Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr5

Orthogroup ID

OG0003077

Physical Location & Seq

Genomic Coordinates Reverse (-)

2956431 .. 2957654

Gene Structure 1224 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw5G003190.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1116 bp

ATGACTCAACCTCCTGGTTTTATTGATCAAACTAGGCCAACTCATGTTTGTAAGCTCCACAAGGCCCTTTATGGCCTTAAACAGGCTCCTCGAGCATTGTTCCAGAGAATGCGCTCTTTTCTATTGTCAGTTGGGTTTTTCCAAAGTTTGGCAGATTCCTTTTTGTTCATCTTTCACCACGGTCAAGACACTATTCATTTCTTGCTGTATGTTGACGATATTGTTCATACCGTCTCCCATGGACTGCATATTAATCAAGTGAAATATGCTTATGATCTTCTTTCCAAGCATGATTTGTTGCTCAGTAAGCCAGTTACTACCCCTATGTCTGCCAAACATAACCTCACTACCACTCAGGGTGCTTTACTTGCCGATCCCACAGAGTTTCGTGCACTTGTGGGTGCCTTACAATATCTCACGATTACTCGTTCGGATATCGCTTTTGCGGTCAACTCAGTTTCCCAGTTTATGAGTAAGCCTCGTGACCCTCATCTGGTTGCCGTGAAACGCATCCTCCGCTATGTCAAAGGCACCATGGGTCATGGATTATTTTTTGCGCCTCAGAAGCAACCGGTTCATATTTCTTCTTATTCTGATGTGGATTGGGCGGGCTGCCCTGACTCCCGTCATTCCACATCCGGTTATCTTGTGTATCTTAACTCCAATTTGATATCTTGGTGCTCCAAGAAGCAGCTTACTATTGCTCGATCGAGTGCCGAGTCGGAATATCGTTCTCTTGCTCATGCCTACGCAGAGACTACTTGGTTGGGCTATCTGTTGTATGAACTCCGTGTTAACATTCAGTTCCCCATCTTCTTGCATTGTGATAATCTAAGTGCTACCTATATGGCGTCTAATCCTATGTTTCATGCTCACACCAAACACATTGAGCTGGACTATCATTATGTTCGTGAAAAGGTTGCTCTTGGAAGTCACCATGTCTGCTTCATTCCTTCCATTGATCAGCCTGCTGATTTACTCACCAAACCGCTTCACAAGTCTCATCATCTTCTCTTTTCCGGCAAACTTGTTCGTCCAGAACCGCCAAGTTTGAGGGGGGATGTTAGAGAACTAAATCTTCTCCTAAACTCCAGCCATATGATTCACCTCCATTGA

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 gag_pre-integrs

Protein Analysis

371

Amino Acids

42.13

Weight (kDa)

9.14

Isoelectric Point (pI)

40.99

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RVT_2	PF07727	1 - 89	3.5e-16	Reverse transcriptase (RNA-dependent DNA polymerase)

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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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: OG0003077)

Species	Orthologous Gene IDs
arabidopsis_thaliana	ATMG00810
fragaria_vesca	FvH4_3g08011 FvH4_5g11221 FvH4_6g11491 FvH4_6g53931 FvH4_6g53931 FvH4_6g53931 FvH4_6g53931
rosa_chinensis	RchiOBHm_Chr1g0347991 RchiOBHm_Chr1g0348001 RchiOBHm_Chr1g0350631 RchiOBHm_Chr2g0100361 RchiOBHm_Chr2g0102931 RchiOBHm_Chr2g0122981 RchiOBHm_Chr2g0124571 RchiOBHm_Chr2g0134981 RchiOBHm_Chr4g0410941 RchiOBHm_Chr4g0410951 RchiOBHm_Chr5g0026511 RchiOBHm_Chr5g0078261 RchiOBHm_Chr5g0082731 RchiOBHm_Chr6g0261771 RchiOBHm_Chr6g0261781 RchiOBHm_Chr6g0276521 RchiOBHm_Chr6g0310171 RchiOBHm_Chr7g0180521 RchiOBHm_Chr7g0182281 RchiOBHm_Chr7g0231781 RchiOBHm_Chr7g0231971
rosa_roxburghii	Rroxscaffold_3G00242950
rosa_wichuraiana	Rw0G003700 Rw0G012710 Rw4G014500 Rw4G035380 Rw5G003190 Rw5G018810 Rw7G035270

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	2 cut(s)	401, 530
AccB7I	CCANNNNNTGG	1 cut(s)	148
AciI	CCGC	5 cut(s)	446, 517, 608, 989, 1043
AclWI	GGATC	1 cut(s)	368
AcyI	GRCGYC	1 cut(s)	851
AfiI	CCNNNNNNNGG	3 cut(s)	82, 148, 493
AgeI	ACCGGT	1 cut(s)	571
AjnI	CCWGG	1 cut(s)	13
AluBI	AGCT	3 cut(s)	55, 694, 892
AluI	AGCT	3 cut(s)	55, 694, 892
Alw21I	GWGCWC	2 cut(s)	394, 683
Alw26I	GTCTC	3 cut(s)	238, 749, 1005
Alw44I	GTGCAC	1 cut(s)	390
AlwI	GGATC	1 cut(s)	368
Ama87I	CYCGRG	1 cut(s)	90
AoxI	GGCC	3 cut(s)	35, 63, 73
ApaLI	GTGCAC	1 cut(s)	390
ApeKI	GCWGC	2 cut(s)	612, 691
AseI	ATTAAT	1 cut(s)	252
AsiGI	ACCGGT	1 cut(s)	571
AspLEI	GCGC	2 cut(s)	114, 559
AspS9I	GGNCC	1 cut(s)	64
AsuHPI	GGTGA	4 cut(s)	167, 926, 973, 1097
AvaI	CYCGRG	1 cut(s)	90
BaeGI	GKGCMC	1 cut(s)	394
BanI	GGYRCC	2 cut(s)	401, 530
BauI	CACGAG	1 cut(s)	480
Bbv12I	GWGCWC	2 cut(s)	394, 683
BbvI	GCAGC	2 cut(s)	599, 703
BccI	CCATC	1 cut(s)	818
BceAI	ACGGC	1 cut(s)	485
BciT130I	CCWGG	1 cut(s)	15
BclI	TGATCA	2 cut(s)	25, 961
BcoDI	GTCTC	3 cut(s)	238, 749, 1005
BfaI	CTAG	1 cut(s)	33
BisI	GCNGC	2 cut(s)	613, 692
BlsI	GCNGC	2 cut(s)	614, 693
Bme1390I	CCNGG	1 cut(s)	15
BmeT110I	CYCGRG	1 cut(s)	90
BmgT120I	GGNCC	1 cut(s)	64
BmiI	GGNNCC	3 cut(s)	87, 403, 532
BmrFI	CCNGG	1 cut(s)	15
BmrI	ACTGGG	1 cut(s)	457
BmsI	GCATC	1 cut(s)	519
BmuI	ACTGGG	1 cut(s)	457
BoxI	GACNNNNGTC	1 cut(s)	624
BplI	GAGNNNNNCTC	2 cut(s)	463, 495
BpmI	CTGGAG	1 cut(s)	1075
BsaHI	GRCGYC	1 cut(s)	851
BsaJI	CCNNGG	3 cut(s)	178, 238, 534
BsaWI	WCCGGW	2 cut(s)	571, 638
BsaXI	ACNNNNNCTCC	3 cut(s)	25, 498, 528
Bsc4I	CCNNNNNNNGG	3 cut(s)	82, 148, 493
Bse118I	RCCGGY	1 cut(s)	571
Bse1I	ACTGG	2 cut(s)	311, 463
BseBI	CCWGG	1 cut(s)	15
BseDI	CCNNGG	3 cut(s)	178, 238, 534
BseGI	GGATG	3 cut(s)	510, 635, 1066
BseLI	CCNNNNNNNGG	3 cut(s)	82, 148, 493
BseMII	CTCAG	4 cut(s)	316, 368, 468, 575
BseNI	ACTGG	2 cut(s)	311, 463
BseRI	GAGGAG	1 cut(s)	78
BseSI	GKGCMC	1 cut(s)	394
BseXI	GCAGC	2 cut(s)	599, 703
Bsh1285I	CGRYCG	1 cut(s)	710
BshFI	GGCC	3 cut(s)	37, 65, 75
BshNI	GGYRCC	2 cut(s)	401, 530
BshTI	ACCGGT	1 cut(s)	571
BsiEI	CGRYCG	1 cut(s)	710
BsiHKAI	GWGCWC	2 cut(s)	394, 683
BsiHKCI	CYCGRG	1 cut(s)	90
BsiSI	CCGG	3 cut(s)	572, 639, 1020
BslI	CCNNNNNNNGG	3 cut(s)	82, 148, 493
BsmAI	GTCTC	3 cut(s)	238, 749, 1005
BsmBI	CGTCTC	1 cut(s)	238
BsmI	GAATGC	1 cut(s)	114
BsnI	GGCC	3 cut(s)	37, 65, 75
BsoBI	CYCGRG	1 cut(s)	90
Bsp1286I	GDGCHC	2 cut(s)	394, 683
Bsp143I	GATC	5 cut(s)	25, 274, 373, 707, 961
Bsp19I	CCATGG	2 cut(s)	238, 534
BspACI	CCGC	5 cut(s)	446, 517, 608, 989, 1043
BspANI	GGCC	3 cut(s)	37, 65, 75
BspCNI	CTCAG	4 cut(s)	315, 367, 467, 574
BspLI	GGNNCC	3 cut(s)	87, 403, 532
BspPI	GGATC	1 cut(s)	368
BspT107I	GGYRCC	2 cut(s)	401, 530
BsrFI	RCCGGY	1 cut(s)	571
BsrI	ACTGG	2 cut(s)	311, 463
BssAI	RCCGGY	1 cut(s)	571
BssECI	CCNNGG	3 cut(s)	178, 238, 534
BssMI	GATC	5 cut(s)	25, 274, 373, 707, 961
BssNI	GRCGYC	1 cut(s)	851
BssSI	CACGAG	1 cut(s)	480
BssT1I	CCWWGG	2 cut(s)	238, 534
Bst2BI	CACGAG	1 cut(s)	480
Bst2UI	CCWGG	1 cut(s)	15
Bst4CI	ACNGT	2 cut(s)	182, 232
BstACI	GRCGYC	1 cut(s)	851
BstC8I	GCNNGC	2 cut(s)	610, 969
BstDEI	CTNAG	5 cut(s)	302, 354, 454, 561, 833
BstDSI	CCRYGG	3 cut(s)	178, 238, 534
BstENI	CCTNNNNNAGG	1 cut(s)	80
BstF5I	GGATG	3 cut(s)	510, 635, 1066
BstHHI	GCGC	2 cut(s)	114, 559
BstKTI	GATC	5 cut(s)	28, 277, 376, 710, 964
BstMAI	GTCTC	3 cut(s)	238, 749, 1005
BstMBI	GATC	5 cut(s)	25, 274, 373, 707, 961
BstMCI	CGRYCG	1 cut(s)	710
BstMWI	GCNNNNNNNGC	5 cut(s)	92, 307, 368, 516, 565
BstNI	CCWGG	1 cut(s)	15
BstPAI	GACNNNNGTC	1 cut(s)	624
BstSCI	CCNGG	1 cut(s)	13
BstSLI	GKGCMC	1 cut(s)	394
BstV1I	GCAGC	2 cut(s)	599, 703
BsuRI	GGCC	3 cut(s)	37, 65, 75
BtgI	CCRYGG	3 cut(s)	178, 238, 534
BtsCI	GGATG	3 cut(s)	510, 635, 1066
Cac8I	GCNNGC	2 cut(s)	610, 969
CfoI	GCGC	2 cut(s)	114, 559
Cfr10I	RCCGGY	1 cut(s)	571
Cfr13I	GGNCC	1 cut(s)	64
CseI	GACGC	1 cut(s)	840
CspAI	ACCGGT	1 cut(s)	571
CviAII	CATG	8 cut(s)	44, 239, 290, 535, 542, 743, 869, 938
DdeI	CTNAG	5 cut(s)	302, 354, 454, 561, 833
DpnI	GATC	5 cut(s)	27, 276, 375, 709, 963
DpnII	GATC	5 cut(s)	25, 274, 373, 707, 961
Eco130I	CCWWGG	2 cut(s)	238, 534
Eco32I	GATATC	2 cut(s)	436, 672
Eco88I	CYCGRG	1 cut(s)	90
EcoNI	CCTNNNNNAGG	1 cut(s)	80
EcoO109I	RGGNCCY	1 cut(s)	64
EcoRII	CCWGG	1 cut(s)	13
EcoRV	GATATC	2 cut(s)	436, 672
EcoT14I	CCWWGG	2 cut(s)	238, 534
ErhI	CCWWGG	2 cut(s)	238, 534
Esp3I	CGTCTC	1 cut(s)	238
FaeI	CATG	8 cut(s)	47, 242, 293, 538, 545, 746, 872, 941
FatI	CATG	8 cut(s)	43, 238, 289, 534, 541, 742, 868, 937
FauI	CCCGC	1 cut(s)	601
FauNDI	CATATG	1 cut(s)	1098
FbaI	TGATCA	2 cut(s)	25, 961
Fnu4HI	GCNGC	2 cut(s)	613, 692
FokI	GGATG	3 cut(s)	497, 622, 1073
Fsp4HI	GCNGC	2 cut(s)	613, 692
FspBI	CTAG	1 cut(s)	33
GlaI	GCGC	2 cut(s)	113, 558
GluI	GCNGC	2 cut(s)	613, 692
GsuI	CTGGAG	1 cut(s)	1075
HaeIII	GGCC	3 cut(s)	37, 65, 75
HapII	CCGG	3 cut(s)	572, 639, 1020
HgaI	GACGC	1 cut(s)	840
HhaI	GCGC	2 cut(s)	114, 559
Hin1I	GRCGYC	1 cut(s)	851
Hin1II	CATG	8 cut(s)	47, 242, 293, 538, 545, 746, 872, 941
Hin6I	GCGC	2 cut(s)	112, 557
HinP1I	GCGC	2 cut(s)	112, 557
HincII	GTYRAC	3 cut(s)	214, 451, 796
HindII	GTYRAC	3 cut(s)	214, 451, 796
HinfI	GANTC	5 cut(s)	4, 155, 620, 719, 1102
HpaI	GTTAAC	1 cut(s)	796
HpaII	CCGG	3 cut(s)	572, 639, 1020
HphI	GGTGA	4 cut(s)	167, 926, 973, 1097
Hpy166II	GTNNAC	4 cut(s)	214, 392, 451, 796
Hpy188I	TCNGA	4 cut(s)	433, 564, 595, 724
Hpy188III	TCNNGA	6 cut(s)	103, 185, 418, 482, 911, 1037
Hpy8I	GTNNAC	4 cut(s)	214, 392, 451, 796
HpyAV	CCTTC	1 cut(s)	963
HpyCH4III	ACNGT	2 cut(s)	182, 232
HpyCH4V	TGCA	3 cut(s)	247, 392, 820
HpyF10VI	GCNNNNNNNGC	5 cut(s)	92, 307, 368, 516, 565
HpyF3I	CTNAG	5 cut(s)	302, 354, 454, 561, 833
Hsp92I	GRCGYC	1 cut(s)	851
Hsp92II	CATG	8 cut(s)	47, 242, 293, 538, 545, 746, 872, 941
HspAI	GCGC	2 cut(s)	112, 557
Ksp22I	TGATCA	2 cut(s)	25, 961
KspAI	GTTAAC	1 cut(s)	796
Kzo9I	GATC	5 cut(s)	25, 274, 373, 707, 961
LmnI	GCTCC	3 cut(s)	60, 91, 686
Lsp1109I	GCAGC	2 cut(s)	599, 703
LweI	GCATC	1 cut(s)	519
MaeI	CTAG	1 cut(s)	33
MaeIII	GTNAC	3 cut(s)	313, 482, 932
MalI	GATC	5 cut(s)	27, 276, 375, 709, 963
MboI	GATC	5 cut(s)	25, 274, 373, 707, 961
MboII	GAAGA	5 cut(s)	269, 576, 805, 1001, 1070
MhlI	GDGCHC	2 cut(s)	394, 683
MluCI	AATT	1 cut(s)	664
MlyI	GAGTC	2 cut(s)	614, 728
MmeI	TCCRAC	1 cut(s)	702
MnlI	CCTC	8 cut(s)	21, 99, 353, 489, 498, 524, 570, 1047
MseI	TTAA	4 cut(s)	78, 252, 657, 795
MspI	CCGG	3 cut(s)	572, 639, 1020
MspR9I	CCNGG	1 cut(s)	15
Mva1269I	GAATGC	1 cut(s)	114
MvaI	CCWGG	1 cut(s)	15
MwoI	GCNNNNNNNGC	5 cut(s)	92, 307, 368, 516, 565
NcoI	CCATGG	2 cut(s)	238, 534
NdeI	CATATG	1 cut(s)	1098
NdeII	GATC	5 cut(s)	25, 274, 373, 707, 961
NlaIII	CATG	8 cut(s)	47, 242, 293, 538, 545, 746, 872, 941
NlaIV	GGNNCC	3 cut(s)	87, 403, 532
NmeAIII	GCCGAG	1 cut(s)	742
NmuCI	GTSAC	2 cut(s)	482, 932
PaeR7I	CTCGAG	1 cut(s)	90
PctI	GAATGC	1 cut(s)	114
PfeI	GAWTC	2 cut(s)	155, 1102
PflMI	CCANNNNNTGG	1 cut(s)	148
PinAI	ACCGGT	1 cut(s)	571
PkrI	GCNGC	2 cut(s)	614, 693
Ple19I	CGATCG	1 cut(s)	710
PleI	GAGTC	2 cut(s)	614, 727
PpsI	GAGTC	2 cut(s)	614, 727
PshAI	GACNNNNGTC	1 cut(s)	624
PshBI	ATTAAT	1 cut(s)	252
Psp6I	CCWGG	1 cut(s)	13
PspGI	CCWGG	1 cut(s)	13
PspN4I	GGNNCC	3 cut(s)	87, 403, 532
PspPI	GGNCC	1 cut(s)	64
PspXI	VCTCGAGB	1 cut(s)	90
PvuI	CGATCG	1 cut(s)	710
SaqAI	TTAA	4 cut(s)	78, 252, 657, 795
SatI	GCNGC	2 cut(s)	613, 692
Sau3AI	GATC	5 cut(s)	25, 274, 373, 707, 961
Sau96I	GGNCC	1 cut(s)	64
SchI	GAGTC	2 cut(s)	614, 728
ScrFI	CCNGG	1 cut(s)	15
SduI	GDGCHC	2 cut(s)	394, 683
SetI	ASST	8 cut(s)	13, 57, 345, 696, 845, 894, 921, 1110
SfaNI	GCATC	1 cut(s)	519
Sfr274I	CTCGAG	1 cut(s)	90
SlaI	CTCGAG	1 cut(s)	90
SmlI	CTYRAG	1 cut(s)	90
SmoI	CTYRAG	1 cut(s)	90
Sse9I	AATT	1 cut(s)	664
SsiI	CCGC	5 cut(s)	446, 517, 608, 989, 1043
SspMI	CTAG	1 cut(s)	33
StyD4I	CCNGG	1 cut(s)	13
StyI	CCWWGG	2 cut(s)	238, 534
TaaI	ACNGT	2 cut(s)	182, 232
TaqI	TCGA	3 cut(s)	91, 706, 710
TasI	AATT	1 cut(s)	664
TfiI	GAWTC	2 cut(s)	155, 1102
Tru1I	TTAA	4 cut(s)	78, 252, 657, 795
Tru9I	TTAA	4 cut(s)	78, 252, 657, 795
TseFI	GTSAC	2 cut(s)	482, 932
TseI	GCWGC	2 cut(s)	612, 691
Tsp45I	GTSAC	2 cut(s)	482, 932
TspDTI	ATGAA	7 cut(s)	157, 185, 215, 566, 798, 857, 937
TspGWI	ACGGA	1 cut(s)	779
Van91I	CCANNNNNTGG	1 cut(s)	148
VneI	GTGCAC	1 cut(s)	390
VspI	ATTAAT	1 cut(s)	252
XagI	CCTNNNNNAGG	1 cut(s)	80
XhoI	CTCGAG	1 cut(s)	90
XspI	CTAG	1 cut(s)	33

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