Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0000370

Physical Location & Seq

Genomic Coordinates Forward (+)

28541364 .. 28542194

Gene Structure 831 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG142700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 831 bp

ATGCAACAAGGTGTTAGAGGAGTAAACAAAGTGGTTGAGCACTTTAGAAAAAATAATCCACCTGCTTTCGATGGACACGAAGACGCACTTGCTGCTGAAGAATGGGTTAATGAGTTGGATAGCATATTCAGGCTTATGGAATGTACTGATGCGCATAAAGTTACTTACGCAATTTACATGCTGAAGAAGGATGCCAGATATTGGTGGGATACTATGTGTAGAGCCCACAACATTGATGTGAATCCCATTAGTTGGACAAGATTTAAGGAGTTATTTTATGAAAAGTATTTCCCTGAGCCATTGAGAGCAGAGAAGGAATCTAAGTTTCTGTTGTTGAAAATTGAATCAATGCCTTACCCAGAGTATGAGAGGAAGTTTGAGTCACTATCAAGGTTTGCTCCACATCTTGTGGATACTGAGGAGCTCAAAGCAAGGAGATTTGTGCAAGGTCTCAGGTTAGAAATCAGGAGAGCTGTGGAGGTCCTTGATTTGCATACATACACAGAAGTGGTAAGAAGAGCTCAAATTGTGGCTAAGCATGATGTGCCAATGGCTACTAGAGAGATAATTGACAAAGACAAGGGTTCAGTACAAAAGAGACCATGTGAAAGTGGTAGCCAAGTAGTGGTCCAAAATCAGGTTGGAGGAAATAAGAGGCCTAGAACAGGTGACATAAGTAGGGGTACCTCACAAACTTGTCAGACCTGTGGGAAGAAGCATGTTGGGTTATGCCATAGAAACACTGGTGCTTACTTTAGGTGTGGGAAAATAGGACACTTCATACAAAACTGCCCTAACACGAAGAATGGTCATGACGATTCACACCAATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000943 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0003887 GO:0003964 GO:0004518 GO:0004540 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006259 GO:0006278 GO:0006508 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0008233 GO:0009058 GO:0009059 GO:0009987 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0016787 GO:0016788 GO:0018130 GO:0019438 GO:0019538 GO:0032196 GO:0032197 GO:0034061 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0071704 GO:0071897 GO:0090304 GO:0090305 GO:0090501 GO:0097159 GO:0140096 GO:0140097 GO:0140098 GO:1901360 GO:1901362 GO:1901363 GO:1901564 GO:1901576

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RVP_2 RVT_1 Retrotrans_gag rve zf-CCHC

Protein Analysis

276

Amino Acids

32.05

Weight (kDa)

8.93

Isoelectric Point (pI)

41.32

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ty3_capsid	PF19259	15 - 187	1.9e-09	Ty3 transposon capsid-like protein
Retrotrans_gag	PF03732	57 - 152	4.1e-13	Retrotransposon gag 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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Tree File

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Publication-ready

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Orthologous Genes (Group: OG0000370)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica	MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica	Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis	pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis	RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata	RLG00000029892
rosa_multiflora	Rmu_sc0001866.1_g000007
rosa_roxburghii	Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa	Rorug05G0160500 Rorug06G0096500
rosa_samantha	Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana	Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	70
Acc16I	TGCGCA	1 cut(s)	153
Acc36I	ACCTGC	1 cut(s)	70
Acc65I	GGTACC	1 cut(s)	683
AccB1I	GGYRCC	1 cut(s)	683
AccB7I	CCANNNNNTGG	3 cut(s)	201, 252, 625
AcuI	CTGAAG	2 cut(s)	117, 203
AfaI	GTAC	3 cut(s)	145, 591, 685
AfiI	CCNNNNNNNGG	5 cut(s)	201, 252, 625, 637, 665
AgsI	TTSAA	2 cut(s)	337, 344
AleI	CACNNNNGTG	1 cut(s)	506
AluBI	AGCT	3 cut(s)	424, 473, 521
AluI	AGCT	3 cut(s)	424, 473, 521
Alw21I	GWGCWC	3 cut(s)	42, 426, 523
Alw26I	GTCTC	2 cut(s)	455, 592
AoxI	GGCC	1 cut(s)	656
ApeKI	GCWGC	1 cut(s)	92
Asp718I	GGTACC	1 cut(s)	683
AspLEI	GCGC	1 cut(s)	154
AspS9I	GGNCC	2 cut(s)	481, 628
AsuHPI	GGTGA	1 cut(s)	680
AvaII	GGWCC	2 cut(s)	481, 628
BanI	GGYRCC	1 cut(s)	683
BanII	GRGCYC	3 cut(s)	226, 426, 523
BbsI	GAAGAC	1 cut(s)	87
Bbv12I	GWGCWC	3 cut(s)	42, 426, 523
BbvI	GCAGC	1 cut(s)	79
BccI	CCATC	1 cut(s)	65
BciVI	GTATCC	2 cut(s)	202, 406
BcoDI	GTCTC	2 cut(s)	455, 592
BfaI	CTAG	2 cut(s)	558, 660
BfuAI	ACCTGC	1 cut(s)	70
BfuI	GTATCC	2 cut(s)	202, 406
BisI	GCNGC	1 cut(s)	93
BlpI	GCTNAGC	1 cut(s)	534
BlsI	GCNGC	1 cut(s)	94
Bme18I	GGWCC	2 cut(s)	481, 628
BmgT120I	GGNCC	2 cut(s)	481, 628
BmiI	GGNNCC	1 cut(s)	685
BmsI	GCATC	2 cut(s)	139, 181
BpiI	GAAGAC	1 cut(s)	87
Bpu10I	CCTNAGC	1 cut(s)	294
Bpu1102I	GCTNAGC	1 cut(s)	534
BsaBI	GATNNNNATC	1 cut(s)	240
BsaI	GGTCTC	2 cut(s)	455, 592
Bsc4I	CCNNNNNNNGG	5 cut(s)	201, 252, 625, 637, 665
Bse1I	ACTGG	1 cut(s)	748
Bse8I	GATNNNNATC	1 cut(s)	240
BseGI	GGATG	1 cut(s)	196
BseJI	GATNNNNATC	1 cut(s)	240
BseLI	CCNNNNNNNGG	5 cut(s)	201, 252, 625, 637, 665
BseMII	CTCAG	3 cut(s)	285, 408, 466
BseNI	ACTGG	1 cut(s)	748
BseRI	GAGGAG	2 cut(s)	33, 434
BseXI	GCAGC	1 cut(s)	79
BshFI	GGCC	1 cut(s)	658
BshNI	GGYRCC	1 cut(s)	683
BsiHKAI	GWGCWC	3 cut(s)	42, 426, 523
BslI	CCNNNNNNNGG	5 cut(s)	201, 252, 625, 637, 665
BsmAI	GTCTC	2 cut(s)	455, 592
BsnI	GGCC	1 cut(s)	658
Bso31I	GGTCTC	2 cut(s)	455, 592
Bsp1286I	GDGCHC	4 cut(s)	42, 226, 426, 523
Bsp1720I	GCTNAGC	1 cut(s)	534
BspANI	GGCC	1 cut(s)	658
BspCNI	CTCAG	3 cut(s)	286, 409, 465
BspHI	TCATGA	1 cut(s)	811
BspLI	GGNNCC	1 cut(s)	685
BspMI	ACCTGC	1 cut(s)	70
BspQI	GCTCTTC	1 cut(s)	511
BspT107I	GGYRCC	1 cut(s)	683
BspTNI	GGTCTC	2 cut(s)	455, 592
BsrI	ACTGG	1 cut(s)	748
Bst6I	CTCTTC	1 cut(s)	511
BstAPI	GCANNNNNTGC	2 cut(s)	92, 544
BstDEI	CTNAG	5 cut(s)	294, 321, 417, 452, 534
BstENI	CCTNNNNNAGG	1 cut(s)	663
BstF5I	GGATG	1 cut(s)	196
BstHHI	GCGC	1 cut(s)	154
BstMAI	GTCTC	2 cut(s)	455, 592
BstMWI	GCNNNNNNNGC	2 cut(s)	92, 544
BstNSI	RCATGY	2 cut(s)	181, 722
BstV1I	GCAGC	1 cut(s)	79
BstV2I	GAAGAC	1 cut(s)	87
BsuI	GTATCC	2 cut(s)	202, 406
BsuRI	GGCC	1 cut(s)	658
BtsCI	GGATG	1 cut(s)	196
BtsIMutI	CAGTG	1 cut(s)	741
BveI	ACCTGC	1 cut(s)	70
CciI	TCATGA	1 cut(s)	811
CfoI	GCGC	1 cut(s)	154
Cfr13I	GGNCC	2 cut(s)	481, 628
CseI	GACGC	1 cut(s)	92
Csp6I	GTAC	3 cut(s)	144, 590, 684
CviAII	CATG	5 cut(s)	178, 539, 603, 719, 812
CviQI	GTAC	3 cut(s)	144, 590, 684
DdeI	CTNAG	5 cut(s)	294, 321, 417, 452, 534
Eam1104I	CTCTTC	1 cut(s)	511
EarI	CTCTTC	1 cut(s)	511
Ecl136II	GAGCTC	2 cut(s)	424, 521
Eco147I	AGGCCT	1 cut(s)	658
Eco24I	GRGCYC	3 cut(s)	226, 426, 523
Eco31I	GGTCTC	2 cut(s)	455, 592
Eco47I	GGWCC	2 cut(s)	481, 628
Eco53kI	GAGCTC	2 cut(s)	424, 521
Eco57I	CTGAAG	2 cut(s)	117, 203
EcoICRI	GAGCTC	2 cut(s)	424, 521
EcoNI	CCTNNNNNAGG	1 cut(s)	663
EcoO109I	RGGNCCY	1 cut(s)	481
EcoT38I	GRGCYC	3 cut(s)	226, 426, 523
FaeI	CATG	5 cut(s)	181, 542, 606, 722, 815
FalI	AAGNNNNNCTT	2 cut(s)	72, 104
FatI	CATG	5 cut(s)	177, 538, 602, 718, 811
Fnu4HI	GCNGC	1 cut(s)	93
FokI	GGATG	1 cut(s)	203
FriOI	GRGCYC	3 cut(s)	226, 426, 523
Fsp4HI	GCNGC	1 cut(s)	93
FspAI	RTGCGCAY	1 cut(s)	153
FspBI	CTAG	2 cut(s)	558, 660
FspI	TGCGCA	1 cut(s)	153
GlaI	GCGC	1 cut(s)	153
GluI	GCNGC	1 cut(s)	93
HaeIII	GGCC	1 cut(s)	658
HgaI	GACGC	1 cut(s)	92
HhaI	GCGC	1 cut(s)	154
Hin1II	CATG	5 cut(s)	181, 542, 606, 722, 815
Hin6I	GCGC	1 cut(s)	152
HinP1I	GCGC	1 cut(s)	152
HinfI	GANTC	5 cut(s)	241, 317, 344, 380, 818
HphI	GGTGA	1 cut(s)	680
Hpy166II	GTNNAC	1 cut(s)	25
Hpy188I	TCNGA	1 cut(s)	702
Hpy188III	TCNNGA	2 cut(s)	466, 812
Hpy8I	GTNNAC	1 cut(s)	25
HpyAV	CCTTC	2 cut(s)	181, 307
HpyCH4V	TGCA	3 cut(s)	4, 445, 493
HpyF10VI	GCNNNNNNNGC	2 cut(s)	92, 544
HpyF3I	CTNAG	5 cut(s)	294, 321, 417, 452, 534
Hsp92II	CATG	5 cut(s)	181, 542, 606, 722, 815
HspAI	GCGC	1 cut(s)	152
KpnI	GGTACC	1 cut(s)	687
LguI	GCTCTTC	1 cut(s)	511
LmnI	GCTCC	2 cut(s)	403, 421
Lsp1109I	GCAGC	1 cut(s)	79
LweI	GCATC	2 cut(s)	139, 181
MaeI	CTAG	2 cut(s)	558, 660
MaeIII	GTNAC	3 cut(s)	160, 381, 668
MboII	GAAGA	6 cut(s)	92, 110, 196, 528, 724, 814
MhlI	GDGCHC	4 cut(s)	42, 226, 426, 523
MluCI	AATT	4 cut(s)	171, 339, 525, 567
MlyI	GAGTC	1 cut(s)	389
MmeI	TCCRAC	3 cut(s)	96, 233, 622
MnlI	CCTC	7 cut(s)	11, 363, 412, 472, 638, 648, 697
MseI	TTAA	2 cut(s)	108, 264
MslI	CAYNNNNRTG	2 cut(s)	236, 506
MwoI	GCNNNNNNNGC	2 cut(s)	92, 544
NlaIII	CATG	5 cut(s)	181, 542, 606, 722, 815
NlaIV	GGNNCC	1 cut(s)	685
NmuCI	GTSAC	2 cut(s)	381, 668
NsbI	TGCGCA	1 cut(s)	153
NspI	RCATGY	2 cut(s)	181, 722
OliI	CACNNNNGTG	1 cut(s)	506
PagI	TCATGA	1 cut(s)	811
PaqCI	CACCTGC	1 cut(s)	70
PceI	AGGCCT	1 cut(s)	658
PciSI	GCTCTTC	1 cut(s)	511
PcsI	WCGNNNNNNNCGW	1 cut(s)	75
PfeI	GAWTC	4 cut(s)	241, 317, 344, 818
PflMI	CCANNNNNTGG	3 cut(s)	201, 252, 625
PkrI	GCNGC	1 cut(s)	94
PleI	GAGTC	1 cut(s)	388
PpsI	GAGTC	1 cut(s)	388
PpuMI	RGGWCCY	1 cut(s)	481
Psp124BI	GAGCTC	2 cut(s)	426, 523
Psp5II	RGGWCCY	1 cut(s)	481
PspN4I	GGNNCC	1 cut(s)	685
PspPI	GGNCC	2 cut(s)	481, 628
PspPPI	RGGWCCY	1 cut(s)	481
RsaI	GTAC	3 cut(s)	145, 591, 685
RsaNI	GTAC	3 cut(s)	144, 590, 684
RseI	CAYNNNNRTG	2 cut(s)	236, 506
SacI	GAGCTC	2 cut(s)	426, 523
SapI	GCTCTTC	1 cut(s)	511
SaqAI	TTAA	2 cut(s)	108, 264
SatI	GCNGC	1 cut(s)	93
Sau96I	GGNCC	2 cut(s)	481, 628
SchI	GAGTC	1 cut(s)	389
SduI	GDGCHC	4 cut(s)	42, 226, 426, 523
SfaNI	GCATC	2 cut(s)	139, 181
SinI	GGWCC	2 cut(s)	481, 628
SmiMI	CAYNNNNRTG	2 cut(s)	236, 506
Sse9I	AATT	4 cut(s)	171, 339, 525, 567
SseBI	AGGCCT	1 cut(s)	658
SspMI	CTAG	2 cut(s)	558, 660
SstI	GAGCTC	2 cut(s)	426, 523
StuI	AGGCCT	1 cut(s)	658
TaqI	TCGA	1 cut(s)	69
TasI	AATT	4 cut(s)	171, 339, 525, 567
TatI	WGTACW	2 cut(s)	143, 589
TfiI	GAWTC	4 cut(s)	241, 317, 344, 818
Tru1I	TTAA	2 cut(s)	108, 264
Tru9I	TTAA	2 cut(s)	108, 264
TscAI	CASTG	1 cut(s)	748
TseFI	GTSAC	2 cut(s)	381, 668
TseI	GCWGC	1 cut(s)	92
Tsp45I	GTSAC	2 cut(s)	381, 668
TspDTI	ATGAA	2 cut(s)	294, 769
TspRI	CASTG	1 cut(s)	748
Van91I	CCANNNNNTGG	3 cut(s)	201, 252, 625
VpaK11BI	GGWCC	2 cut(s)	481, 628
XagI	CCTNNNNNAGG	1 cut(s)	663
XceI	RCATGY	2 cut(s)	181, 722
XcmI	CCANNNNNNNNNTGG	2 cut(s)	638, 740
XspI	CTAG	2 cut(s)	558, 660

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