Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0004190

Physical Location & Seq

Genomic Coordinates Reverse (-)

1346093 .. 1348114

Gene Structure 2022 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG018900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1242 bp

ATGATTGTTTTGATATCTTCCCTAGTCTTTCGGACTTTCTTGTTTTTGTTCTTGTTGGCATGGATAACAGAAGGCCATAAACTCTATCGTCAAACAGCACGTCTTGGTAGACCCATGGTTTTCAATGTGATGCGTTATGGAGCTATTGAAGGAGGAAGAACTGATAATAGTCAGGCATTTTTGAAAGCATGGAGTGAAGCATGTAAATGGGATGGAAGAGCAAAGGTTGTGATTCCGCCCGGAACATTCAAGTTGTTCCCAGTTGTATTCTCAGGTCCATGCAAGGGTAACATGGCCTTTGTAATCAAGGGAACTTTGTTGGCTTCTACTAGTCCATCAGCATTGAGTTCTGAAAATTGGATAAACTTTCGGAACATTGAACAATTAACTGTAGCCGGGGGAGGTACGCTGGACGGCCAAGGATCCTCGGTTTGGTCTCTTAACGATTGCAAAACTAATCCCGTATGCAAAGCTCTCCCAACTTCAATGACTTTCGACTTCGTAACAAATGCAAGTGTTCATCACTTAAGATCATTCAACAGCCAAAATGGTCATTTTAAGGTTCATGGATGCCAGAAGATAGACTTCGGAAACATTAGAATATCGGCTCCTGAGGACAGTCCAAACACCGATGGCATAAAAATTGGAAACTCATACCGCATCAGAATTAGACGAACGATCATTGAGACCGGCGATGATTGTATAGGAATTGTATCGGGAAGTCAAAAAATCCACATTTCTAATGTCTTTTGCGGTCCCGGACATGGAATTAGCGTTGGAAGTCTTGGAGGGCATAGTTATACAGAATATGATGTGGAGGGAATTTTTGTGAAAAATAGCGTTTTCAAAAAGACTGATAATGGTTTGAGAATCAAAACATGGGCTCGAGATACTCCAAAACCATTGAAGGCTTCAAATATTGTGTATGAAGATATTAACATGATTGATGTCATGAATCCCATTGTCATCGATCAACAATATTGTCCGAACAATCAATGCAATCAACAGGATACTTCATCAAATGTGCAAATCAGCGATGTAACATTCAGAAACATATGGGGAACCTCGTCTTCCCAAGAAGCAGTGACTCTGAAATGCAGCAAAAGCAAGCCATGCAAGAATATAGTGATGGAGAATATCAAGTTACCTCATACTGATTCCAAAGGAGCTGCGACGACTTCCATCTGTAATAATGTCATCGGCAACTCTTATGGCTCACACATCCCTCCTAGTTGCATATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

ko00040 ko01100 map00040 map01100

Pfam Domains

Protein Families

Glyco_hydro_28

Protein Analysis

413

Amino Acids

45.3

Weight (kDa)

9.04

Isoelectric Point (pI)

31.86

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pect-lyase_RHGA_epim	PF12708	41 - 261	8.3e-06	Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28	PF00295	70 - 399	1.1e-93	Glycosyl hydrolases family 28

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: OG0004190)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G78400
fragaria_vesca	FvH4_3g01611 FvH4_3g01620 FvH4_3g16670 FvH4_6g48250
malus_domestica	MD05G1208400.v1.1 MD10G1194900.v1.1
prunus_persica	Prupe.4G149100_v2.0.a1
pyrus_communis	pycom10g16830
rosa_chinensis	RchiOBHm_Chr5g0002411 RchiOBHm_Chr5g0027771
rosa_laevigata	RLG00000015288 RLG00000031030 RLG00000033042
rosa_multiflora	Rmu_co8379139.1_g000001 Rmu_sc0000920.1_g000006
rosa_roxburghii	Rroxscaffold_1G00051830 Rroxscaffold_1G00051840 Rroxscaffold_1G00073440
rosa_rugosa	Rorug04G0396100 Rorug05G0101000 Rorug05G0517000
rosa_samantha	Rh5AG018900 Rh5AG195300 Rh5BG193600 Rh5CG020800 Rh5CG213900 Rh5DG019900 Rh5DG195600 Rh6CG028000 Rh6DG027300
rosa_wichuraiana	Rw5G001770 Rw5G017820

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	109
AciI	CCGC	3 cut(s)	236, 658, 753
AclWI	GGATC	2 cut(s)	417, 430
AcoI	YGGCCR	1 cut(s)	415
AcsI	RAATTY	1 cut(s)	822
AfaI	GTAC	1 cut(s)	406
AfiI	CCNNNNNNNGG	3 cut(s)	284, 432, 764
AflII	CTTAAG	1 cut(s)	526
AhlI	ACTAGT	1 cut(s)	329
AjiI	CACGTC	1 cut(s)	101
AluBI	AGCT	3 cut(s)	143, 473, 1169
AluI	AGCT	3 cut(s)	143, 473, 1169
Alw26I	GTCTC	2 cut(s)	441, 680
AlwI	GGATC	2 cut(s)	417, 430
Ama87I	CYCGRG	1 cut(s)	885
AoxI	GGCC	3 cut(s)	73, 294, 415
ApeKI	GCWGC	2 cut(s)	1098, 1169
ApoI	RAATTY	1 cut(s)	822
ArsI	GACNNNNNNTTYG	2 cut(s)	85, 117
AspS9I	GGNCC	2 cut(s)	275, 755
AsuC2I	CCSGG	3 cut(s)	240, 397, 759
AvaI	CYCGRG	1 cut(s)	885
AvaII	GGWCC	2 cut(s)	275, 755
AxyI	CCTNAGG	1 cut(s)	612
BamHI	GGATCC	1 cut(s)	422
BanII	GRGCYC	1 cut(s)	886
BbsI	GAAGAC	1 cut(s)	1062
BbvI	GCAGC	2 cut(s)	1110, 1156
BccI	CCATC	5 cut(s)	206, 343, 626, 1123, 1190
BceAI	ACGGC	1 cut(s)	430
BciVI	GTATCC	1 cut(s)	1003
BcnI	CCSGG	3 cut(s)	240, 397, 759
BcoDI	GTCTC	2 cut(s)	441, 680
BcuI	ACTAGT	1 cut(s)	329
BfaI	CTAG	3 cut(s)	23, 330, 1230
BfmI	CTRYAG	1 cut(s)	390
BfrI	CTTAAG	1 cut(s)	526
BfuI	GTATCC	1 cut(s)	1003
BisI	GCNGC	2 cut(s)	1099, 1170
BlsI	GCNGC	2 cut(s)	1100, 1171
Bme1390I	CCNGG	3 cut(s)	240, 397, 759
Bme18I	GGWCC	2 cut(s)	275, 755
BmeT110I	CYCGRG	1 cut(s)	885
BmgBI	CACGTC	1 cut(s)	101
BmgT120I	GGNCC	2 cut(s)	275, 755
BmiI	GGNNCC	4 cut(s)	424, 609, 757, 1063
BmrFI	CCNGG	3 cut(s)	240, 397, 759
BmrI	ACTGGG	1 cut(s)	254
BmsI	GCATC	3 cut(s)	120, 560, 669
BmuI	ACTGGG	1 cut(s)	254
BpiI	GAAGAC	1 cut(s)	1062
BpuMI	CCSGG	3 cut(s)	240, 397, 759
Bsa29I	ATCGAT	1 cut(s)	969
BsaI	GGTCTC	2 cut(s)	441, 680
BsaJI	CCNNGG	4 cut(s)	114, 396, 418, 426
Bsc4I	CCNNNNNNNGG	3 cut(s)	284, 432, 764
Bse118I	RCCGGY	1 cut(s)	689
Bse1I	ACTGG	1 cut(s)	260
Bse21I	CCTNAGG	1 cut(s)	612
BseCI	ATCGAT	1 cut(s)	969
BseDI	CCNNGG	4 cut(s)	114, 396, 418, 426
BseGI	GGATG	3 cut(s)	217, 575, 1221
BseLI	CCNNNNNNNGG	3 cut(s)	284, 432, 764
BseMII	CTCAG	2 cut(s)	285, 603
BseNI	ACTGG	1 cut(s)	260
BseXI	GCAGC	2 cut(s)	1110, 1156
BshFI	GGCC	3 cut(s)	75, 296, 417
BshVI	ATCGAT	1 cut(s)	969
BsiHKCI	CYCGRG	1 cut(s)	885
BsiSI	CCGG	4 cut(s)	240, 396, 690, 759
BslFI	GGGAC	1 cut(s)	741
BslI	CCNNNNNNNGG	3 cut(s)	284, 432, 764
BsmAI	GTCTC	2 cut(s)	441, 680
BsmFI	GGGAC	1 cut(s)	741
BsnI	GGCC	3 cut(s)	75, 296, 417
Bso31I	GGTCTC	2 cut(s)	441, 680
BsoBI	CYCGRG	1 cut(s)	885
Bsp1286I	GDGCHC	1 cut(s)	886
Bsp143I	GATC	4 cut(s)	422, 530, 678, 970
Bsp19I	CCATGG	1 cut(s)	114
BspACI	CCGC	3 cut(s)	236, 658, 753
BspANI	GGCC	3 cut(s)	75, 296, 417
BspCNI	CTCAG	2 cut(s)	284, 604
BspDI	ATCGAT	1 cut(s)	969
BspHI	TCATGA	1 cut(s)	951
BspLI	GGNNCC	4 cut(s)	424, 609, 757, 1063
BspPI	GGATC	2 cut(s)	417, 430
BspQI	GCTCTTC	1 cut(s)	211
BspTI	CTTAAG	1 cut(s)	526
BspTNI	GGTCTC	2 cut(s)	441, 680
BsrFI	RCCGGY	1 cut(s)	689
BsrI	ACTGG	1 cut(s)	260
BssAI	RCCGGY	1 cut(s)	689
BssECI	CCNNGG	4 cut(s)	114, 396, 418, 426
BssMI	GATC	4 cut(s)	422, 530, 678, 970
BssT1I	CCWWGG	2 cut(s)	114, 418
Bst4CI	ACNGT	2 cut(s)	391, 620
Bst6I	CTCTTC	1 cut(s)	211
BstAFI	CTTAAG	1 cut(s)	526
BstAPI	GCANNNNNTGC	1 cut(s)	1113
BstC8I	GCNNGC	1 cut(s)	1109
BstDEI	CTNAG	2 cut(s)	271, 612
BstDSI	CCRYGG	1 cut(s)	114
BstF5I	GGATG	3 cut(s)	217, 575, 1221
BstKTI	GATC	4 cut(s)	425, 533, 681, 973
BstMAI	GTCTC	2 cut(s)	441, 680
BstMBI	GATC	4 cut(s)	422, 530, 678, 970
BstMWI	GCNNNNNNNGC	2 cut(s)	1104, 1113
BstNSI	RCATGY	1 cut(s)	204
BstSCI	CCNGG	3 cut(s)	238, 395, 757
BstSFI	CTRYAG	1 cut(s)	390
BstV1I	GCAGC	2 cut(s)	1110, 1156
BstV2I	GAAGAC	1 cut(s)	1062
BstX2I	RGATCY	1 cut(s)	422
BstYI	RGATCY	1 cut(s)	422
Bsu15I	ATCGAT	1 cut(s)	969
Bsu36I	CCTNAGG	1 cut(s)	612
BsuI	GTATCC	1 cut(s)	1003
BsuRI	GGCC	3 cut(s)	75, 296, 417
BsuTUI	ATCGAT	1 cut(s)	969
BtgI	CCRYGG	1 cut(s)	114
BtgZI	GCGATG	2 cut(s)	708, 1050
BtrI	CACGTC	1 cut(s)	101
BtsCI	GGATG	3 cut(s)	217, 575, 1221
BtsI	GCAGTG	1 cut(s)	1089
BtsIMutI	CAGTG	1 cut(s)	1089
Cac8I	GCNNGC	1 cut(s)	1109
CciI	TCATGA	1 cut(s)	951
Cfr10I	RCCGGY	1 cut(s)	689
Cfr13I	GGNCC	2 cut(s)	275, 755
ClaI	ATCGAT	1 cut(s)	969
Csp6I	GTAC	1 cut(s)	405
CviQI	GTAC	1 cut(s)	405
DdeI	CTNAG	2 cut(s)	271, 612
DpnI	GATC	4 cut(s)	424, 532, 680, 972
DpnII	GATC	4 cut(s)	422, 530, 678, 970
EaeI	YGGCCR	1 cut(s)	415
Eam1104I	CTCTTC	1 cut(s)	211
EarI	CTCTTC	1 cut(s)	211
EciI	GGCGGA	1 cut(s)	225
Eco130I	CCWWGG	2 cut(s)	114, 418
Eco24I	GRGCYC	1 cut(s)	886
Eco31I	GGTCTC	2 cut(s)	441, 680
Eco32I	GATATC	1 cut(s)	15
Eco47I	GGWCC	2 cut(s)	275, 755
Eco81I	CCTNAGG	1 cut(s)	612
Eco88I	CYCGRG	1 cut(s)	885
EcoRV	GATATC	1 cut(s)	15
EcoT14I	CCWWGG	2 cut(s)	114, 418
EcoT38I	GRGCYC	1 cut(s)	886
ErhI	CCWWGG	2 cut(s)	114, 418
FalI	AAGNNNNNCTT	2 cut(s)	569, 601
FaqI	GGGAC	1 cut(s)	741
FauNDI	CATATG	1 cut(s)	1055
FblI	GTMKAC	1 cut(s)	109
Fnu4HI	GCNGC	2 cut(s)	1099, 1170
FokI	GGATG	3 cut(s)	224, 582, 1208
FriOI	GRGCYC	1 cut(s)	886
Fsp4HI	GCNGC	2 cut(s)	1099, 1170
FspBI	CTAG	3 cut(s)	23, 330, 1230
GluI	GCNGC	2 cut(s)	1099, 1170
HaeIII	GGCC	3 cut(s)	75, 296, 417
HapII	CCGG	4 cut(s)	240, 396, 690, 759
HinfI	GANTC	5 cut(s)	232, 870, 955, 1087, 1157
HpaII	CCGG	4 cut(s)	240, 396, 690, 759
Hpy166II	GTNNAC	1 cut(s)	110
Hpy188I	TCNGA	8 cut(s)	33, 352, 372, 590, 665, 987, 1049, 1092
Hpy188III	TCNNGA	4 cut(s)	611, 717, 887, 952
Hpy8I	GTNNAC	1 cut(s)	110
Hpy99I	CGWCG	1 cut(s)	1177
HpyAV	CCTTC	3 cut(s)	65, 143, 901
HpyCH4III	ACNGT	2 cut(s)	391, 620
HpyCH4IV	ACGT	1 cut(s)	100
HpyCH4V	TGCA	9 cut(s)	282, 450, 468, 512, 999, 1027, 1098, 1116, 1236
HpyF10VI	GCNNNNNNNGC	2 cut(s)	1104, 1113
HpyF3I	CTNAG	2 cut(s)	271, 612
HpySE526I	ACGT	1 cut(s)	100
Kzo9I	GATC	4 cut(s)	422, 530, 678, 970
LguI	GCTCTTC	1 cut(s)	211
LmnI	GCTCC	3 cut(s)	140, 613, 1166
Lsp1109I	GCAGC	2 cut(s)	1110, 1156
LweI	GCATC	3 cut(s)	120, 560, 669
MaeI	CTAG	3 cut(s)	23, 330, 1230
MaeII	ACGT	1 cut(s)	100
MaeIII	GTNAC	5 cut(s)	287, 502, 1039, 1084, 1143
MalI	GATC	4 cut(s)	424, 532, 680, 972
MboI	GATC	4 cut(s)	422, 530, 678, 970
MboII	GAAGA	6 cut(s)	9, 168, 228, 589, 941, 1062
MflI	RGATCY	1 cut(s)	422
MhlI	GDGCHC	1 cut(s)	886
MluCI	AATT	7 cut(s)	355, 383, 642, 666, 708, 768, 822
MlyI	GAGTC	1 cut(s)	1081
MmeI	TCCRAC	1 cut(s)	757
MnlI	CCTC	9 cut(s)	146, 395, 436, 607, 782, 811, 1075, 1158, 1236
MseI	TTAA	5 cut(s)	386, 441, 527, 558, 936
MslI	CAYNNNNRTG	1 cut(s)	205
MspCI	CTTAAG	1 cut(s)	526
MspI	CCGG	4 cut(s)	240, 396, 690, 759
MspR9I	CCNGG	3 cut(s)	240, 397, 759
MwoI	GCNNNNNNNGC	2 cut(s)	1104, 1113
NciI	CCSGG	3 cut(s)	240, 397, 759
NcoI	CCATGG	1 cut(s)	114
NdeI	CATATG	1 cut(s)	1055
NdeII	GATC	4 cut(s)	422, 530, 678, 970
NlaIV	GGNNCC	4 cut(s)	424, 609, 757, 1063
NmuCI	GTSAC	1 cut(s)	1084
NspI	RCATGY	1 cut(s)	204
PaeR7I	CTCGAG	1 cut(s)	885
PagI	TCATGA	1 cut(s)	951
PciSI	GCTCTTC	1 cut(s)	211
PfeI	GAWTC	4 cut(s)	232, 870, 955, 1157
PfoI	TCCNGGA	1 cut(s)	757
PkrI	GCNGC	2 cut(s)	1100, 1171
PleI	GAGTC	1 cut(s)	1081
PpsI	GAGTC	1 cut(s)	1081
PspN4I	GGNNCC	4 cut(s)	424, 609, 757, 1063
PspPI	GGNCC	2 cut(s)	275, 755
PsuI	RGATCY	1 cut(s)	422
RsaI	GTAC	1 cut(s)	406
RsaNI	GTAC	1 cut(s)	405
RseI	CAYNNNNRTG	1 cut(s)	205
SapI	GCTCTTC	1 cut(s)	211
SaqAI	TTAA	5 cut(s)	386, 441, 527, 558, 936
SatI	GCNGC	2 cut(s)	1099, 1170
Sau3AI	GATC	4 cut(s)	422, 530, 678, 970
Sau96I	GGNCC	2 cut(s)	275, 755
SchI	GAGTC	1 cut(s)	1081
ScrFI	CCNGG	3 cut(s)	240, 397, 759
SduI	GDGCHC	1 cut(s)	886
SfaNI	GCATC	3 cut(s)	120, 560, 669
SfcI	CTRYAG	1 cut(s)	390
Sfr274I	CTCGAG	1 cut(s)	885
SinI	GGWCC	2 cut(s)	275, 755
SlaI	CTCGAG	1 cut(s)	885
SmiMI	CAYNNNNRTG	1 cut(s)	205
SmlI	CTYRAG	2 cut(s)	526, 885
SmoI	CTYRAG	2 cut(s)	526, 885
SpeI	ACTAGT	1 cut(s)	329
Sse9I	AATT	7 cut(s)	355, 383, 642, 666, 708, 768, 822
SsiI	CCGC	3 cut(s)	236, 658, 753
SspI	AATATT	2 cut(s)	919, 980
SspMI	CTAG	3 cut(s)	23, 330, 1230
StyD4I	CCNGG	3 cut(s)	238, 395, 757
StyI	CCWWGG	2 cut(s)	114, 418
TaaI	ACNGT	2 cut(s)	391, 620
TaiI	ACGT	1 cut(s)	103
TaqI	TCGA	3 cut(s)	495, 886, 969
TasI	AATT	7 cut(s)	355, 383, 642, 666, 708, 768, 822
TfiI	GAWTC	4 cut(s)	232, 870, 955, 1157
Tru1I	TTAA	5 cut(s)	386, 441, 527, 558, 936
Tru9I	TTAA	5 cut(s)	386, 441, 527, 558, 936
TscAI	CASTG	1 cut(s)	1089
TseFI	GTSAC	1 cut(s)	1084
TseI	GCWGC	2 cut(s)	1098, 1169
Tsp45I	GTSAC	1 cut(s)	1084
TspDTI	ATGAA	5 cut(s)	509, 554, 942, 968, 1005
TspRI	CASTG	1 cut(s)	1089
Vha464I	CTTAAG	1 cut(s)	526
VpaK11BI	GGWCC	2 cut(s)	275, 755
XapI	RAATTY	1 cut(s)	822
XceI	RCATGY	1 cut(s)	204
XhoI	CTCGAG	1 cut(s)	885
XmiI	GTMKAC	1 cut(s)	109
XspI	CTAG	3 cut(s)	23, 330, 1230

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