Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0006436

Physical Location & Seq

Genomic Coordinates Reverse (-)

14755346 .. 14757574

Gene Structure 2229 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG086000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 669 bp

ATGGAGAATGCTCAGGTGCTTACTTGGTTCCATAACTCTGTTGAATCAAGCATTGGTCAGAACTTTTCAAAGTTCGAAACTGCAAAGAGAGTATGGGAGTATTTGCAACTGTTATATCAAGAGTCTAACTTTGCCAAGCAATATCAGCTGGAAATGGAAATTCAAGGTGCCCAGCAAGGTGATAAGACCATTCAAGACTTCTACAATCAGATGACTTGTTTCTGGGATCAATTAGCACTTATGGAATTAGCTGACCTCTTGGCATTAGATAGTTATGTTAACTATAGAGAGCGTCAGAGACTTGTCCAATTTCTTATGGCACTTAAGGAACAGTTTGAACCTTTGTGTGGTGCTATGCTGCATCGTGTTCCTCTACCCACTGTTGATGGAGCGGTTAAAGAACTTCTAGCTGAGGAGACTCGATTTAAGGTTGCTCATAATGTTTCTCCCTCCCCATCAGTGTTTGCAACCTCTATGTTGCAACCTCCTTTACTGCCTACTCCACCTCAAAGTTTGATACAGATTACTGGCAAACCTAAGCAACGTGTCAGCAATGATGAATGCAGTTTTTGCCATCAAAAAGGACATTGGAAGGTCTCTTGCCCAAAATTACAGAAGGGGCGTCCATTCTCTCAGTATAATCATCGGCCCCCTCACCACAATTCTTAG

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

Retrotran_gag_2 Retrotran_gag_3

Protein Analysis

222

Amino Acids

25.69

Weight (kDa)

7.08

Isoelectric Point (pI)

45.45

Instability Index

Protein Domains (Pfam)

No Pfam domains detected for this protein.

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: OG0006436)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G21280
fragaria_vesca	FvH4_3g37931 FvH4_3g37931 FvH4_3g37931
malus_domestica	MD01G1094300.v1.1 MD02G1156200.v1.1 MD10G1309400.v1.1 MD14G1005300.v1.1
pyrus_communis	pycom02g16670 pycom03g10030 pycom04g21390 pycom05g29420 pycom07g08570 pycom08g06430 pycom15g03080 pycom15g21690
rosa_chinensis	RchiOBHm_Chr4g0394011 RchiOBHm_Chr4g0436631
rosa_multiflora	Rmu_sc0002646.1_g000018 Rmu_sc0004135.1_g000007
rosa_roxburghii	Rroxscaffold_2G00099130
rosa_samantha	Rh1AG086000 Rh2BG003200 Rh5DG450100 Rh7AG095400
rosa_wichuraiana	Rw1G012660

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	167
AccBSI	CCGCTC	1 cut(s)	392
AciI	CCGC	1 cut(s)	392
AclWI	GGATC	1 cut(s)	234
AcsI	RAATTY	1 cut(s)	159
AcyI	GRCGYC	1 cut(s)	622
AfiI	CCNNNNNNNGG	1 cut(s)	347
AflII	CTTAAG	1 cut(s)	323
AflIII	ACRYGT	1 cut(s)	544
AgsI	TTSAA	5 cut(s)	44, 69, 164, 194, 338
AjuI	GAANNNNNNNTTGG	2 cut(s)	36, 68
AluBI	AGCT	3 cut(s)	148, 251, 410
AluI	AGCT	3 cut(s)	148, 251, 410
Alw26I	GTCTC	3 cut(s)	292, 410, 601
AlwI	GGATC	1 cut(s)	234
AoxI	GGCC	1 cut(s)	647
ApeKI	GCWGC	1 cut(s)	358
ApoI	RAATTY	1 cut(s)	159
AspS9I	GGNCC	1 cut(s)	648
AsuHPI	GGTGA	2 cut(s)	191, 647
AsuII	TTCGAA	1 cut(s)	75
BaeGI	GKGCMC	1 cut(s)	172
BanI	GGYRCC	1 cut(s)	167
BbvCI	CCTCAGC	1 cut(s)	411
BbvI	GCAGC	1 cut(s)	345
BccI	CCATC	3 cut(s)	380, 463, 582
BcoDI	GTCTC	3 cut(s)	292, 410, 601
BfaI	CTAG	1 cut(s)	407
BfmI	CTRYAG	1 cut(s)	283
BfrI	CTTAAG	1 cut(s)	323
BisI	GCNGC	1 cut(s)	359
BlsI	GCNGC	1 cut(s)	360
BmgT120I	GGNCC	1 cut(s)	648
BmiI	GGNNCC	3 cut(s)	29, 169, 650
BmsI	GCATC	1 cut(s)	370
Bpu10I	CCTNAGC	3 cut(s)	12, 411, 537
Bpu14I	TTCGAA	1 cut(s)	75
BsaHI	GRCGYC	1 cut(s)	622
BsaI	GGTCTC	1 cut(s)	601
Bsc4I	CCNNNNNNNGG	1 cut(s)	347
Bse1I	ACTGG	1 cut(s)	532
Bse3DI	GCAATG	1 cut(s)	559
BseLI	CCNNNNNNNGG	1 cut(s)	347
BseMI	GCAATG	1 cut(s)	559
BseMII	CTCAG	3 cut(s)	26, 402, 647
BseNI	ACTGG	1 cut(s)	532
BseRI	GAGGAG	1 cut(s)	428
BseSI	GKGCMC	1 cut(s)	172
BseXI	GCAGC	1 cut(s)	345
BseYI	CCCAGC	1 cut(s)	171
BshFI	GGCC	1 cut(s)	649
BshNI	GGYRCC	1 cut(s)	167
BslI	CCNNNNNNNGG	1 cut(s)	347
BsmAI	GTCTC	3 cut(s)	292, 410, 601
BsmI	GAATGC	2 cut(s)	13, 566
BsnI	GGCC	1 cut(s)	649
Bso31I	GGTCTC	1 cut(s)	601
Bsp119I	TTCGAA	1 cut(s)	75
Bsp1286I	GDGCHC	1 cut(s)	172
Bsp143I	GATC	1 cut(s)	226
BspACI	CCGC	1 cut(s)	392
BspANI	GGCC	1 cut(s)	649
BspCNI	CTCAG	3 cut(s)	25, 403, 646
BspLI	GGNNCC	3 cut(s)	29, 169, 650
BspPI	GGATC	1 cut(s)	234
BspT104I	TTCGAA	1 cut(s)	75
BspT107I	GGYRCC	1 cut(s)	167
BspTI	CTTAAG	1 cut(s)	323
BspTNI	GGTCTC	1 cut(s)	601
BsrBI	CCGCTC	1 cut(s)	392
BsrDI	GCAATG	1 cut(s)	559
BsrI	ACTGG	1 cut(s)	532
BssMI	GATC	1 cut(s)	226
BssNI	GRCGYC	1 cut(s)	622
Bst4CI	ACNGT	3 cut(s)	111, 333, 382
BstACI	GRCGYC	1 cut(s)	622
BstAFI	CTTAAG	1 cut(s)	323
BstAPI	GCANNNNNTGC	1 cut(s)	570
BstBI	TTCGAA	1 cut(s)	75
BstDEI	CTNAG	5 cut(s)	12, 411, 537, 633, 666
BstKTI	GATC	1 cut(s)	229
BstMAI	GTCTC	3 cut(s)	292, 410, 601
BstMBI	GATC	1 cut(s)	226
BstMWI	GCNNNNNNNGC	2 cut(s)	145, 570
BstSFI	CTRYAG	1 cut(s)	283
BstSLI	GKGCMC	1 cut(s)	172
BstV1I	GCAGC	1 cut(s)	345
BsuRI	GGCC	1 cut(s)	649
BtsIMutI	CAGTG	2 cut(s)	378, 465
Cfr13I	GGNCC	1 cut(s)	648
CseI	GACGC	2 cut(s)	281, 611
CviJI	RGCY	4 cut(s)	148, 251, 410, 649
CviKI_1	RGCY	4 cut(s)	148, 251, 410, 649
DdeI	CTNAG	5 cut(s)	12, 411, 537, 633, 666
DpnI	GATC	1 cut(s)	228
DpnII	GATC	1 cut(s)	226
Eco31I	GGTCTC	1 cut(s)	601
Fnu4HI	GCNGC	1 cut(s)	359
Fsp4HI	GCNGC	1 cut(s)	359
FspBI	CTAG	1 cut(s)	407
GluI	GCNGC	1 cut(s)	359
GsaI	CCCAGC	1 cut(s)	175
HaeIII	GGCC	1 cut(s)	649
HgaI	GACGC	2 cut(s)	281, 611
Hin1I	GRCGYC	1 cut(s)	622
HincII	GTYRAC	1 cut(s)	280
HindII	GTYRAC	1 cut(s)	280
HinfI	GANTC	3 cut(s)	44, 122, 418
HpaI	GTTAAC	1 cut(s)	280
HphI	GGTGA	2 cut(s)	191, 647
Hpy166II	GTNNAC	1 cut(s)	280
Hpy188I	TCNGA	3 cut(s)	60, 210, 297
Hpy188III	TCNNGA	2 cut(s)	119, 194
Hpy8I	GTNNAC	1 cut(s)	280
HpyAV	CCTTC	2 cut(s)	586, 610
HpyCH4III	ACNGT	3 cut(s)	111, 333, 382
HpyCH4IV	ACGT	1 cut(s)	544
HpyCH4V	TGCA	6 cut(s)	83, 106, 361, 467, 481, 564
HpyF10VI	GCNNNNNNNGC	2 cut(s)	145, 570
HpyF3I	CTNAG	5 cut(s)	12, 411, 537, 633, 666
HpySE526I	ACGT	1 cut(s)	544
Hsp92I	GRCGYC	1 cut(s)	622
KspAI	GTTAAC	1 cut(s)	280
Kzo9I	GATC	1 cut(s)	226
LmnI	GCTCC	1 cut(s)	389
LpnPI	CCDG	4 cut(s)	134, 185, 208, 513
Lsp1109I	GCAGC	1 cut(s)	345
LweI	GCATC	1 cut(s)	370
MaeI	CTAG	1 cut(s)	407
MaeII	ACGT	1 cut(s)	544
MalI	GATC	1 cut(s)	228
MbiI	CCGCTC	1 cut(s)	392
MboI	GATC	1 cut(s)	226
MhlI	GDGCHC	1 cut(s)	172
MluCI	AATT	6 cut(s)	159, 230, 245, 308, 608, 661
MlyI	GAGTC	2 cut(s)	131, 412
MnlI	CCTC	8 cut(s)	266, 381, 406, 460, 481, 495, 516, 663
MseI	TTAA	4 cut(s)	279, 324, 396, 426
MspA1I	CMGCKG	1 cut(s)	148
MspCI	CTTAAG	1 cut(s)	323
Mva1269I	GAATGC	2 cut(s)	13, 566
MwoI	GCNNNNNNNGC	2 cut(s)	145, 570
NdeII	GATC	1 cut(s)	226
NlaIV	GGNNCC	3 cut(s)	29, 169, 650
NspV	TTCGAA	1 cut(s)	75
PctI	GAATGC	2 cut(s)	13, 566
PfeI	GAWTC	1 cut(s)	44
PkrI	GCNGC	1 cut(s)	360
PleI	GAGTC	2 cut(s)	130, 412
PpsI	GAGTC	2 cut(s)	130, 412
PspFI	CCCAGC	1 cut(s)	171
PspN4I	GGNNCC	3 cut(s)	29, 169, 650
PspPI	GGNCC	1 cut(s)	648
PvuII	CAGCTG	1 cut(s)	148
SaqAI	TTAA	4 cut(s)	279, 324, 396, 426
SatI	GCNGC	1 cut(s)	359
Sau3AI	GATC	1 cut(s)	226
Sau96I	GGNCC	1 cut(s)	648
SchI	GAGTC	2 cut(s)	131, 412
SduI	GDGCHC	1 cut(s)	172
SfaNI	GCATC	1 cut(s)	370
SfcI	CTRYAG	1 cut(s)	283
SfuI	TTCGAA	1 cut(s)	75
SmlI	CTYRAG	1 cut(s)	323
SmoI	CTYRAG	1 cut(s)	323
Sse9I	AATT	6 cut(s)	159, 230, 245, 308, 608, 661
SsiI	CCGC	1 cut(s)	392
SspMI	CTAG	1 cut(s)	407
TaaI	ACNGT	3 cut(s)	111, 333, 382
TaiI	ACGT	1 cut(s)	547
TaqI	TCGA	2 cut(s)	75, 421
TasI	AATT	6 cut(s)	159, 230, 245, 308, 608, 661
TfiI	GAWTC	1 cut(s)	44
Tru1I	TTAA	4 cut(s)	279, 324, 396, 426
Tru9I	TTAA	4 cut(s)	279, 324, 396, 426
TscAI	CASTG	2 cut(s)	385, 465
TseI	GCWGC	1 cut(s)	358
TspDTI	ATGAA	1 cut(s)	573
TspRI	CASTG	2 cut(s)	385, 465
Vha464I	CTTAAG	1 cut(s)	323
XapI	RAATTY	1 cut(s)	159
XspI	CTAG	1 cut(s)	407

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