Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr6

Orthogroup ID

OG0003287

Physical Location & Seq

Genomic Coordinates Reverse (-)

62377325 .. 62378227

Gene Structure 903 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw6G038170.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 618 bp

ATGGCTCATGTGGAGAGGAATGACTCCAAGTGTGAAGATGTGTGGTTTCTAGATAATGGTTGCAGCAATCATATGTGCTGCAACAAGGATTGGTTCACTAACATTGATGAGGAATTTAGGCACTCTGTGAAACTTGGCAACAATGCAAGGATGTCGGTGATGGGCAAGGGAAGCATCAGGTTAAAGGTGGATGGCTTGACTCAGGTAATCAGTGATGTTTACTTTGTTCCTGAGTTAAGAAATAACCTGCTAAGTATAGGACAATTGCAAGAGAAAGGCTTAGCCATTTTGATACAACATGGGGTCTGCAAAATTTATCATTCGAAGAGGGGACTCATTATGCAGATTCCTATGACCGCAAATCGCATGTTTGTACTTTTGGCTAATGTTGTGCTCACAGACTTCTCCACATGTATGCAAGCTTCTTCAGATGACCTATCACGCTTATGGCACTGCCGTTACAATCACCTAAATTACAAGGGACTCAAAACGCTGCATTATAGAAAGATGGTTAAGGGGCTGCCTCAAATCAAAGCTTATGCAAGGGTTTGTCATGATTGCCTGGTGGGAAAGCAAAGTCGGGATTCAATTCCGAAGAGTAGCCAGTGGAGAGCTTAA

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

RVT_2 Retrotran_gag_2 Retrotran_gag_3 Retrotrans_gag gag_pre-integrs rve zf-CCHC

Protein Analysis

205

Amino Acids

23.53

Weight (kDa)

9.26

Isoelectric Point (pI)

38.33

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pol_BBD	PF22936	15 - 93	3.1e-30	Pol polyprotein, beta-barrel domain
gag_pre-integrs	PF13976	136 - 192	1.5e-13	GAG-pre-integrase domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

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Orthologous Genes (Group: OG0003287)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G11591
fragaria_vesca	FvH4_2g20411 FvH4_2g29931 FvH4_3g14181 FvH4_4g00781 FvH4_4g12541 FvH4_5g22143 FvH4_7g24581
pyrus_communis	pycom04g03170 pycom05g18080 pycom12g05030 pycom13g18540
rosa_chinensis	RchiOBHm_Chr1g0313681 RchiOBHm_Chr1g0344501 RchiOBHm_Chr2g0157511
rosa_laevigata	RLG00000008144 RLG00000008360
rosa_multiflora	Rmu_sc0003765.1_g000035 Rmu_sc0004343.1_g000026 Rmu_sc0006087.1_g000011
rosa_roxburghii	Rroxscaffold_1G00038680 Rroxscaffold_3G00247490 Rroxscaffold_4G00315330 Rroxscaffold_5G00355970 Rroxscaffold_7G00214090
rosa_rugosa	Rorug04G0109300 Rorug04G0109400
rosa_samantha	Rh1AG403200 Rh4AG167500 Rh4BG164600 Rh4CG179400 Rh4DG162300
rosa_wichuraiana	Rw4G013620 Rw4G013850 Rw4G013950 Rw6G038170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	255
AciI	CCGC	1 cut(s)	357
AcsI	RAATTY	2 cut(s)	113, 312
AcuI	CTGAAG	1 cut(s)	411
AdeI	CACNNNGTG	1 cut(s)	127
AfaI	GTAC	1 cut(s)	375
AflIII	ACRYGT	1 cut(s)	410
AgsI	TTSAA	1 cut(s)	588
AjnI	CCWGG	1 cut(s)	561
AluBI	AGCT	3 cut(s)	422, 536, 614
AluI	AGCT	3 cut(s)	422, 536, 614
Alw21I	GWGCWC	1 cut(s)	396
ApeKI	GCWGC	4 cut(s)	63, 78, 493, 520
ApoI	RAATTY	2 cut(s)	113, 312
AsuHPI	GGTGA	2 cut(s)	169, 458
AsuII	TTCGAA	1 cut(s)	323
BarI	GAAGNNNNNNTAC	2 cut(s)	406, 438
Bbv12I	GWGCWC	1 cut(s)	396
BbvI	GCAGC	4 cut(s)	65, 75, 480, 507
BccI	CCATC	3 cut(s)	154, 185, 502
BceAI	ACGGC	1 cut(s)	441
BcgI	CGANNNNNNTGC	2 cut(s)	135, 169
BciT130I	CCWGG	1 cut(s)	563
BfaI	CTAG	1 cut(s)	50
BfuAI	ACCTGC	1 cut(s)	255
BisI	GCNGC	4 cut(s)	64, 79, 494, 521
BlpI	GCTNAGC	1 cut(s)	280
BlsI	GCNGC	4 cut(s)	65, 80, 495, 522
Bme1390I	CCNGG	1 cut(s)	563
BmrFI	CCNGG	1 cut(s)	563
BmsI	GCATC	1 cut(s)	183
Bpu1102I	GCTNAGC	1 cut(s)	280
Bpu14I	TTCGAA	1 cut(s)	323
Bse1I	ACTGG	1 cut(s)	604
BseBI	CCWGG	1 cut(s)	563
BseGI	GGATG	2 cut(s)	156, 196
BseMII	CTCAG	2 cut(s)	215, 222
BseNI	ACTGG	1 cut(s)	604
BseXI	GCAGC	4 cut(s)	65, 75, 480, 507
BsiHKAI	GWGCWC	1 cut(s)	396
BslFI	GGGAC	2 cut(s)	345, 495
BsmFI	GGGAC	2 cut(s)	345, 495
Bsp119I	TTCGAA	1 cut(s)	323
Bsp1286I	GDGCHC	1 cut(s)	396
Bsp1720I	GCTNAGC	1 cut(s)	280
BspACI	CCGC	1 cut(s)	357
BspCNI	CTCAG	2 cut(s)	214, 223
BspHI	TCATGA	1 cut(s)	553
BspMI	ACCTGC	1 cut(s)	255
BspT104I	TTCGAA	1 cut(s)	323
BsrI	ACTGG	1 cut(s)	604
Bst2UI	CCWGG	1 cut(s)	563
Bst6I	CTCTTC	2 cut(s)	320, 590
BstBI	TTCGAA	1 cut(s)	323
BstC8I	GCNNGC	1 cut(s)	420
BstDEI	CTNAG	4 cut(s)	201, 231, 251, 280
BstF5I	GGATG	2 cut(s)	156, 196
BstMWI	GCNNNNNNNGC	1 cut(s)	171
BstNI	CCWGG	1 cut(s)	563
BstNSI	RCATGY	2 cut(s)	370, 414
BstSCI	CCNGG	1 cut(s)	561
BstV1I	GCAGC	4 cut(s)	65, 75, 480, 507
BtsCI	GGATG	2 cut(s)	156, 196
BtsI	GCAGTG	1 cut(s)	451
BtsIMutI	CAGTG	3 cut(s)	217, 451, 611
BveI	ACCTGC	1 cut(s)	255
Cac8I	GCNNGC	1 cut(s)	420
CciI	TCATGA	1 cut(s)	553
Csp6I	GTAC	1 cut(s)	374
CviAII	CATG	5 cut(s)	8, 299, 367, 411, 554
CviQI	GTAC	1 cut(s)	374
DdeI	CTNAG	4 cut(s)	201, 231, 251, 280
DraIII	CACNNNGTG	1 cut(s)	127
Eam1104I	CTCTTC	2 cut(s)	320, 590
EarI	CTCTTC	2 cut(s)	320, 590
Eco57I	CTGAAG	1 cut(s)	411
EcoRII	CCWGG	1 cut(s)	561
FaeI	CATG	5 cut(s)	11, 302, 370, 414, 557
FaqI	GGGAC	2 cut(s)	345, 495
FatI	CATG	5 cut(s)	7, 298, 366, 410, 553
FauNDI	CATATG	1 cut(s)	72
Fnu4HI	GCNGC	4 cut(s)	64, 79, 494, 521
FokI	GGATG	2 cut(s)	163, 203
Fsp4HI	GCNGC	4 cut(s)	64, 79, 494, 521
FspBI	CTAG	1 cut(s)	50
GluI	GCNGC	4 cut(s)	64, 79, 494, 521
Hin1II	CATG	5 cut(s)	11, 302, 370, 414, 557
HindIII	AAGCTT	2 cut(s)	420, 534
HinfI	GANTC	6 cut(s)	23, 199, 333, 346, 483, 584
HphI	GGTGA	2 cut(s)	169, 458
Hpy166II	GTNNAC	2 cut(s)	96, 220
Hpy188I	TCNGA	2 cut(s)	430, 594
Hpy188III	TCNNGA	4 cut(s)	50, 230, 554, 581
Hpy8I	GTNNAC	2 cut(s)	96, 220
HpyCH4V	TGCA	9 cut(s)	63, 81, 146, 268, 309, 343, 418, 496, 542
HpyF10VI	GCNNNNNNNGC	1 cut(s)	171
HpyF3I	CTNAG	4 cut(s)	201, 231, 251, 280
Hsp92II	CATG	5 cut(s)	11, 302, 370, 414, 557
LpnPI	CCDG	6 cut(s)	163, 188, 243, 260, 548, 575
Lsp1109I	GCAGC	4 cut(s)	65, 75, 480, 507
LweI	GCATC	1 cut(s)	183
MaeI	CTAG	1 cut(s)	50
MaeIII	GTNAC	1 cut(s)	458
MboII	GAAGA	4 cut(s)	47, 337, 417, 607
MfeI	CAATTG	1 cut(s)	263
MhlI	GDGCHC	1 cut(s)	396
MluCI	AATT	5 cut(s)	113, 263, 312, 472, 588
MlyI	GAGTC	4 cut(s)	17, 193, 327, 477
MnlI	CCTC	4 cut(s)	9, 103, 321, 534
MseI	TTAA	4 cut(s)	182, 236, 513, 616
MslI	CAYNNNNRTG	2 cut(s)	413, 445
MspR9I	CCNGG	1 cut(s)	563
MunI	CAATTG	1 cut(s)	263
MvaI	CCWGG	1 cut(s)	563
MwoI	GCNNNNNNNGC	1 cut(s)	171
NdeI	CATATG	1 cut(s)	72
NlaIII	CATG	5 cut(s)	11, 302, 370, 414, 557
NspI	RCATGY	2 cut(s)	370, 414
NspV	TTCGAA	1 cut(s)	323
PagI	TCATGA	1 cut(s)	553
PciI	ACATGT	1 cut(s)	410
PfeI	GAWTC	2 cut(s)	346, 584
PkrI	GCNGC	4 cut(s)	65, 80, 495, 522
PleI	GAGTC	4 cut(s)	17, 193, 327, 477
PpsI	GAGTC	4 cut(s)	17, 193, 327, 477
PscI	ACATGT	1 cut(s)	410
Psp6I	CCWGG	1 cut(s)	561
PspGI	CCWGG	1 cut(s)	561
RsaI	GTAC	1 cut(s)	375
RsaNI	GTAC	1 cut(s)	374
RseI	CAYNNNNRTG	2 cut(s)	413, 445
SaqAI	TTAA	4 cut(s)	182, 236, 513, 616
SatI	GCNGC	4 cut(s)	64, 79, 494, 521
SchI	GAGTC	4 cut(s)	17, 193, 327, 477
ScrFI	CCNGG	1 cut(s)	563
SduI	GDGCHC	1 cut(s)	396
SetI	ASST	9 cut(s)	182, 189, 207, 249, 424, 438, 471, 538, 616
SfaNI	GCATC	1 cut(s)	183
SfuI	TTCGAA	1 cut(s)	323
SmiMI	CAYNNNNRTG	2 cut(s)	413, 445
Sse9I	AATT	5 cut(s)	113, 263, 312, 472, 588
SsiI	CCGC	1 cut(s)	357
SspMI	CTAG	1 cut(s)	50
StyD4I	CCNGG	1 cut(s)	561
TaqI	TCGA	1 cut(s)	323
TasI	AATT	5 cut(s)	113, 263, 312, 472, 588
TatI	WGTACW	1 cut(s)	373
TfiI	GAWTC	2 cut(s)	346, 584
Tru1I	TTAA	4 cut(s)	182, 236, 513, 616
Tru9I	TTAA	4 cut(s)	182, 236, 513, 616
TscAI	CASTG	3 cut(s)	217, 458, 611
TseI	GCWGC	4 cut(s)	63, 78, 493, 520
TspRI	CASTG	3 cut(s)	217, 458, 611
XapI	RAATTY	2 cut(s)	113, 312
XbaI	TCTAGA	1 cut(s)	49
XceI	RCATGY	2 cut(s)	370, 414
XspI	CTAG	1 cut(s)	50

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