Basic Information

Type: gene

Biological Identity

Species

fragaria_vesca

Chromosome

Fvb5

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

12997407 .. 13000321

Gene Structure 2915 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

FvH4_5g21560.t1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 621 bp

ATGGCTCTATCAGAAGAAGAAATCACAAGGCTTTACAGAGTTCGAAGAACGGTGATGCAAATGTTGAAAGATGGGGAGTATTTAGTTACAGAATCTGATATCAACATGACAAAAGAACAATTCAGGAGCACATATGGAGAGAACATGAAAAGGGAAGATCTAGACATCAATAAAGAAAAGCGGAGTGACAGCTCTGATCAGATATATGTCTTCTTCCCTAATGAAGCCAAGGTTGGGGTAAATACAATGAGGGACTACACCAAGCGCATGCAGTCGCAGAATGTGTTCAGAGCAATCTTGGTGTCTCAAACAAAGCTGACTCCTTTCGCAACCAGATGTATAAGTGAGATGTCTACAAGGTTCCAGATGGAGGTTTTCCAGGAAGCAGAACTGTTGGTGAATATTAAAGAGCATGTTCTAGTTCCTGAGCATCAGGTGCTTACAAATGAGGAAAAGAAGACTCTGCTGCAGAGGTATACCGTGAAAGAAACACAGCTTCCTCGGATGCAGGTGATAGATCCAATCGCAAGGTATTACGGGCTTACACGTGGACAAGTTGTGAAGATAATCAGGCCAAGTGAGACTGCTGGAAGATATGTCACCTACCGTTATGTTGTTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006366 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb5_C RNA_pol_Rpb5_N

Protein Analysis

207

Amino Acids

24.37

Weight (kDa)

9.06

Isoelectric Point (pI)

41.22

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	5 - 90	1.6e-30	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	133 - 205	4.6e-35	RNA polymerase Rpb5, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000701)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G22320
fragaria_vesca	FvH4_5g21560 FvH4_7g09301 FvH4_7g09301
malus_domestica	MD02G1080800.v1.1 MD02G1093900.v1.1 MD15G1208600.v1.1
prunus_persica	Prupe.2G121300_v2.0.a1 Prupe.2G121300_v2.0.a1 Prupe.2G121400_v2.0.a1 Prupe.2G121400_v2.0.a1
pyrus_communis	pycom02g06410 pycom02g07430 pycom15g18470
rosa_chinensis	RchiOBHm_Chr1g0332791 RchiOBHm_Chr1g0344101 RchiOBHm_Chr1g0344151 RchiOBHm_Chr1g0344171 RchiOBHm_Chr1g0345361 RchiOBHm_Chr1g0345421 RchiOBHm_Chr1g0345561 RchiOBHm_Chr1g0345591 RchiOBHm_Chr1g0345671 RchiOBHm_Chr1g0345701 RchiOBHm_Chr1g0345711 RchiOBHm_Chr1g0345721 RchiOBHm_Chr1g0345801 RchiOBHm_Chr1g0345851 RchiOBHm_Chr1g0345901 RchiOBHm_Chr1g0345921 RchiOBHm_Chr1g0345931 RchiOBHm_Chr1g0345951 RchiOBHm_Chr1g0345961 RchiOBHm_Chr7g0208981
rosa_laevigata	RLG00000003175 RLG00000029644
rosa_multiflora	Rmu_co8382943.1_g000001 Rmu_sc0000532.1_g000035 Rmu_sc0001292.1_g000003 Rmu_sc0001349.1_g000004 Rmu_sc0001692.1_g000006 Rmu_sc0001692.1_g000027 Rmu_sc0002329.1_g000024 Rmu_sc0002329.1_g000032 Rmu_sc0004239.1_g000023 Rmu_sc0008115.1_g000011
rosa_roxburghii	Rroxscaffold_3G00238160 Rroxscaffold_3G00249920 Rroxscaffold_4G00310020 Rroxscaffold_4G00317980 Rroxscaffold_5G00344600
rosa_rugosa	Rorug01G0103700 Rorug01G0103800 Rorug01G0103900 Rorug01G0171800 Rorug07G0107800
rosa_samantha	Rh1BG097500 Rh1BG161500 Rh1CG122000 Rh1CG173900 Rh1CG180700 Rh1CG181100 Rh1DG133900 Rh1DG191900 Rh7AG242600 Rh7BG237400 Rh7DG249500
rosa_wichuraiana	Rw1G010510 Rw1G016120 Rw1G016200 Rw1G016220 Rw1G016430 Rw1G016490 Rw7G020550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	499
Acc36I	ACCTGC	1 cut(s)	499
AccI	GTMKAC	2 cut(s)	353, 476
AciI	CCGC	1 cut(s)	181
AclWI	GGATC	1 cut(s)	512
AcvI	CACGTG	1 cut(s)	548
AfiI	CCNNNNNNNGG	2 cut(s)	234, 370
AflIII	ACRYGT	1 cut(s)	545
AgsI	TTSAA	1 cut(s)	67
AjnI	CCWGG	1 cut(s)	378
AjuI	GAANNNNNNNTTGG	2 cut(s)	216, 248
AluBI	AGCT	3 cut(s)	192, 316, 496
AluI	AGCT	3 cut(s)	192, 316, 496
Alw21I	GWGCWC	1 cut(s)	131
Alw26I	GTCTC	2 cut(s)	309, 575
AlwI	GGATC	1 cut(s)	512
AlwNI	CAGNNNCTG	1 cut(s)	95
AoxI	GGCC	1 cut(s)	572
ApeKI	GCWGC	1 cut(s)	466
Asp700I	GAANNNNTTC	1 cut(s)	284
AspLEI	GCGC	1 cut(s)	267
AsuHPI	GGTGA	4 cut(s)	64, 409, 523, 592
AsuII	TTCGAA	1 cut(s)	43
BbrPI	CACGTG	1 cut(s)	548
BbsI	GAAGAC	2 cut(s)	202, 464
Bbv12I	GWGCWC	1 cut(s)	131
BbvI	GCAGC	1 cut(s)	453
BccI	CCATC	2 cut(s)	65, 361
BciT130I	CCWGG	1 cut(s)	380
BclI	TGATCA	1 cut(s)	196
BcoDI	GTCTC	2 cut(s)	309, 575
BfaI	CTAG	2 cut(s)	161, 419
BfmI	CTRYAG	1 cut(s)	467
BfuAI	ACCTGC	1 cut(s)	499
BglII	AGATCT	1 cut(s)	157
BisI	GCNGC	1 cut(s)	467
BlsI	GCNGC	1 cut(s)	468
Bme1390I	CCNGG	1 cut(s)	380
BmiI	GGNNCC	1 cut(s)	362
BmrFI	CCNGG	1 cut(s)	380
BmsI	GCATC	3 cut(s)	45, 439, 495
BpiI	GAAGAC	2 cut(s)	202, 464
Bpu10I	CCTNAGC	1 cut(s)	426
Bpu14I	TTCGAA	1 cut(s)	43
BsaAI	YACGTR	1 cut(s)	548
BsaJI	CCNNGG	2 cut(s)	228, 500
Bsc4I	CCNNNNNNNGG	2 cut(s)	234, 370
BseBI	CCWGG	1 cut(s)	380
BseDI	CCNNGG	2 cut(s)	228, 500
BseGI	GGATG	1 cut(s)	510
BseLI	CCNNNNNNNGG	2 cut(s)	234, 370
BseMII	CTCAG	1 cut(s)	417
BseXI	GCAGC	1 cut(s)	453
BshFI	GGCC	1 cut(s)	574
BsiHKAI	GWGCWC	1 cut(s)	131
BslFI	GGGAC	1 cut(s)	266
BslI	CCNNNNNNNGG	2 cut(s)	234, 370
BsmAI	GTCTC	2 cut(s)	309, 575
BsmFI	GGGAC	1 cut(s)	266
BsnI	GGCC	1 cut(s)	574
Bsp119I	TTCGAA	1 cut(s)	43
Bsp1286I	GDGCHC	1 cut(s)	131
Bsp143I	GATC	3 cut(s)	157, 196, 517
BspACI	CCGC	1 cut(s)	181
BspANI	GGCC	1 cut(s)	574
BspCNI	CTCAG	1 cut(s)	418
BspLI	GGNNCC	1 cut(s)	362
BspMAI	CTGCAG	1 cut(s)	471
BspMI	ACCTGC	1 cut(s)	499
BspPI	GGATC	1 cut(s)	512
BspT104I	TTCGAA	1 cut(s)	43
BssECI	CCNNGG	2 cut(s)	228, 500
BssMI	GATC	3 cut(s)	157, 196, 517
BssNAI	GTATAC	1 cut(s)	477
BssT1I	CCWWGG	1 cut(s)	228
Bst1107I	GTATAC	1 cut(s)	477
Bst2UI	CCWGG	1 cut(s)	380
Bst4CI	ACNGT	4 cut(s)	52, 393, 481, 608
BstAPI	GCANNNNNTGC	1 cut(s)	436
BstBAI	YACGTR	1 cut(s)	548
BstBI	TTCGAA	1 cut(s)	43
BstC8I	GCNNGC	1 cut(s)	269
BstDEI	CTNAG	1 cut(s)	426
BstF5I	GGATG	1 cut(s)	510
BstHHI	GCGC	1 cut(s)	267
BstKTI	GATC	3 cut(s)	160, 199, 520
BstMAI	GTCTC	2 cut(s)	309, 575
BstMBI	GATC	3 cut(s)	157, 196, 517
BstMWI	GCNNNNNNNGC	1 cut(s)	436
BstNI	CCWGG	1 cut(s)	380
BstNSI	RCATGY	2 cut(s)	271, 416
BstSCI	CCNGG	1 cut(s)	378
BstSFI	CTRYAG	1 cut(s)	467
BstV1I	GCAGC	1 cut(s)	453
BstV2I	GAAGAC	2 cut(s)	202, 464
BstX2I	RGATCY	2 cut(s)	157, 517
BstYI	RGATCY	2 cut(s)	157, 517
BstZ17I	GTATAC	1 cut(s)	477
BsuRI	GGCC	1 cut(s)	574
BtsCI	GGATG	1 cut(s)	510
BveI	ACCTGC	1 cut(s)	499
Cac8I	GCNNGC	1 cut(s)	269
CaiI	CAGNNNCTG	1 cut(s)	95
CfoI	GCGC	1 cut(s)	267
CviAII	CATG	4 cut(s)	106, 145, 268, 413
CviJI	RGCY	8 cut(s)	5, 31, 192, 227, 316, 496, 541, 574
CviKI_1	RGCY	8 cut(s)	5, 31, 192, 227, 316, 496, 541, 574
DdeI	CTNAG	1 cut(s)	426
DpnI	GATC	3 cut(s)	159, 198, 519
DpnII	GATC	3 cut(s)	157, 196, 517
Eco130I	CCWWGG	1 cut(s)	228
Eco32I	GATATC	1 cut(s)	100
Eco72I	CACGTG	1 cut(s)	548
EcoRII	CCWGG	1 cut(s)	378
EcoRV	GATATC	1 cut(s)	100
EcoT14I	CCWWGG	1 cut(s)	228
ErhI	CCWWGG	1 cut(s)	228
FaeI	CATG	4 cut(s)	109, 148, 271, 416
FaqI	GGGAC	1 cut(s)	266
FatI	CATG	4 cut(s)	105, 144, 267, 412
FauNDI	CATATG	1 cut(s)	133
FbaI	TGATCA	1 cut(s)	196
FblI	GTMKAC	2 cut(s)	353, 476
Fnu4HI	GCNGC	1 cut(s)	467
FokI	GGATG	1 cut(s)	517
Fsp4HI	GCNGC	1 cut(s)	467
FspBI	CTAG	2 cut(s)	161, 419
GlaI	GCGC	1 cut(s)	266
GluI	GCNGC	1 cut(s)	467
HaeIII	GGCC	1 cut(s)	574
HhaI	GCGC	1 cut(s)	267
Hin1II	CATG	4 cut(s)	109, 148, 271, 416
Hin6I	GCGC	1 cut(s)	265
HinP1I	GCGC	1 cut(s)	265
HinfI	GANTC	3 cut(s)	92, 319, 460
HphI	GGTGA	4 cut(s)	64, 409, 523, 592
Hpy166II	GTNNAC	3 cut(s)	354, 477, 551
Hpy188I	TCNGA	6 cut(s)	13, 97, 196, 201, 290, 504
Hpy188III	TCNNGA	4 cut(s)	124, 161, 364, 425
Hpy8I	GTNNAC	3 cut(s)	354, 477, 551
HpyCH4III	ACNGT	4 cut(s)	52, 393, 481, 608
HpyCH4IV	ACGT	1 cut(s)	547
HpyCH4V	TGCA	4 cut(s)	58, 271, 469, 508
HpyF10VI	GCNNNNNNNGC	1 cut(s)	436
HpyF3I	CTNAG	1 cut(s)	426
HpySE526I	ACGT	1 cut(s)	547
Hsp92II	CATG	4 cut(s)	109, 148, 271, 416
HspAI	GCGC	1 cut(s)	265
Ksp22I	TGATCA	1 cut(s)	196
Kzo9I	GATC	3 cut(s)	157, 196, 517
LmnI	GCTCC	1 cut(s)	126
Lsp1109I	GCAGC	1 cut(s)	453
LweI	GCATC	3 cut(s)	45, 439, 495
MaeI	CTAG	2 cut(s)	161, 419
MaeII	ACGT	1 cut(s)	547
MaeIII	GTNAC	3 cut(s)	85, 185, 598
MalI	GATC	3 cut(s)	159, 198, 519
MboI	GATC	3 cut(s)	157, 196, 517
MboII	GAAGA	9 cut(s)	26, 29, 57, 167, 202, 205, 469, 574, 603
MflI	RGATCY	2 cut(s)	157, 517
MhlI	GDGCHC	1 cut(s)	131
MluCI	AATT	1 cut(s)	119
MlyI	GAGTC	2 cut(s)	313, 454
MnlI	CCTC	5 cut(s)	243, 364, 442, 465, 510
MroXI	GAANNNNTTC	1 cut(s)	284
MseI	TTAA	2 cut(s)	405, 619
MspR9I	CCNGG	1 cut(s)	380
MvaI	CCWGG	1 cut(s)	380
MwoI	GCNNNNNNNGC	1 cut(s)	436
NdeI	CATATG	1 cut(s)	133
NdeII	GATC	3 cut(s)	157, 196, 517
NlaIII	CATG	4 cut(s)	109, 148, 271, 416
NlaIV	GGNNCC	1 cut(s)	362
NmuCI	GTSAC	2 cut(s)	185, 598
NspI	RCATGY	2 cut(s)	271, 416
NspV	TTCGAA	1 cut(s)	43
PaeI	GCATGC	1 cut(s)	271
PaqCI	CACCTGC	1 cut(s)	499
PdmI	GAANNNNTTC	1 cut(s)	284
PfeI	GAWTC	1 cut(s)	92
PfoI	TCCNGGA	1 cut(s)	378
PkrI	GCNGC	1 cut(s)	468
PleI	GAGTC	2 cut(s)	313, 454
PmaCI	CACGTG	1 cut(s)	548
PmlI	CACGTG	1 cut(s)	548
PpsI	GAGTC	2 cut(s)	313, 454
Ppu21I	YACGTR	1 cut(s)	548
Psp6I	CCWGG	1 cut(s)	378
PspCI	CACGTG	1 cut(s)	548
PspGI	CCWGG	1 cut(s)	378
PspN4I	GGNNCC	1 cut(s)	362
PstI	CTGCAG	1 cut(s)	471
PstNI	CAGNNNCTG	1 cut(s)	95
PsuI	RGATCY	2 cut(s)	157, 517
SaqAI	TTAA	2 cut(s)	405, 619
SatI	GCNGC	1 cut(s)	467
Sau3AI	GATC	3 cut(s)	157, 196, 517
SchI	GAGTC	2 cut(s)	313, 454
ScrFI	CCNGG	1 cut(s)	380
SduI	GDGCHC	1 cut(s)	131
SfaNI	GCATC	3 cut(s)	45, 439, 495
SfcI	CTRYAG	1 cut(s)	467
SfuI	TTCGAA	1 cut(s)	43
SphI	GCATGC	1 cut(s)	271
Sse9I	AATT	1 cut(s)	119
SsiI	CCGC	1 cut(s)	181
SspI	AATATT	1 cut(s)	403
SspMI	CTAG	2 cut(s)	161, 419
StyD4I	CCNGG	1 cut(s)	378
StyI	CCWWGG	1 cut(s)	228
TaaI	ACNGT	4 cut(s)	52, 393, 481, 608
TaiI	ACGT	1 cut(s)	550
TaqI	TCGA	1 cut(s)	43
TasI	AATT	1 cut(s)	119
TfiI	GAWTC	1 cut(s)	92
Tru1I	TTAA	2 cut(s)	405, 619
Tru9I	TTAA	2 cut(s)	405, 619
TseFI	GTSAC	2 cut(s)	185, 598
TseI	GCWGC	1 cut(s)	466
Tsp45I	GTSAC	2 cut(s)	185, 598
TspDTI	ATGAA	2 cut(s)	161, 237
XbaI	TCTAGA	1 cut(s)	160
XceI	RCATGY	2 cut(s)	271, 416
XmiI	GTMKAC	2 cut(s)	353, 476
XmnI	GAANNNNTTC	1 cut(s)	284
XspI	CTAG	2 cut(s)	161, 419

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