Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0000756

Physical Location & Seq

Genomic Coordinates Forward (+)

3333921 .. 3335771

Gene Structure 1851 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00280870.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 873 bp

ATGCCTGAGAGCATTATCAGTGATAGGGATCCCATATTTCTCAGTGCATTTTGGAAAAATTTCTTTGAATTACAAGGGTCAAAGCTGTGTATGAGTACCGCATACCATCCGCAAACTGACGGTCAAACTGAATGCTTAAATAGAGTCTTGGAACAATATTTAAGATGTGTGATTTTGGAGGAGAAAGGTCACTGGACAGATATTTTGCCTTGGGCCGAGTGGTGGTACAATACCACTTATCACTCAACTATTAAGATGTCTCCTTATCAAGCTCTTTATGGAATTCCTCCTCCTCAAGTGAGAAAATATGTCCCTGGTAGTACTGCTGTTCATCAAGTGGATCTAGTACTGAGGAACAGAGATGAATTACTAAGCAAGCTCAAGTGTAACATGGAACAAGCTCAGGCCAGAATGAAGGTTTACTATGACAAACGTCACACCGAAAGAGAGTTTGACATTGGTGATTGGGTATTCCTCAAATTGCAGCCATACAAACAAAAGTCAGTGCAGGTTAGGAAATCCCACAAATTGTCTCCAAAATACTTTGGTCCTTATCAGGTGATAGAAAAGATTGGTAAAGTGGCATACAAGTTAGAGCTCCCCGCTTCTGCGAGGGTGCATCCAGTGTTTCATGTATCTCTTCTAAAGAAGAAACTTGGAAGCTCAGTGGTTCCTTCTCCAACCTTGCCTCCTAGTTTTGATACCAACAAGAGCAATTGGGTTCCTGCCAAGGTGCTTCAGCGAGCTTTATTCAAGAATGGTAACAAACCTGAGGTGAGATGGTTGATTCAATGGAAGAATGGTTCAGAGGATGATGCCACGTGGGAATGTGCAGAAGAATTTCAGAAGCGTTTTCCAGATTTTAAGGGGTAA

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

Chromo RVP_2 RVT_1 Retrotrans_gag rve

Protein Analysis

290

Amino Acids

33.91

Weight (kDa)

9.29

Isoelectric Point (pI)

47.99

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SH3_Tf2-1	PF24626	154 - 217	5.3e-26	Tf2-1-like, SH3 domain
Integrase_p58_C	PF22938	183 - 217	6.3e-06	Integrase p58, C-terminal 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

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Orthologous Genes (Group: OG0000756)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G00155
fragaria_vesca	FvH4_2g19791 FvH4_3g30422 FvH4_3g30933 FvH4_3g30934 FvH4_3g31635 FvH4_4g05353 FvH4_4g06571 FvH4_4g06572 FvH4_4g06573 FvH4_4g08682 FvH4_4g12501 FvH4_5g33111 FvH4_6g20641 FvH4_6g22262 FvH4_6g24731 FvH4_6g52751
pyrus_communis	pycom10g18150
rosa_chinensis	RchiOBHm_Chr1g0321671 RchiOBHm_Chr2g0126521 RchiOBHm_Chr3g0451511 RchiOBHm_Chr3g0473251 RchiOBHm_Chr4g0397431 RchiOBHm_Chr4g0399101 RchiOBHm_Chr4g0399111 RchiOBHm_Chr4g0414841 RchiOBHm_Chr5g0021471 RchiOBHm_Chr5g0021481 RchiOBHm_Chr5g0075951 RchiOBHm_Chr5g0078051 RchiOBHm_Chr6g0286161 RchiOBHm_Chr6g0286171 RchiOBHm_Chr7g0185771
rosa_laevigata	RLG00000010238 RLG00000030464
rosa_roxburghii	Rroxscaffold_1G00071870 Rroxscaffold_2G00080460 Rroxscaffold_2G00085610 Rroxscaffold_2G00093090 Rroxscaffold_2G00134320 Rroxscaffold_3G00238340 Rroxscaffold_3G00255160 Rroxscaffold_4G00280870 Rroxscaffold_6G00402930 Rroxscaffold_6G00428840 Rroxscaffold_7G00197340
rosa_samantha	Rh3CG229300 Rh7BG226300
rosa_wichuraiana	Rw0G002510 Rw0G003200 Rw0G021820 Rw0G023810 Rw1G014640 Rw2G004390 Rw2G007910 Rw2G018470 Rw2G037630 Rw2G044860 Rw2G053420 Rw3G002230 Rw3G028200 Rw4G004770 Rw4G006640 Rw5G005440 Rw5G024120 Rw5G028050 Rw5G028410 Rw6G004650 Rw6G019400 Rw7G026910

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	499
AciI	CCGC	3 cut(s)	99, 110, 603
AclWI	GGATC	3 cut(s)	23, 36, 348
AcsI	RAATTY	3 cut(s)	58, 282, 839
AcuI	CTGAAG	1 cut(s)	722
AcvI	CACGTG	1 cut(s)	822
AfaI	GTAC	4 cut(s)	97, 227, 322, 348
AfiI	CCNNNNNNNGG	1 cut(s)	222
AgsI	TTSAA	3 cut(s)	68, 754, 791
AjnI	CCWGG	1 cut(s)	313
AloI	GAACNNNNNNTCC	2 cut(s)	787, 819
AluBI	AGCT	7 cut(s)	85, 272, 379, 401, 598, 663, 746
AluI	AGCT	7 cut(s)	85, 272, 379, 401, 598, 663, 746
Alw21I	GWGCWC	1 cut(s)	600
Alw26I	GTCTC	2 cut(s)	264, 537
AlwI	GGATC	3 cut(s)	23, 36, 348
AoxI	GGCC	2 cut(s)	213, 405
ApeKI	GCWGC	1 cut(s)	484
ApoI	RAATTY	3 cut(s)	58, 282, 839
ArsI	GACNNNNNNTTYG	4 cut(s)	106, 138, 187, 219
Asp700I	GAANNNNTTC	2 cut(s)	59, 840
AspS9I	GGNCC	2 cut(s)	213, 548
AsuHPI	GGTGA	3 cut(s)	473, 571, 787
AvaII	GGWCC	1 cut(s)	548
AxyI	CCTNAGG	1 cut(s)	771
BamHI	GGATCC	1 cut(s)	28
BanII	GRGCYC	1 cut(s)	600
BbrPI	CACGTG	1 cut(s)	822
Bbv12I	GWGCWC	1 cut(s)	600
BbvI	GCAGC	1 cut(s)	496
BccI	CCATC	2 cut(s)	114, 774
BciT130I	CCWGG	1 cut(s)	315
BcoDI	GTCTC	2 cut(s)	264, 537
BfaI	CTAG	2 cut(s)	344, 693
BfuAI	ACCTGC	1 cut(s)	499
BisI	GCNGC	1 cut(s)	485
BlsI	GCNGC	1 cut(s)	486
BmcAI	AGTACT	2 cut(s)	322, 348
Bme1390I	CCNGG	1 cut(s)	315
Bme18I	GGWCC	1 cut(s)	548
BmgT120I	GGNCC	2 cut(s)	213, 548
BmiI	GGNNCC	3 cut(s)	30, 672, 723
BmrFI	CCNGG	1 cut(s)	315
BmsI	GCATC	2 cut(s)	628, 805
BoxI	GACNNNNGTC	1 cut(s)	432
Bpu10I	CCTNAGC	1 cut(s)	402
BpuEI	CTTGAG	2 cut(s)	279, 365
BsaAI	YACGTR	1 cut(s)	822
BsaBI	GATNNNNATC	1 cut(s)	27
BsaJI	CCNNGG	3 cut(s)	209, 313, 729
BsaXI	ACNNNNNCTCC	2 cut(s)	673, 703
Bsc4I	CCNNNNNNNGG	1 cut(s)	222
Bse1I	ACTGG	2 cut(s)	197, 623
Bse21I	CCTNAGG	1 cut(s)	771
Bse8I	GATNNNNATC	1 cut(s)	27
BseBI	CCWGG	1 cut(s)	315
BseDI	CCNNGG	3 cut(s)	209, 313, 729
BseGI	GGATG	3 cut(s)	106, 619, 817
BseJI	GATNNNNATC	1 cut(s)	27
BseLI	CCNNNNNNNGG	1 cut(s)	222
BseMII	CTCAG	5 cut(s)	55, 341, 416, 678, 762
BseNI	ACTGG	2 cut(s)	197, 623
BseRI	GAGGAG	3 cut(s)	194, 279, 282
BseXI	GCAGC	1 cut(s)	496
BsgI	GTGCAG	2 cut(s)	527, 852
BshFI	GGCC	2 cut(s)	215, 407
BsiHKAI	GWGCWC	1 cut(s)	600
BslFI	GGGAC	1 cut(s)	296
BslI	CCNNNNNNNGG	1 cut(s)	222
BsmAI	GTCTC	2 cut(s)	264, 537
BsmFI	GGGAC	1 cut(s)	296
BsmI	GAATGC	1 cut(s)	137
BsnI	GGCC	2 cut(s)	215, 407
Bsp1286I	GDGCHC	1 cut(s)	600
Bsp143I	GATC	2 cut(s)	28, 340
BspACI	CCGC	3 cut(s)	99, 110, 603
BspANI	GGCC	2 cut(s)	215, 407
BspCNI	CTCAG	5 cut(s)	54, 342, 415, 677, 763
BspLI	GGNNCC	3 cut(s)	30, 672, 723
BspMI	ACCTGC	1 cut(s)	499
BspPI	GGATC	3 cut(s)	23, 36, 348
BsrI	ACTGG	2 cut(s)	197, 623
BssECI	CCNNGG	3 cut(s)	209, 313, 729
BssMI	GATC	2 cut(s)	28, 340
BssT1I	CCWWGG	2 cut(s)	209, 729
Bst2UI	CCWGG	1 cut(s)	315
Bst4CI	ACNGT	1 cut(s)	122
Bst6I	CTCTTC	1 cut(s)	645
BstBAI	YACGTR	1 cut(s)	822
BstC8I	GCNNGC	2 cut(s)	377, 744
BstDEI	CTNAG	7 cut(s)	6, 41, 350, 371, 402, 664, 771
BstF5I	GGATG	3 cut(s)	106, 619, 817
BstKTI	GATC	2 cut(s)	31, 343
BstMAI	GTCTC	2 cut(s)	264, 537
BstMBI	GATC	2 cut(s)	28, 340
BstNI	CCWGG	1 cut(s)	315
BstPAI	GACNNNNGTC	1 cut(s)	432
BstSCI	CCNGG	1 cut(s)	313
BstV1I	GCAGC	1 cut(s)	496
BstX2I	RGATCY	2 cut(s)	28, 340
BstYI	RGATCY	2 cut(s)	28, 340
Bsu36I	CCTNAGG	1 cut(s)	771
BsuRI	GGCC	2 cut(s)	215, 407
BtsCI	GGATG	3 cut(s)	106, 619, 817
BtsIMutI	CAGTG	6 cut(s)	25, 49, 190, 510, 630, 672
BveI	ACCTGC	1 cut(s)	499
Cac8I	GCNNGC	2 cut(s)	377, 744
Cfr13I	GGNCC	2 cut(s)	213, 548
Csp6I	GTAC	4 cut(s)	96, 226, 321, 347
CviAII	CATG	2 cut(s)	391, 632
CviQI	GTAC	4 cut(s)	96, 226, 321, 347
DdeI	CTNAG	7 cut(s)	6, 41, 350, 371, 402, 664, 771
DpnI	GATC	2 cut(s)	30, 342
DpnII	GATC	2 cut(s)	28, 340
Eam1104I	CTCTTC	1 cut(s)	645
EarI	CTCTTC	1 cut(s)	645
Ecl136II	GAGCTC	1 cut(s)	598
Eco130I	CCWWGG	2 cut(s)	209, 729
Eco24I	GRGCYC	1 cut(s)	600
Eco47I	GGWCC	1 cut(s)	548
Eco53kI	GAGCTC	1 cut(s)	598
Eco57I	CTGAAG	1 cut(s)	722
Eco72I	CACGTG	1 cut(s)	822
Eco81I	CCTNAGG	1 cut(s)	771
EcoICRI	GAGCTC	1 cut(s)	598
EcoRI	GAATTC	1 cut(s)	282
EcoRII	CCWGG	1 cut(s)	313
EcoT14I	CCWWGG	2 cut(s)	209, 729
EcoT38I	GRGCYC	1 cut(s)	600
ErhI	CCWWGG	2 cut(s)	209, 729
FaeI	CATG	2 cut(s)	394, 635
FaqI	GGGAC	1 cut(s)	296
FatI	CATG	2 cut(s)	390, 631
FauI	CCCGC	1 cut(s)	610
Fnu4HI	GCNGC	1 cut(s)	485
FokI	GGATG	3 cut(s)	93, 606, 824
FriOI	GRGCYC	1 cut(s)	600
Fsp4HI	GCNGC	1 cut(s)	485
FspBI	CTAG	2 cut(s)	344, 693
GluI	GCNGC	1 cut(s)	485
HaeIII	GGCC	2 cut(s)	215, 407
Hin1II	CATG	2 cut(s)	394, 635
HinfI	GANTC	2 cut(s)	144, 787
HphI	GGTGA	3 cut(s)	473, 571, 787
Hpy166II	GTNNAC	1 cut(s)	421
Hpy188I	TCNGA	2 cut(s)	808, 846
Hpy188III	TCNNGA	2 cut(s)	754, 857
Hpy8I	GTNNAC	1 cut(s)	421
HpyAV	CCTTC	2 cut(s)	409, 684
HpyCH4III	ACNGT	1 cut(s)	122
HpyCH4IV	ACGT	2 cut(s)	433, 821
HpyCH4V	TGCA	5 cut(s)	47, 484, 508, 619, 833
HpyF3I	CTNAG	7 cut(s)	6, 41, 350, 371, 402, 664, 771
HpySE526I	ACGT	2 cut(s)	433, 821
Hsp92II	CATG	2 cut(s)	394, 635
Kzo9I	GATC	2 cut(s)	28, 340
LmnI	GCTCC	1 cut(s)	603
Lsp1109I	GCAGC	1 cut(s)	496
LweI	GCATC	2 cut(s)	628, 805
MaeI	CTAG	2 cut(s)	344, 693
MaeII	ACGT	2 cut(s)	433, 821
MaeIII	GTNAC	4 cut(s)	188, 386, 434, 761
MalI	GATC	2 cut(s)	30, 342
MboI	GATC	2 cut(s)	28, 340
MboII	GAAGA	4 cut(s)	632, 661, 808, 848
MfeI	CAATTG	1 cut(s)	715
MflI	RGATCY	2 cut(s)	28, 340
MhlI	GDGCHC	1 cut(s)	600
MluCI	AATT	8 cut(s)	58, 68, 282, 365, 479, 527, 715, 839
MlyI	GAGTC	1 cut(s)	153
MmeI	TCCRAC	1 cut(s)	704
MroXI	GAANNNNTTC	2 cut(s)	59, 840
MseI	TTAA	4 cut(s)	137, 161, 252, 864
MspR9I	CCNGG	1 cut(s)	315
MunI	CAATTG	1 cut(s)	715
Mva1269I	GAATGC	1 cut(s)	137
MvaI	CCWGG	1 cut(s)	315
NdeII	GATC	2 cut(s)	28, 340
NlaIII	CATG	2 cut(s)	394, 635
NlaIV	GGNNCC	3 cut(s)	30, 672, 723
NmeAIII	GCCGAG	1 cut(s)	241
NmuCI	GTSAC	2 cut(s)	188, 434
PctI	GAATGC	1 cut(s)	137
PdmI	GAANNNNTTC	2 cut(s)	59, 840
PfeI	GAWTC	1 cut(s)	787
PkrI	GCNGC	1 cut(s)	486
PleI	GAGTC	1 cut(s)	152
PmaCI	CACGTG	1 cut(s)	822
PmlI	CACGTG	1 cut(s)	822
PpsI	GAGTC	1 cut(s)	152
Ppu21I	YACGTR	1 cut(s)	822
PshAI	GACNNNNGTC	1 cut(s)	432
Psp124BI	GAGCTC	1 cut(s)	600
Psp6I	CCWGG	1 cut(s)	313
PspCI	CACGTG	1 cut(s)	822
PspGI	CCWGG	1 cut(s)	313
PspN4I	GGNNCC	3 cut(s)	30, 672, 723
PspPI	GGNCC	2 cut(s)	213, 548
PsuI	RGATCY	2 cut(s)	28, 340
RsaI	GTAC	4 cut(s)	97, 227, 322, 348
RsaNI	GTAC	4 cut(s)	96, 226, 321, 347
SacI	GAGCTC	1 cut(s)	600
SaqAI	TTAA	4 cut(s)	137, 161, 252, 864
SatI	GCNGC	1 cut(s)	485
Sau3AI	GATC	2 cut(s)	28, 340
Sau96I	GGNCC	2 cut(s)	213, 548
ScaI	AGTACT	2 cut(s)	322, 348
SchI	GAGTC	1 cut(s)	153
ScrFI	CCNGG	1 cut(s)	315
SduI	GDGCHC	1 cut(s)	600
SfaNI	GCATC	2 cut(s)	628, 805
SinI	GGWCC	1 cut(s)	548
SmlI	CTYRAG	2 cut(s)	294, 380
SmoI	CTYRAG	2 cut(s)	294, 380
Sse9I	AATT	8 cut(s)	58, 68, 282, 365, 479, 527, 715, 839
SsiI	CCGC	3 cut(s)	99, 110, 603
SspI	AATATT	1 cut(s)	158
SspMI	CTAG	2 cut(s)	344, 693
SstI	GAGCTC	1 cut(s)	600
StyD4I	CCNGG	1 cut(s)	313
StyI	CCWWGG	2 cut(s)	209, 729
TaaI	ACNGT	1 cut(s)	122
TaiI	ACGT	2 cut(s)	436, 824
TasI	AATT	8 cut(s)	58, 68, 282, 365, 479, 527, 715, 839
TatI	WGTACW	2 cut(s)	320, 346
TfiI	GAWTC	1 cut(s)	787
Tru1I	TTAA	4 cut(s)	137, 161, 252, 864
Tru9I	TTAA	4 cut(s)	137, 161, 252, 864
TscAI	CASTG	6 cut(s)	25, 49, 197, 510, 630, 672
TseFI	GTSAC	2 cut(s)	188, 434
TseI	GCWGC	1 cut(s)	484
Tsp45I	GTSAC	2 cut(s)	188, 434
TspDTI	ATGAA	4 cut(s)	320, 378, 428, 620
TspRI	CASTG	6 cut(s)	25, 49, 197, 510, 630, 672
VpaK11BI	GGWCC	1 cut(s)	548
XapI	RAATTY	3 cut(s)	58, 282, 839
XmnI	GAANNNNTTC	2 cut(s)	59, 840
XspI	CTAG	2 cut(s)	344, 693
ZrmI	AGTACT	2 cut(s)	322, 348

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