Basic Information

Type: gene

Biological Identity

Species

rosa_rugosa

Chromosome

GWHBQTZ00000007

Orthogroup ID

OG0003905

Physical Location & Seq

Genomic Coordinates Forward (+)

23885373 .. 23887797

Gene Structure 2425 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rorug07G0255600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 837 bp

ATGGCCACAATGTCACGCCCAATGGCTTCTCGGAGCAACAGAGAGGGAAGAGGACATGCCTTCCCAGTGGACTCTCCAAGCTTCTACTTGAAGATTGTTACTGCTGTGGATCTCCAAGATGGGAAGGAACTTCCAGAGCCAGCTGTGACGAAGTATGGGAATTGTATGGCAGACTCCATATTCCTCAAGGTTCCCAATTGCGGAACACCATGGCCAGTAGAACTAAAAAAAACGATTCGTGGTAGCCGAATCTGGTTACAAAAAGGATGGGAACTATTCACAGACTTTTACTCCATAGACCAAGATTACTTCATAGTGTTCAGCTATGAAGGCGAACATTCTTATTTCCAAGTACACATTTTCAACTGCAACAATATGGAAATAGGTTATTCAATTCGTGGAGGTGCTGGTGGATGCATGTCTACACCCAATTCAAAAGGTACCTCCTTTCCCTCTGCATCATCTGCTGGCAGAGACCAAAACAATGACAACAAACGTGACTTTTATGGAGCTAACAATTTCAAATTCGGGGACAAGCCTAGTTTTCGGGTCATAATGACTGAAAAATACTTATCATCTTTCTTGAAAGTACCTTCGTACTTCACCATCGAACATCTGTGTGAAATAGGGTCTCATTCTACTGTGACCTTACAGACTTCAGGTGAAAGAACTTGGACTGTTCAGTGTGCTGTCAGCAAATGTGGGAAAAATGCAAGATTCAATCGTGCTAGTTGGAGAGGATTTGTGAAGGGCAATCAATTGGAAGCACGTGATGATTGTCTGTTTGAGTTGATAGGCGTTCGTATGCTCAAAGTCAACATATCCCGAGCTAAATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000184 GO:0000956 GO:0001101 GO:0003674 GO:0003676 GO:0003723 GO:0003729 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005730 GO:0006139 GO:0006401 GO:0006402 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0007154 GO:0007165 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009314 GO:0009416 GO:0009605 GO:0009607 GO:0009611 GO:0009617 GO:0009628 GO:0009648 GO:0009719 GO:0009725 GO:0009751 GO:0009753 GO:0009755 GO:0009863 GO:0009867 GO:0009892 GO:0009987 GO:0010033 GO:0010468 GO:0010605 GO:0010629 GO:0014070 GO:0016070 GO:0016071 GO:0019222 GO:0019439 GO:0023052 GO:0031974 GO:0031981 GO:0032870 GO:0034641 GO:0034655 GO:0035690 GO:0042221 GO:0042493 GO:0042742 GO:0043170 GO:0043207 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044248 GO:0044260 GO:0044265 GO:0044270 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0046677 GO:0046700 GO:0048519 GO:0048571 GO:0050789 GO:0050794 GO:0050896 GO:0051704 GO:0051707 GO:0051716 GO:0060255 GO:0065007 GO:0070013 GO:0070887 GO:0071229 GO:0071236 GO:0071310 GO:0071395 GO:0071407 GO:0071446 GO:0071495 GO:0071704 GO:0090304 GO:0097159 GO:0098542 GO:1901360 GO:1901361 GO:1901363 GO:1901575 GO:1901700 GO:1901701

KEGG Pathways

Metabolic & Signaling

ko03013 ko03015 map03013 map03015

Pfam Domains

Protein Families

Smg4_UPF3

Protein Analysis

278

Amino Acids

31.33

Weight (kDa)

9.04

Isoelectric Point (pI)

38.06

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
B3	PF02362	42 - 122	3.2e-07	B3 DNA binding domain
B3	PF02362	186 - 276	7.9e-11	B3 DNA binding 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: OG0003905)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G33980 AT1G33980
fragaria_vesca	FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510 FvH4_5g32510
malus_domestica	MD08G1216600.v1.1 MD15G1403800.v1.1
prunus_persica	Prupe.1G550000_v2.0.a1
pyrus_communis	pycom08g18750 pycom15g36110
rosa_chinensis	RchiOBHm_Chr6g0271031 RchiOBHm_Chr7g0229091
rosa_laevigata	RLG00000001531
rosa_multiflora	Rmu_sc0000271.1_g000018
rosa_roxburghii	Rroxscaffold_3G00230720
rosa_rugosa	Rorug07G0255600 Rorug07G0255700 Rorug07G0255700 Rorug07G0255800 Rorug07G0255900 Rorug07G0256000
rosa_samantha	Rh7AG406900 Rh7BG386300 Rh7CG424600 Rh7DG400900
rosa_wichuraiana	Rw7G033780

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	440
AccB1I	GGYRCC	1 cut(s)	440
AccI	GTMKAC	1 cut(s)	422
AciI	CCGC	1 cut(s)	201
AclWI	GGATC	1 cut(s)	117
AcoI	YGGCCR	2 cut(s)	3, 212
AcsI	RAATTY	1 cut(s)	524
AcuI	CTGAAG	1 cut(s)	642
AcvI	CACGTG	1 cut(s)	770
AfaI	GTAC	4 cut(s)	354, 442, 591, 599
AfiI	CCNNNNNNNGG	1 cut(s)	200
AgsI	TTSAA	7 cut(s)	91, 364, 393, 435, 523, 586, 721
AluBI	AGCT	5 cut(s)	81, 143, 324, 512, 830
AluI	AGCT	5 cut(s)	81, 143, 324, 512, 830
Alw26I	GTCTC	2 cut(s)	468, 636
AlwI	GGATC	1 cut(s)	117
Ama87I	CYCGRG	1 cut(s)	825
AoxI	GGCC	2 cut(s)	3, 212
ApoI	RAATTY	1 cut(s)	524
Asp718I	GGTACC	1 cut(s)	440
AsuHPI	GGTGA	2 cut(s)	595, 674
AvaI	CYCGRG	1 cut(s)	825
BalI	TGGCCA	2 cut(s)	5, 214
BanI	GGYRCC	1 cut(s)	440
BbrPI	CACGTG	1 cut(s)	770
BccI	CCATC	3 cut(s)	113, 261, 614
BcoDI	GTCTC	2 cut(s)	468, 636
BfaI	CTAG	2 cut(s)	540, 729
BmeT110I	CYCGRG	1 cut(s)	825
BmiI	GGNNCC	2 cut(s)	192, 442
BmrI	ACTGGG	1 cut(s)	59
BmsI	GCATC	2 cut(s)	404, 467
BmuI	ACTGGG	1 cut(s)	59
BpuEI	CTTGAG	1 cut(s)	170
BsaAI	YACGTR	1 cut(s)	770
BsaI	GGTCTC	2 cut(s)	468, 636
BsaJI	CCNNGG	1 cut(s)	209
BsaXI	ACNNNNNCTCC	2 cut(s)	275, 305
Bsc4I	CCNNNNNNNGG	1 cut(s)	200
Bse1I	ACTGG	2 cut(s)	65, 215
BseDI	CCNNGG	1 cut(s)	209
BseGI	GGATG	2 cut(s)	272, 419
BseLI	CCNNNNNNNGG	1 cut(s)	200
BseNI	ACTGG	2 cut(s)	65, 215
BshFI	GGCC	2 cut(s)	5, 214
BshNI	GGYRCC	1 cut(s)	440
BsiHKCI	CYCGRG	1 cut(s)	825
BslFI	GGGAC	1 cut(s)	545
BslI	CCNNNNNNNGG	1 cut(s)	200
BsmAI	GTCTC	2 cut(s)	468, 636
BsmFI	GGGAC	1 cut(s)	545
BsnI	GGCC	2 cut(s)	5, 214
Bso31I	GGTCTC	2 cut(s)	468, 636
BsoBI	CYCGRG	1 cut(s)	825
Bsp143I	GATC	1 cut(s)	109
Bsp19I	CCATGG	1 cut(s)	209
BspACI	CCGC	1 cut(s)	201
BspANI	GGCC	2 cut(s)	5, 214
BspLI	GGNNCC	2 cut(s)	192, 442
BspPI	GGATC	1 cut(s)	117
BspT107I	GGYRCC	1 cut(s)	440
BspTNI	GGTCTC	2 cut(s)	468, 636
BsrI	ACTGG	2 cut(s)	65, 215
BssECI	CCNNGG	1 cut(s)	209
BssMI	GATC	1 cut(s)	109
BssT1I	CCWWGG	1 cut(s)	209
Bst4CI	ACNGT	2 cut(s)	643, 679
Bst6I	CTCTTC	1 cut(s)	43
BstAPI	GCANNNNNTGC	1 cut(s)	464
BstBAI	YACGTR	1 cut(s)	770
BstC8I	GCNNGC	2 cut(s)	141, 469
BstDSI	CCRYGG	1 cut(s)	209
BstF5I	GGATG	2 cut(s)	272, 419
BstKTI	GATC	1 cut(s)	112
BstMAI	GTCTC	2 cut(s)	468, 636
BstMBI	GATC	1 cut(s)	109
BstMWI	GCNNNNNNNGC	2 cut(s)	330, 464
BstNSI	RCATGY	2 cut(s)	59, 421
BstX2I	RGATCY	1 cut(s)	109
BstYI	RGATCY	1 cut(s)	109
BsuRI	GGCC	2 cut(s)	5, 214
BtgI	CCRYGG	1 cut(s)	209
BtsCI	GGATG	2 cut(s)	272, 419
BtsIMutI	CAGTG	2 cut(s)	72, 689
Cac8I	GCNNGC	2 cut(s)	141, 469
Csp6I	GTAC	4 cut(s)	353, 441, 590, 598
CviAII	CATG	3 cut(s)	56, 210, 418
CviQI	GTAC	4 cut(s)	353, 441, 590, 598
DpnI	GATC	1 cut(s)	111
DpnII	GATC	1 cut(s)	109
EaeI	YGGCCR	2 cut(s)	3, 212
Eam1104I	CTCTTC	1 cut(s)	43
EarI	CTCTTC	1 cut(s)	43
Eco130I	CCWWGG	1 cut(s)	209
Eco31I	GGTCTC	2 cut(s)	468, 636
Eco57I	CTGAAG	1 cut(s)	642
Eco72I	CACGTG	1 cut(s)	770
Eco88I	CYCGRG	1 cut(s)	825
EcoT14I	CCWWGG	1 cut(s)	209
EcoT22I	ATGCAT	1 cut(s)	419
ErhI	CCWWGG	1 cut(s)	209
FaeI	CATG	3 cut(s)	59, 213, 421
FaqI	GGGAC	1 cut(s)	545
FatI	CATG	3 cut(s)	55, 209, 417
FblI	GTMKAC	1 cut(s)	422
FokI	GGATG	2 cut(s)	279, 426
FspBI	CTAG	2 cut(s)	540, 729
HaeIII	GGCC	2 cut(s)	5, 214
Hin1II	CATG	3 cut(s)	59, 213, 421
HincII	GTYRAC	1 cut(s)	817
HindII	GTYRAC	1 cut(s)	817
HindIII	AAGCTT	1 cut(s)	79
HinfI	GANTC	5 cut(s)	71, 173, 235, 249, 717
HphI	GGTGA	2 cut(s)	595, 674
Hpy166II	GTNNAC	4 cut(s)	70, 355, 423, 817
Hpy188I	TCNGA	1 cut(s)	33
Hpy188III	TCNNGA	3 cut(s)	134, 583, 825
Hpy8I	GTNNAC	4 cut(s)	70, 355, 423, 817
HpyAV	CCTTC	5 cut(s)	70, 118, 323, 603, 742
HpyCH4III	ACNGT	2 cut(s)	643, 679
HpyCH4IV	ACGT	2 cut(s)	496, 769
HpyCH4V	TGCA	4 cut(s)	369, 417, 458, 713
HpyF10VI	GCNNNNNNNGC	2 cut(s)	330, 464
HpySE526I	ACGT	2 cut(s)	496, 769
Hsp92II	CATG	3 cut(s)	59, 213, 421
KpnI	GGTACC	1 cut(s)	444
Kzo9I	GATC	1 cut(s)	109
LmnI	GCTCC	2 cut(s)	33, 509
LpnPI	CCDG	8 cut(s)	78, 147, 153, 228, 238, 393, 453, 645
LweI	GCATC	2 cut(s)	404, 467
MaeI	CTAG	2 cut(s)	540, 729
MaeII	ACGT	2 cut(s)	496, 769
MaeIII	GTNAC	6 cut(s)	12, 97, 145, 255, 497, 643
MalI	GATC	1 cut(s)	111
MboI	GATC	1 cut(s)	109
MboII	GAAGA	2 cut(s)	60, 103
MfeI	CAATTG	2 cut(s)	196, 758
MflI	RGATCY	1 cut(s)	109
MlsI	TGGCCA	2 cut(s)	5, 214
MluCI	AATT	7 cut(s)	160, 196, 393, 430, 517, 524, 758
MluNI	TGGCCA	2 cut(s)	5, 214
MlyI	GAGTC	2 cut(s)	65, 167
MmeI	TCCRAC	1 cut(s)	713
MnlI	CCTC	7 cut(s)	37, 44, 194, 395, 454, 463, 731
Mox20I	TGGCCA	2 cut(s)	5, 214
Mph1103I	ATGCAT	1 cut(s)	419
MscI	TGGCCA	2 cut(s)	5, 214
MslI	CAYNNNNRTG	1 cut(s)	618
Msp20I	TGGCCA	2 cut(s)	5, 214
MspA1I	CMGCKG	1 cut(s)	143
MunI	CAATTG	2 cut(s)	196, 758
MwoI	GCNNNNNNNGC	2 cut(s)	330, 464
NcoI	CCATGG	1 cut(s)	209
NdeII	GATC	1 cut(s)	109
NlaIII	CATG	3 cut(s)	59, 213, 421
NlaIV	GGNNCC	2 cut(s)	192, 442
NmuCI	GTSAC	4 cut(s)	12, 145, 497, 643
NsiI	ATGCAT	1 cut(s)	419
NspI	RCATGY	2 cut(s)	59, 421
PcsI	WCGNNNNNNNCGW	1 cut(s)	244
PfeI	GAWTC	3 cut(s)	235, 249, 717
PleI	GAGTC	2 cut(s)	65, 167
PmaCI	CACGTG	1 cut(s)	770
PmlI	CACGTG	1 cut(s)	770
PpsI	GAGTC	2 cut(s)	65, 167
Ppu21I	YACGTR	1 cut(s)	770
PspCI	CACGTG	1 cut(s)	770
PspN4I	GGNNCC	2 cut(s)	192, 442
PsuI	RGATCY	1 cut(s)	109
PvuII	CAGCTG	1 cut(s)	143
RsaI	GTAC	4 cut(s)	354, 442, 591, 599
RsaNI	GTAC	4 cut(s)	353, 441, 590, 598
RseI	CAYNNNNRTG	1 cut(s)	618
Sau3AI	GATC	1 cut(s)	109
SchI	GAGTC	2 cut(s)	65, 167
SfaNI	GCATC	2 cut(s)	404, 467
SmiMI	CAYNNNNRTG	1 cut(s)	618
SmlI	CTYRAG	1 cut(s)	185
SmoI	CTYRAG	1 cut(s)	185
Sse9I	AATT	7 cut(s)	160, 196, 393, 430, 517, 524, 758
SsiI	CCGC	1 cut(s)	201
SspMI	CTAG	2 cut(s)	540, 729
StyI	CCWWGG	1 cut(s)	209
TaaI	ACNGT	2 cut(s)	643, 679
TaiI	ACGT	2 cut(s)	499, 772
TaqI	TCGA	1 cut(s)	609
TasI	AATT	7 cut(s)	160, 196, 393, 430, 517, 524, 758
TatI	WGTACW	1 cut(s)	352
TfiI	GAWTC	3 cut(s)	235, 249, 717
TscAI	CASTG	2 cut(s)	72, 689
TseFI	GTSAC	4 cut(s)	12, 145, 497, 643
Tsp45I	GTSAC	4 cut(s)	12, 145, 497, 643
TspDTI	ATGAA	2 cut(s)	301, 342
TspRI	CASTG	2 cut(s)	72, 689
XapI	RAATTY	1 cut(s)	524
XceI	RCATGY	2 cut(s)	59, 421
XmiI	GTMKAC	1 cut(s)	422
XspI	CTAG	2 cut(s)	540, 729
Zsp2I	ATGCAT	1 cut(s)	419

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