Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000001

Orthogroup ID

OG0002557

Physical Location & Seq

Genomic Coordinates Forward (+)

1430831 .. 1435323

Gene Structure 4493 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_1G00001000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1044 bp

ATGCACACAATTTTACTCTTCCAAGGGCATTTTACATCAAACCGGTTGCATCAACACGCCCCAACGAATGGCGTCGCCGAGCGCAAACACGAGCACTTGTTGAACGTTGCTCGTGCACTTCTCTTTCAATCAAACTTGCCTAAATCATTTTGGGGGGATGCCATACTCACCGCTGCCTATCTAATAAATAGGACACCGACACCAATTTTGCAAGGTAAAACACCTTTTGAAACGTTATTTCACAAATCACCAAACTACTCTCATTTGCGTGTTTTTGGTTGTCGTTGCTTTGTGTCTACTCATCCACTCCGGCCCAGCAAGTTTGATCCACGCTCTACCGAGTGTATCTTCCTTGGTTACCCTCATGGTCAAAAGGGATATAAAGTCTATAGCCCGAAAGATAAGAAAATGTTAGTCTCACGAGATGTCATCTTCTTTGAAACCGAGTTTCCTTATCAATCCAAACTCTCCACATCTTCGCCTTCATCGGTCCTCCAACACCTCCTCAATTCTTTCCTTCTTTATCTACCTCCTCAATTCTTGACGATCAAATCTTCTCAAATCACTCGGAATCAAATCTTGATTCTAATCCCACAACTTCCGCCGATATCAATCCCACAAATCACTCGGAATCAAATCTTGATTCTAATCCCACAACTTCCGCCGATATTAATCCCACAAATCACTCGGAATCAAATCTTGATTCTAATCCCACAACTTCCGCTGATATCAATCCCACAAATCACTCGGATTCAAATATTCCACTATCTCATTTTCCAAATACGTCACCACCGGACTTATCCGTATCCCAAGATGCAATATCTCATTCTTCATTGTCACAACCACGAAGATCATCACGGCCAACTAGGACTCCAACCACATTGCAAGGCTTTCATATTGAGGCAGCCCTTCCTTCACGTACTGCACCATCATCTTCCACGAGCGAGGTTACTCATCCAGGTACCCCTCATTCTATTGCTCATGTTTTATCCTATGATAGACTCTCTCCTACACATAAAGCTTTCACCGTTAACATTACACTAG

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

Protein Analysis

347

Amino Acids

40.35

Weight (kDa)

10.05

Isoelectric Point (pI)

56.57

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SH3_retrovirus	PF25597	94 - 155	6.9e-25	Retroviral polymerase SH3-like domain

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)

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: OG0002557)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G48720
fragaria_vesca	FvH4_2g28692 FvH4_5g18842 FvH4_6g09151
malus_domestica	MD02G1224100.v1.1 MD05G1187300.v1.1 MD05G1333300.v1.1 MD11G1249500.v1.1 MD16G1029500.v1.1
prunus_persica	Prupe.5G008900_v2.0.a1 Prupe.6G200700_v2.0.a1 Prupe.7G019700_v2.0.a1
pyrus_communis	pycom01g03530 pycom02g12970 pycom02g19220 pycom05g10750 pycom09g02370 pycom10g16330 pycom14g07330 pycom15g16240
rosa_chinensis	RchiOBHm_Chr1g0340271 RchiOBHm_Chr1g0362001 RchiOBHm_Chr1g0382731 RchiOBHm_Chr2g0152171 RchiOBHm_Chr3g0480511 RchiOBHm_Chr4g0398841 RchiOBHm_Chr5g0081101 RchiOBHm_Chr7g0182361 RchiOBHm_Chr7g0237371
rosa_roxburghii	Rroxscaffold_160G00433850 Rroxscaffold_1G00001000 Rroxscaffold_1G00046300 Rroxscaffold_3G00252380 Rroxscaffold_3G00254550 Rroxscaffold_4G00320010 Rroxscaffold_4G00327310 Rroxscaffold_5G00336230 Rroxscaffold_7G00179260
rosa_samantha	Rh3BG173000
rosa_wichuraiana	Rw4G008490

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	961
AccB1I	GGYRCC	1 cut(s)	961
AccB7I	CCANNNNNTGG	1 cut(s)	68
AccI	GTMKAC	1 cut(s)	296
AciI	CCGC	4 cut(s)	171, 602, 662, 722
AclI	AACGTT	2 cut(s)	105, 233
AclWI	GGATC	1 cut(s)	320
AcoI	YGGCCR	1 cut(s)	859
AcyI	GRCGYC	1 cut(s)	72
AfaI	GTAC	2 cut(s)	921, 963
AfiI	CCNNNNNNNGG	1 cut(s)	68
AgeI	ACCGGT	1 cut(s)	42
AgsI	TTSAA	5 cut(s)	103, 128, 230, 440, 755
AjnI	CCWGG	1 cut(s)	957
AluBI	AGCT	1 cut(s)	1021
AluI	AGCT	1 cut(s)	1021
Alw21I	GWGCWC	2 cut(s)	96, 118
Alw26I	GTCTC	1 cut(s)	421
Alw44I	GTGCAC	1 cut(s)	114
AlwI	GGATC	1 cut(s)	320
AoxI	GGCC	2 cut(s)	311, 859
ApaLI	GTGCAC	1 cut(s)	114
ApeKI	GCWGC	2 cut(s)	173, 904
ArsI	GACNNNNNNTTYG	2 cut(s)	190, 222
AseI	ATTAAT	1 cut(s)	671
AsiGI	ACCGGT	1 cut(s)	42
Asp718I	GGTACC	1 cut(s)	961
AspLEI	GCGC	1 cut(s)	84
AspS9I	GGNCC	2 cut(s)	312, 490
AsuHPI	GGTGA	4 cut(s)	160, 240, 779, 1017
AvaII	GGWCC	1 cut(s)	490
BaeGI	GKGCMC	1 cut(s)	118
BanI	GGYRCC	1 cut(s)	961
BauI	CACGAG	4 cut(s)	89, 111, 420, 939
Bbv12I	GWGCWC	2 cut(s)	96, 118
BbvI	GCAGC	2 cut(s)	160, 916
BccI	CCATC	1 cut(s)	936
BceAI	ACGGC	1 cut(s)	874
BciT130I	CCWGG	1 cut(s)	959
BciVI	GTATCC	1 cut(s)	816
BcoDI	GTCTC	1 cut(s)	421
BfaI	CTAG	2 cut(s)	866, 1042
BfmI	CTRYAG	1 cut(s)	388
BfuI	GTATCC	1 cut(s)	816
BisI	GCNGC	2 cut(s)	174, 905
BlsI	GCNGC	2 cut(s)	175, 906
Bme1390I	CCNGG	1 cut(s)	959
Bme18I	GGWCC	1 cut(s)	490
BmgT120I	GGNCC	2 cut(s)	312, 490
BmiI	GGNNCC	1 cut(s)	963
BmrFI	CCNGG	1 cut(s)	959
BmsI	GCATC	3 cut(s)	58, 148, 804
BsaAI	YACGTR	1 cut(s)	919
BsaBI	GATNNNNATC	6 cut(s)	587, 611, 647, 671, 707, 731
BsaHI	GRCGYC	1 cut(s)	72
BsaJI	CCNNGG	2 cut(s)	22, 352
BsaWI	WCCGGW	2 cut(s)	42, 792
BsaXI	ACNNNNNCTCC	2 cut(s)	855, 885
Bsc4I	CCNNNNNNNGG	1 cut(s)	68
Bse118I	RCCGGY	1 cut(s)	42
Bse3DI	GCAATG	1 cut(s)	880
Bse8I	GATNNNNATC	6 cut(s)	587, 611, 647, 671, 707, 731
BseBI	CCWGG	1 cut(s)	959
BseDI	CCNNGG	2 cut(s)	22, 352
BseGI	GGATG	3 cut(s)	163, 301, 954
BseJI	GATNNNNATC	6 cut(s)	587, 611, 647, 671, 707, 731
BseLI	CCNNNNNNNGG	1 cut(s)	68
BseMI	GCAATG	1 cut(s)	880
BseRI	GAGGAG	2 cut(s)	494, 522
BseSI	GKGCMC	1 cut(s)	118
BseXI	GCAGC	2 cut(s)	160, 916
BseYI	CCCAGC	1 cut(s)	314
BsgI	GTGCAG	1 cut(s)	908
BshFI	GGCC	2 cut(s)	313, 861
BshNI	GGYRCC	1 cut(s)	961
BshTI	ACCGGT	1 cut(s)	42
BsiHKAI	GWGCWC	2 cut(s)	96, 118
BsiSI	CCGG	3 cut(s)	43, 310, 793
BslI	CCNNNNNNNGG	1 cut(s)	68
BsmAI	GTCTC	1 cut(s)	421
BsnI	GGCC	2 cut(s)	313, 861
Bsp1286I	GDGCHC	2 cut(s)	96, 118
Bsp143I	GATC	3 cut(s)	325, 546, 850
BspACI	CCGC	4 cut(s)	171, 602, 662, 722
BspANI	GGCC	2 cut(s)	313, 861
BspLI	GGNNCC	1 cut(s)	963
BspPI	GGATC	1 cut(s)	320
BspT107I	GGYRCC	1 cut(s)	961
BsrDI	GCAATG	1 cut(s)	880
BsrFI	RCCGGY	1 cut(s)	42
BssAI	RCCGGY	1 cut(s)	42
BssECI	CCNNGG	2 cut(s)	22, 352
BssMI	GATC	3 cut(s)	325, 546, 850
BssNI	GRCGYC	1 cut(s)	72
BssSI	CACGAG	4 cut(s)	89, 111, 420, 939
BssT1I	CCWWGG	2 cut(s)	22, 352
Bst2BI	CACGAG	4 cut(s)	89, 111, 420, 939
Bst2UI	CCWGG	1 cut(s)	959
Bst4CI	ACNGT	1 cut(s)	1029
Bst6I	CTCTTC	1 cut(s)	23
BstACI	GRCGYC	1 cut(s)	72
BstBAI	YACGTR	1 cut(s)	919
BstEII	GGTNACC	1 cut(s)	356
BstF5I	GGATG	3 cut(s)	163, 301, 954
BstHHI	GCGC	1 cut(s)	84
BstKTI	GATC	3 cut(s)	328, 549, 853
BstMAI	GTCTC	1 cut(s)	421
BstMBI	GATC	3 cut(s)	325, 546, 850
BstNI	CCWGG	1 cut(s)	959
BstPI	GGTNACC	1 cut(s)	356
BstSCI	CCNGG	1 cut(s)	957
BstSFI	CTRYAG	1 cut(s)	388
BstSLI	GKGCMC	1 cut(s)	118
BstV1I	GCAGC	2 cut(s)	160, 916
BsuI	GTATCC	1 cut(s)	816
BsuRI	GGCC	2 cut(s)	313, 861
BtsCI	GGATG	3 cut(s)	163, 301, 954
CfoI	GCGC	1 cut(s)	84
Cfr10I	RCCGGY	1 cut(s)	42
Cfr13I	GGNCC	2 cut(s)	312, 490
CseI	GACGC	1 cut(s)	61
Csp6I	GTAC	2 cut(s)	920, 962
CspAI	ACCGGT	1 cut(s)	42
CviAII	CATG	2 cut(s)	365, 982
CviJI	RGCY	6 cut(s)	313, 393, 861, 890, 907, 1021
CviKI_1	RGCY	6 cut(s)	313, 393, 861, 890, 907, 1021
CviQI	GTAC	2 cut(s)	920, 962
DpnI	GATC	3 cut(s)	327, 548, 852
DpnII	GATC	3 cut(s)	325, 546, 850
EaeI	YGGCCR	1 cut(s)	859
Eam1104I	CTCTTC	1 cut(s)	23
EarI	CTCTTC	1 cut(s)	23
EciI	GGCGGA	2 cut(s)	591, 651
Eco130I	CCWWGG	2 cut(s)	22, 352
Eco32I	GATATC	2 cut(s)	609, 729
Eco47I	GGWCC	1 cut(s)	490
Eco91I	GGTNACC	1 cut(s)	356
EcoO65I	GGTNACC	1 cut(s)	356
EcoRII	CCWGG	1 cut(s)	957
EcoRV	GATATC	2 cut(s)	609, 729
EcoT14I	CCWWGG	2 cut(s)	22, 352
ErhI	CCWWGG	2 cut(s)	22, 352
FaeI	CATG	2 cut(s)	368, 985
FaiI	YATR	8 cut(s)	164, 366, 381, 390, 896, 983, 995, 1016
FatI	CATG	2 cut(s)	364, 981
FblI	GTMKAC	1 cut(s)	296
Fnu4HI	GCNGC	2 cut(s)	174, 905
FokI	GGATG	3 cut(s)	170, 288, 941
Fsp4HI	GCNGC	2 cut(s)	174, 905
FspBI	CTAG	2 cut(s)	866, 1042
GlaI	GCGC	1 cut(s)	83
GluI	GCNGC	2 cut(s)	174, 905
GsaI	CCCAGC	1 cut(s)	318
HaeIII	GGCC	2 cut(s)	313, 861
HapII	CCGG	3 cut(s)	43, 310, 793
HgaI	GACGC	1 cut(s)	61
HhaI	GCGC	1 cut(s)	84
Hin1I	GRCGYC	1 cut(s)	72
Hin1II	CATG	2 cut(s)	368, 985
Hin6I	GCGC	1 cut(s)	82
HinP1I	GCGC	1 cut(s)	82
HincII	GTYRAC	1 cut(s)	1032
HindII	GTYRAC	1 cut(s)	1032
HindIII	AAGCTT	1 cut(s)	1019
HinfI	GANTC	9 cut(s)	571, 583, 631, 643, 691, 703, 751, 870, 1001
HpaI	GTTAAC	1 cut(s)	1032
HpaII	CCGG	3 cut(s)	43, 310, 793
HphI	GGTGA	4 cut(s)	160, 240, 779, 1017
Hpy166II	GTNNAC	3 cut(s)	116, 297, 1032
Hpy188I	TCNGA	4 cut(s)	570, 630, 690, 750
Hpy188III	TCNNGA	5 cut(s)	420, 541, 580, 640, 700
Hpy8I	GTNNAC	3 cut(s)	116, 297, 1032
Hpy99I	CGWCG	1 cut(s)	77
HpyAV	CCTTC	4 cut(s)	492, 527, 919, 923
HpyCH4III	ACNGT	1 cut(s)	1029
HpyCH4IV	ACGT	4 cut(s)	105, 233, 784, 918
HpyCH4V	TGCA	7 cut(s)	4, 49, 116, 211, 817, 885, 925
HpySE526I	ACGT	4 cut(s)	105, 233, 784, 918
Hsp92I	GRCGYC	1 cut(s)	72
Hsp92II	CATG	2 cut(s)	368, 985
HspAI	GCGC	1 cut(s)	82
KpnI	GGTACC	1 cut(s)	965
KspAI	GTTAAC	1 cut(s)	1032
Kzo9I	GATC	3 cut(s)	325, 546, 850
LpnPI	CCDG	6 cut(s)	56, 323, 328, 806, 944, 971
Lsp1109I	GCAGC	2 cut(s)	160, 916
LweI	GCATC	3 cut(s)	58, 148, 804
MaeI	CTAG	2 cut(s)	866, 1042
MaeII	ACGT	4 cut(s)	105, 233, 784, 918
MaeIII	GTNAC	4 cut(s)	356, 785, 836, 948
MalI	GATC	3 cut(s)	327, 548, 852
MboI	GATC	3 cut(s)	325, 546, 850
MboII	GAAGA	8 cut(s)	10, 340, 424, 468, 546, 821, 860, 926
MhlI	GDGCHC	2 cut(s)	96, 118
MluCI	AATT	4 cut(s)	9, 204, 508, 536
MlyI	GAGTC	2 cut(s)	864, 995
MmeI	TCCRAC	2 cut(s)	520, 898
MnlI	CCTC	9 cut(s)	372, 503, 512, 515, 540, 543, 894, 939, 977
MseI	TTAA	2 cut(s)	671, 1031
MslI	CAYNNNNRTG	1 cut(s)	267
MspA1I	CMGCKG	2 cut(s)	173, 724
MspI	CCGG	3 cut(s)	43, 310, 793
MspR9I	CCNGG	1 cut(s)	959
MvaI	CCWGG	1 cut(s)	959
NdeII	GATC	3 cut(s)	325, 546, 850
NlaIII	CATG	2 cut(s)	368, 985
NlaIV	GGNNCC	1 cut(s)	963
NmeAIII	GCCGAG	1 cut(s)	103
NmuCI	GTSAC	2 cut(s)	785, 836
PfeI	GAWTC	7 cut(s)	571, 583, 631, 643, 691, 703, 751
PflMI	CCANNNNNTGG	1 cut(s)	68
PinAI	ACCGGT	1 cut(s)	42
PkrI	GCNGC	2 cut(s)	175, 906
PleI	GAGTC	2 cut(s)	864, 995
PpsI	GAGTC	2 cut(s)	864, 995
Ppu21I	YACGTR	1 cut(s)	919
PshBI	ATTAAT	1 cut(s)	671
Psp1406I	AACGTT	2 cut(s)	105, 233
Psp6I	CCWGG	1 cut(s)	957
PspEI	GGTNACC	1 cut(s)	356
PspFI	CCCAGC	1 cut(s)	314
PspGI	CCWGG	1 cut(s)	957
PspN4I	GGNNCC	1 cut(s)	963
PspPI	GGNCC	2 cut(s)	312, 490
RsaI	GTAC	2 cut(s)	921, 963
RsaNI	GTAC	2 cut(s)	920, 962
RseI	CAYNNNNRTG	1 cut(s)	267
SaqAI	TTAA	2 cut(s)	671, 1031
SatI	GCNGC	2 cut(s)	174, 905
Sau3AI	GATC	3 cut(s)	325, 546, 850
Sau96I	GGNCC	2 cut(s)	312, 490
SchI	GAGTC	2 cut(s)	864, 995
ScrFI	CCNGG	1 cut(s)	959
SduI	GDGCHC	2 cut(s)	96, 118
SfaNI	GCATC	3 cut(s)	58, 148, 804
SfcI	CTRYAG	1 cut(s)	388
SinI	GGWCC	1 cut(s)	490
SmiMI	CAYNNNNRTG	1 cut(s)	267
Sse9I	AATT	4 cut(s)	9, 204, 508, 536
SsiI	CCGC	4 cut(s)	171, 602, 662, 722
SspI	AATATT	1 cut(s)	759
SspMI	CTAG	2 cut(s)	866, 1042
StyD4I	CCNGG	1 cut(s)	957
StyI	CCWWGG	2 cut(s)	22, 352
TaaI	ACNGT	1 cut(s)	1029
TaiI	ACGT	4 cut(s)	108, 236, 787, 921
TaqII	GACCGA	1 cut(s)	478
TasI	AATT	4 cut(s)	9, 204, 508, 536
TfiI	GAWTC	7 cut(s)	571, 583, 631, 643, 691, 703, 751
Tru1I	TTAA	2 cut(s)	671, 1031
Tru9I	TTAA	2 cut(s)	671, 1031
TseFI	GTSAC	2 cut(s)	785, 836
TseI	GCWGC	2 cut(s)	173, 904
Tsp45I	GTSAC	2 cut(s)	785, 836
TspDTI	ATGAA	3 cut(s)	474, 821, 883
TspGWI	ACGGA	1 cut(s)	792
Van91I	CCANNNNNTGG	1 cut(s)	68
VneI	GTGCAC	1 cut(s)	114
VpaK11BI	GGWCC	1 cut(s)	490
VspI	ATTAAT	1 cut(s)	671
XmiI	GTMKAC	1 cut(s)	296
XspI	CTAG	2 cut(s)	866, 1042

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