAGAAAGGAAGATCAGACATCTCACGGAGACATGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DUF4219 RVT_2 Retrotran_gag_2 Retrotran_gag_3 gag_pre-integrs rve zf-CCHC

Protein Analysis

329

Amino Acids

36.97

Weight (kDa)

8.87

Isoelectric Point (pI)

37.48

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pol_BBD	PF22936	19 - 99	1.3e-19	Pol polyprotein, beta-barrel domain
gag_pre-integrs	PF13976	145 - 198	7.2e-16	GAG-pre-integrase domain
rve	PF00665	212 - 296	2.5e-09	Integrase core domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0009688)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_5g19322 FvH4_5g31431
malus_domestica	MD01G1222200.v1.1 MD14G1034300.v1.1
prunus_persica	Prupe.2G033500_v2.0.a1 Prupe.7G032100_v2.0.a1
pyrus_communis	pycom02g19670 pycom03g19000 pycom11g04720 pycom11g04870 pycom11g07640 pycom12g10550 pycom13g07730 pycom16g07450 pycom520g00380
rosa_chinensis	RchiOBHm_Chr3g0481931 RchiOBHm_Chr3g0481941 RchiOBHm_Chr5g0017901 RchiOBHm_Chr5g0017911
rosa_roxburghii	Rroxscaffold_1G00053310 Rroxscaffold_4G00308650
rosa_rugosa	Rorug07G0315400

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	353
AccB1I	GGYRCC	1 cut(s)	576
AccB7I	CCANNNNNTGG	1 cut(s)	128
AccI	GTMKAC	2 cut(s)	407, 532
AciI	CCGC	1 cut(s)	835
AcoI	YGGCCR	1 cut(s)	76
AcsI	RAATTY	6 cut(s)	262, 329, 347, 517, 612, 875
AfiI	CCNNNNNNNGG	2 cut(s)	128, 852
AflIII	ACRYGT	1 cut(s)	984
AgsI	TTSAA	6 cut(s)	499, 732, 788, 796, 809, 826
AjnI	CCWGG	1 cut(s)	247
AjuI	GAANNNNNNNTTGG	2 cut(s)	801, 833
AluBI	AGCT	3 cut(s)	140, 438, 540
AluI	AGCT	3 cut(s)	140, 438, 540
Alw26I	GTCTC	2 cut(s)	597, 975
AoxI	GGCC	2 cut(s)	76, 314
ApeKI	GCWGC	2 cut(s)	438, 838
ApoI	RAATTY	6 cut(s)	262, 329, 347, 517, 612, 875
AseI	ATTAAT	1 cut(s)	39
Asp700I	GAANNNNTTC	3 cut(s)	648, 682, 813
AspS9I	GGNCC	2 cut(s)	314, 668
AsuHPI	GGTGA	5 cut(s)	104, 157, 214, 535, 668
AvaII	GGWCC	1 cut(s)	668
BaeI	ACNNNNGTAYC	2 cut(s)	384, 417
BalI	TGGCCA	1 cut(s)	78
BanI	GGYRCC	1 cut(s)	576
BbsI	GAAGAC	2 cut(s)	593, 689
BbvI	GCAGC	2 cut(s)	425, 825
BccI	CCATC	2 cut(s)	87, 197
BciT130I	CCWGG	1 cut(s)	249
BcoDI	GTCTC	2 cut(s)	597, 975
BfaI	CTAG	4 cut(s)	300, 468, 555, 675
BisI	GCNGC	3 cut(s)	439, 836, 839
BlsI	GCNGC	3 cut(s)	440, 837, 840
Bme1390I	CCNGG	1 cut(s)	249
Bme18I	GGWCC	1 cut(s)	668
BmgT120I	GGNCC	2 cut(s)	314, 668
BmiI	GGNNCC	2 cut(s)	578, 636
BmrFI	CCNGG	1 cut(s)	249
BmsI	GCATC	4 cut(s)	280, 461, 760, 958
BpiI	GAAGAC	2 cut(s)	593, 689
BplI	GAGNNNNNCTC	2 cut(s)	851, 883
BsaJI	CCNNGG	2 cut(s)	27, 639
BsaXI	ACNNNNNCTCC	2 cut(s)	664, 694
Bsc4I	CCNNNNNNNGG	2 cut(s)	128, 852
Bse1I	ACTGG	1 cut(s)	379
Bse3DI	GCAATG	2 cut(s)	139, 448
BseBI	CCWGG	1 cut(s)	249
BseDI	CCNNGG	2 cut(s)	27, 639
BseGI	GGATG	2 cut(s)	295, 452
BseLI	CCNNNNNNNGG	2 cut(s)	128, 852
BseMI	GCAATG	2 cut(s)	139, 448
BseNI	ACTGG	1 cut(s)	379
BseXI	GCAGC	2 cut(s)	425, 825
BseYI	CCCAGC	1 cut(s)	937
BsgI	GTGCAG	1 cut(s)	946
BshFI	GGCC	2 cut(s)	78, 316
BshNI	GGYRCC	1 cut(s)	576
BsiSI	CCGG	1 cut(s)	69
BslI	CCNNNNNNNGG	2 cut(s)	128, 852
BsmAI	GTCTC	2 cut(s)	597, 975
BsmI	GAATGC	3 cut(s)	454, 648, 650
BsnI	GGCC	2 cut(s)	78, 316
Bsp143I	GATC	1 cut(s)	964
Bsp19I	CCATGG	1 cut(s)	27
BspACI	CCGC	1 cut(s)	835
BspANI	GGCC	2 cut(s)	78, 316
BspLI	GGNNCC	2 cut(s)	578, 636
BspT107I	GGYRCC	1 cut(s)	576
BsrDI	GCAATG	2 cut(s)	139, 448
BsrI	ACTGG	1 cut(s)	379
BssECI	CCNNGG	2 cut(s)	27, 639
BssMI	GATC	1 cut(s)	964
BssT1I	CCWWGG	2 cut(s)	27, 639
Bst2UI	CCWGG	1 cut(s)	249
Bst4CI	ACNGT	2 cut(s)	163, 190
Bst6I	CTCTTC	2 cut(s)	418, 905
BstC8I	GCNNGC	1 cut(s)	465
BstDSI	CCRYGG	1 cut(s)	27
BstF5I	GGATG	2 cut(s)	295, 452
BstKTI	GATC	1 cut(s)	967
BstMAI	GTCTC	2 cut(s)	597, 975
BstMBI	GATC	1 cut(s)	964
BstMWI	GCNNNNNNNGC	1 cut(s)	290
BstNI	CCWGG	1 cut(s)	249
BstNSI	RCATGY	3 cut(s)	467, 482, 988
BstSCI	CCNGG	1 cut(s)	247
BstV1I	GCAGC	2 cut(s)	425, 825
BstV2I	GAAGAC	2 cut(s)	593, 689
BstXI	CCANNNNNNTGG	2 cut(s)	248, 945
BsuRI	GGCC	2 cut(s)	78, 316
BtgI	CCRYGG	1 cut(s)	27
BtgZI	GCGATG	1 cut(s)	935
BtsCI	GGATG	2 cut(s)	295, 452
Cac8I	GCNNGC	1 cut(s)	465
Cfr13I	GGNCC	2 cut(s)	314, 668
CspCI	CAANNNNNGTGG	2 cut(s)	267, 302
CviJI	RGCY	9 cut(s)	32, 72, 78, 140, 316, 438, 540, 635, 838
CviKI_1	RGCY	9 cut(s)	32, 72, 78, 140, 316, 438, 540, 635, 838
DpnI	GATC	1 cut(s)	966
DpnII	GATC	1 cut(s)	964
EaeI	YGGCCR	1 cut(s)	76
Eam1104I	CTCTTC	2 cut(s)	418, 905
EarI	CTCTTC	2 cut(s)	418, 905
Eco130I	CCWWGG	2 cut(s)	27, 639
Eco47I	GGWCC	1 cut(s)	668
EcoRII	CCWGG	1 cut(s)	247
EcoT14I	CCWWGG	2 cut(s)	27, 639
EcoT22I	ATGCAT	3 cut(s)	372, 454, 650
ErhI	CCWWGG	2 cut(s)	27, 639
FalI	AAGNNNNNCTT	4 cut(s)	623, 655, 801, 833
FblI	GTMKAC	2 cut(s)	407, 532
Fnu4HI	GCNGC	3 cut(s)	439, 836, 839
FokI	GGATG	2 cut(s)	302, 439
Fsp4HI	GCNGC	3 cut(s)	439, 836, 839
FspBI	CTAG	4 cut(s)	300, 468, 555, 675
GluI	GCNGC	3 cut(s)	439, 836, 839
GsaI	CCCAGC	1 cut(s)	941
HaeIII	GGCC	2 cut(s)	78, 316
HapII	CCGG	1 cut(s)	69
HindIII	AAGCTT	1 cut(s)	538
HinfI	GANTC	5 cut(s)	8, 65, 98, 215, 712
HpaII	CCGG	1 cut(s)	69
HphI	GGTGA	5 cut(s)	104, 157, 214, 535, 668
Hpy166II	GTNNAC	5 cut(s)	64, 166, 408, 484, 533
Hpy188I	TCNGA	5 cut(s)	513, 611, 769, 871, 969
Hpy188III	TCNNGA	4 cut(s)	46, 624, 732, 788
Hpy8I	GTNNAC	5 cut(s)	64, 166, 408, 484, 533
HpyAV	CCTTC	4 cut(s)	176, 566, 693, 803
HpyCH4III	ACNGT	2 cut(s)	163, 190
HpyCH4V	TGCA	5 cut(s)	370, 441, 452, 648, 927
HpyF10VI	GCNNNNNNNGC	1 cut(s)	290
Kzo9I	GATC	1 cut(s)	964
LmnI	GCTCC	1 cut(s)	640
LpnPI	CCDG	9 cut(s)	59, 75, 82, 234, 261, 279, 360, 678, 951
Lsp1109I	GCAGC	2 cut(s)	425, 825
LweI	GCATC	4 cut(s)	280, 461, 760, 958
MaeI	CTAG	4 cut(s)	300, 468, 555, 675
MaeIII	GTNAC	3 cut(s)	114, 145, 209
MalI	GATC	1 cut(s)	966
MboI	GATC	1 cut(s)	964
MboII	GAAGA	8 cut(s)	268, 271, 405, 526, 593, 689, 922, 974
MlsI	TGGCCA	1 cut(s)	78
MluCI	AATT	9 cut(s)	40, 262, 329, 347, 517, 581, 612, 828, 875
MluNI	TGGCCA	1 cut(s)	78
MlyI	GAGTC	2 cut(s)	17, 59
MnlI	CCTC	3 cut(s)	200, 375, 421
Mox20I	TGGCCA	1 cut(s)	78
Mph1103I	ATGCAT	3 cut(s)	372, 454, 650
MroXI	GAANNNNTTC	3 cut(s)	648, 682, 813
MscI	TGGCCA	1 cut(s)	78
MseI	TTAA	7 cut(s)	39, 198, 227, 327, 345, 756, 831
MslI	CAYNNNNRTG	1 cut(s)	457
Msp20I	TGGCCA	1 cut(s)	78
MspI	CCGG	1 cut(s)	69
MspR9I	CCNGG	1 cut(s)	249
Mva1269I	GAATGC	3 cut(s)	454, 648, 650
MvaI	CCWGG	1 cut(s)	249
MwoI	GCNNNNNNNGC	1 cut(s)	290
NcoI	CCATGG	1 cut(s)	27
NdeII	GATC	1 cut(s)	964
NlaIV	GGNNCC	2 cut(s)	578, 636
NmuCI	GTSAC	1 cut(s)	145
NsiI	ATGCAT	3 cut(s)	372, 454, 650
NspI	RCATGY	3 cut(s)	467, 482, 988
PaeI	GCATGC	1 cut(s)	467
PciI	ACATGT	1 cut(s)	984
PctI	GAATGC	3 cut(s)	454, 648, 650
PdmI	GAANNNNTTC	3 cut(s)	648, 682, 813
PfeI	GAWTC	3 cut(s)	98, 215, 712
PflMI	CCANNNNNTGG	1 cut(s)	128
PkrI	GCNGC	3 cut(s)	440, 837, 840
PleI	GAGTC	2 cut(s)	16, 59
PpsI	GAGTC	2 cut(s)	16, 59
PscI	ACATGT	1 cut(s)	984
PshBI	ATTAAT	1 cut(s)	39
PsiI	TTATAA	1 cut(s)	353
Psp6I	CCWGG	1 cut(s)	247
PspFI	CCCAGC	1 cut(s)	937
PspGI	CCWGG	1 cut(s)	247
PspN4I	GGNNCC	2 cut(s)	578, 636
PspPI	GGNCC	2 cut(s)	314, 668
RseI	CAYNNNNRTG	1 cut(s)	457
SaqAI	TTAA	7 cut(s)	39, 198, 227, 327, 345, 756, 831
SatI	GCNGC	3 cut(s)	439, 836, 839
Sau3AI	GATC	1 cut(s)	964
Sau96I	GGNCC	2 cut(s)	314, 668
SchI	GAGTC	2 cut(s)	17, 59
ScrFI	CCNGG	1 cut(s)	249
SfaNI	GCATC	4 cut(s)	280, 461, 760, 958
SinI	GGWCC	1 cut(s)	668
SmiMI	CAYNNNNRTG	1 cut(s)	457
SphI	GCATGC	1 cut(s)	467
Sse9I	AATT	9 cut(s)	40, 262, 329, 347, 517, 581, 612, 828, 875
SsiI	CCGC	1 cut(s)	835
SspI	AATATT	1 cut(s)	343
SspMI	CTAG	4 cut(s)	300, 468, 555, 675
StyD4I	CCNGG	1 cut(s)	247
StyI	CCWWGG	2 cut(s)	27, 639
TaaI	ACNGT	2 cut(s)	163, 190
TaqI	TCGA	1 cut(s)	700
TasI	AATT	9 cut(s)	40, 262, 329, 347, 517, 581, 612, 828, 875
TauI	GCSGC	1 cut(s)	838
TfiI	GAWTC	3 cut(s)	98, 215, 712
Tru1I	TTAA	7 cut(s)	39, 198, 227, 327, 345, 756, 831
Tru9I	TTAA	7 cut(s)	39, 198, 227, 327, 345, 756, 831
TseFI	GTSAC	1 cut(s)	145
TseI	GCWGC	2 cut(s)	438, 838
Tsp45I	GTSAC	1 cut(s)	145
TspDTI	ATGAA	9 cut(s)	111, 150, 195, 269, 405, 641, 675, 853, 888
Van91I	CCANNNNNTGG	1 cut(s)	128
VpaK11BI	GGWCC	1 cut(s)	668
VspI	ATTAAT	1 cut(s)	39
XapI	RAATTY	6 cut(s)	262, 329, 347, 517, 612, 875
XceI	RCATGY	3 cut(s)	467, 482, 988
XmiI	GTMKAC	2 cut(s)	407, 532
XmnI	GAANNNNTTC	3 cut(s)	648, 682, 813
XspI	CTAG	4 cut(s)	300, 468, 555, 675
Zsp2I	ATGCAT	3 cut(s)	372, 454, 650

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