Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000006

Orthogroup ID

OG0011573

Physical Location & Seq

Genomic Coordinates Forward (+)

43276405 .. 43278481

Gene Structure 2077 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_6G00422350.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 621 bp

ATGGCAAACCAATCTGAACCAAGCACTGCTACCAGCACAGATGATCTGAAGTTGCACCGGTGGGCGGTATGGGCCATCCCACCGGATAGCATTTGTAAGAGAGTTAAAACGGTGATGGAGGTCCTCCGGAAGGAATTTGGTGGGCCTGAGGTCGAGCCCCACATCACCGTTGCGGGGTCCATTCTCTTCAATCGCTCAGAGGCCATTGAGAAGTTCATCGGTGCATGTAATGAGATAAACCCCTATGTTTGTCAAGTTGATCAACTTGAGACTAGCAAATTCTACTTCCAATGTGTTTCCCTAGTCTTTCAGACAGATCATCAGTTAACACAGGAAACTGGACTCCTCGCTGGGCGTATGTATTGCAATAGTGCTAATATGCCACATTTGAGCTTGTTCTATGGGGATCTTACAGACGAAGAGAAGAAAAGAGCAGTAGAAATAGTGAAGAGTGTCGATGAGGGACTTTGTAATATGCCACATCTGAGTCTCCTTTATGGGGAGCTGACAGATGAAGAGAAGAAAAGAACTCAAGGAAAAGTTAGTGTTCTGGATGAGACCATTACCAGCCTCAATTTCACCATAGCTGGCCTTGCGCGCACTGTACAAATGTCACGATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000394 GO:0003674 GO:0003824 GO:0004112 GO:0004113 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006388 GO:0006396 GO:0006399 GO:0006725 GO:0006753 GO:0006793 GO:0006796 GO:0006807 GO:0008033 GO:0008081 GO:0008150 GO:0008152 GO:0008380 GO:0009117 GO:0009187 GO:0009987 GO:0010467 GO:0016070 GO:0016787 GO:0016788 GO:0019637 GO:0034470 GO:0034641 GO:0034660 GO:0042578 GO:0043170 GO:0044237 GO:0044238 GO:0044281 GO:0044424 GO:0044464 GO:0046483 GO:0055086 GO:0071704 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

2_5_RNA_ligase2 CPDase

Protein Analysis

206

Amino Acids

23.12

Weight (kDa)

5.29

Isoelectric Point (pI)

45.01

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CPDase	PF07823	22 - 155	9.6e-08	Cyclic phosphodiesterase-like protein

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0011573)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_6g07330
rosa_chinensis	RchiOBHm_Chr3g0456941 RchiOBHm_Chr3g0457361
rosa_laevigata	RLG00000025232 RLG00000025262
rosa_multiflora	Rmu_sc0005442.1_g000007 Rmu_sc0011220.1_g000001 Rmu_sc0016008.1_g000002
rosa_roxburghii	Rroxscaffold_6G00421950 Rroxscaffold_6G00422350
rosa_rugosa	Rorug03G0017500 Rorug03G0020100
rosa_samantha	Rh3AG077500 Rh3AG080300 Rh3BG079400 Rh3BG082100 Rh3CG079300 Rh3CG082400 Rh3DG081100
rosa_wichuraiana	Rw3G006640

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	598
AccIII	TCCGGA	1 cut(s)	126
AciI	CCGC	2 cut(s)	65, 173
AclWI	GGATC	1 cut(s)	414
AcsI	RAATTY	2 cut(s)	134, 278
AcuI	CTGAAG	1 cut(s)	68
AfaI	GTAC	1 cut(s)	606
AfiI	CCNNNNNNNGG	4 cut(s)	64, 130, 174, 499
AgeI	ACCGGT	1 cut(s)	57
AgsI	TTSAA	1 cut(s)	190
AluBI	AGCT	3 cut(s)	393, 505, 587
AluI	AGCT	3 cut(s)	393, 505, 587
Alw26I	GTCTC	3 cut(s)	263, 494, 551
AlwI	GGATC	1 cut(s)	414
Aor13HI	TCCGGA	1 cut(s)	126
AoxI	GGCC	4 cut(s)	72, 143, 201, 589
ApoI	RAATTY	2 cut(s)	134, 278
AsiGI	ACCGGT	1 cut(s)	57
AspLEI	GCGC	2 cut(s)	598, 600
AspS9I	GGNCC	4 cut(s)	72, 121, 143, 177
AsuHPI	GGTGA	3 cut(s)	124, 157, 571
AvaII	GGWCC	2 cut(s)	121, 177
AxyI	CCTNAGG	1 cut(s)	147
BanII	GRGCYC	1 cut(s)	159
BccI	CCATC	2 cut(s)	83, 109
BclI	TGATCA	1 cut(s)	259
BcoDI	GTCTC	3 cut(s)	263, 494, 551
BfaI	CTAG	2 cut(s)	273, 302
Bme18I	GGWCC	2 cut(s)	121, 177
BmgT120I	GGNCC	4 cut(s)	72, 121, 143, 177
BmiI	GGNNCC	1 cut(s)	178
BpuEI	CTTGAG	2 cut(s)	287, 516
BsaI	GGTCTC	1 cut(s)	551
BsaWI	WCCGGW	3 cut(s)	57, 82, 126
Bsc4I	CCNNNNNNNGG	4 cut(s)	64, 130, 174, 499
Bse118I	RCCGGY	1 cut(s)	57
Bse1I	ACTGG	1 cut(s)	343
Bse21I	CCTNAGG	1 cut(s)	147
BseAI	TCCGGA	1 cut(s)	126
BseGI	GGATG	2 cut(s)	75, 559
BseLI	CCNNNNNNNGG	4 cut(s)	64, 130, 174, 499
BseMII	CTCAG	3 cut(s)	138, 210, 476
BseNI	ACTGG	1 cut(s)	343
BsePI	GCGCGC	1 cut(s)	596
BseRI	GAGGAG	1 cut(s)	335
BseYI	CCCAGC	1 cut(s)	350
Bsh1236I	CGCG	1 cut(s)	598
BshFI	GGCC	4 cut(s)	74, 145, 203, 591
BshTI	ACCGGT	1 cut(s)	57
BsiSI	CCGG	3 cut(s)	58, 83, 127
BslFI	GGGAC	1 cut(s)	477
BslI	CCNNNNNNNGG	4 cut(s)	64, 130, 174, 499
BsmAI	GTCTC	3 cut(s)	263, 494, 551
BsmFI	GGGAC	1 cut(s)	477
BsnI	GGCC	4 cut(s)	74, 145, 203, 591
Bso31I	GGTCTC	1 cut(s)	551
Bsp1286I	GDGCHC	1 cut(s)	159
Bsp13I	TCCGGA	1 cut(s)	126
Bsp1407I	TGTACA	1 cut(s)	604
Bsp143I	GATC	4 cut(s)	43, 259, 316, 406
BspACI	CCGC	2 cut(s)	65, 173
BspANI	GGCC	4 cut(s)	74, 145, 203, 591
BspCNI	CTCAG	3 cut(s)	139, 209, 477
BspEI	TCCGGA	1 cut(s)	126
BspFNI	CGCG	1 cut(s)	598
BspLI	GGNNCC	1 cut(s)	178
BspPI	GGATC	1 cut(s)	414
BspTNI	GGTCTC	1 cut(s)	551
BsrFI	RCCGGY	1 cut(s)	57
BsrGI	TGTACA	1 cut(s)	604
BsrI	ACTGG	1 cut(s)	343
BssAI	RCCGGY	1 cut(s)	57
BssHII	GCGCGC	1 cut(s)	596
BssMI	GATC	4 cut(s)	43, 259, 316, 406
Bst4CI	ACNGT	3 cut(s)	112, 169, 604
Bst6I	CTCTTC	4 cut(s)	191, 414, 443, 510
BstAUI	TGTACA	1 cut(s)	604
BstC8I	GCNNGC	2 cut(s)	589, 598
BstDEI	CTNAG	3 cut(s)	147, 196, 485
BstENI	CCTNNNNNAGG	1 cut(s)	128
BstF5I	GGATG	2 cut(s)	75, 559
BstFNI	CGCG	1 cut(s)	598
BstHHI	GCGC	2 cut(s)	598, 600
BstKTI	GATC	4 cut(s)	46, 262, 319, 409
BstMAI	GTCTC	3 cut(s)	263, 494, 551
BstMBI	GATC	4 cut(s)	43, 259, 316, 406
BstMWI	GCNNNNNNNGC	3 cut(s)	71, 593, 597
BstNSI	RCATGY	1 cut(s)	228
BstUI	CGCG	1 cut(s)	598
BstX2I	RGATCY	1 cut(s)	406
BstYI	RGATCY	1 cut(s)	406
Bsu36I	CCTNAGG	1 cut(s)	147
BsuRI	GGCC	4 cut(s)	74, 145, 203, 591
BtsCI	GGATG	2 cut(s)	75, 559
BtsI	GCAGTG	1 cut(s)	24
BtsIMutI	CAGTG	2 cut(s)	24, 600
Cac8I	GCNNGC	2 cut(s)	589, 598
CfoI	GCGC	2 cut(s)	598, 600
Cfr10I	RCCGGY	1 cut(s)	57
Cfr13I	GGNCC	4 cut(s)	72, 121, 143, 177
Csp6I	GTAC	1 cut(s)	605
CspAI	ACCGGT	1 cut(s)	57
CviAII	CATG	1 cut(s)	225
CviJI	RGCY	9 cut(s)	74, 145, 157, 203, 393, 505, 570, 587, 591
CviKI_1	RGCY	9 cut(s)	74, 145, 157, 203, 393, 505, 570, 587, 591
CviQI	GTAC	1 cut(s)	605
DdeI	CTNAG	3 cut(s)	147, 196, 485
DpnI	GATC	4 cut(s)	45, 261, 318, 408
DpnII	GATC	4 cut(s)	43, 259, 316, 406
Eam1104I	CTCTTC	4 cut(s)	191, 414, 443, 510
EarI	CTCTTC	4 cut(s)	191, 414, 443, 510
Eco24I	GRGCYC	1 cut(s)	159
Eco31I	GGTCTC	1 cut(s)	551
Eco47I	GGWCC	2 cut(s)	121, 177
Eco57I	CTGAAG	1 cut(s)	68
Eco81I	CCTNAGG	1 cut(s)	147
EcoNI	CCTNNNNNAGG	1 cut(s)	128
EcoO109I	RGGNCCY	1 cut(s)	121
EcoT38I	GRGCYC	1 cut(s)	159
FaeI	CATG	1 cut(s)	228
FaiI	YATR	9 cut(s)	70, 226, 246, 359, 380, 402, 476, 498, 584
FaqI	GGGAC	1 cut(s)	477
FatI	CATG	1 cut(s)	224
FauI	CCCGC	1 cut(s)	166
FbaI	TGATCA	1 cut(s)	259
FokI	GGATG	2 cut(s)	62, 566
FriOI	GRGCYC	1 cut(s)	159
FspBI	CTAG	2 cut(s)	273, 302
GlaI	GCGC	2 cut(s)	597, 599
GsaI	CCCAGC	1 cut(s)	354
HaeIII	GGCC	4 cut(s)	74, 145, 203, 591
HapII	CCGG	3 cut(s)	58, 83, 127
HhaI	GCGC	2 cut(s)	598, 600
Hin1II	CATG	1 cut(s)	228
Hin6I	GCGC	2 cut(s)	596, 598
HinP1I	GCGC	2 cut(s)	596, 598
HincII	GTYRAC	1 cut(s)	327
HindII	GTYRAC	1 cut(s)	327
HinfI	GANTC	2 cut(s)	342, 487
HpaI	GTTAAC	1 cut(s)	327
HpaII	CCGG	3 cut(s)	58, 83, 127
HphI	GGTGA	3 cut(s)	124, 157, 571
Hpy166II	GTNNAC	1 cut(s)	327
Hpy188I	TCNGA	5 cut(s)	16, 48, 199, 312, 486
Hpy188III	TCNNGA	3 cut(s)	127, 551, 615
Hpy8I	GTNNAC	1 cut(s)	327
HpyAV	CCTTC	1 cut(s)	124
HpyCH4III	ACNGT	3 cut(s)	112, 169, 604
HpyCH4V	TGCA	3 cut(s)	55, 224, 366
HpyF10VI	GCNNNNNNNGC	3 cut(s)	71, 593, 597
HpyF3I	CTNAG	3 cut(s)	147, 196, 485
Hsp92II	CATG	1 cut(s)	228
HspAI	GCGC	2 cut(s)	596, 598
Kpn2I	TCCGGA	1 cut(s)	126
Ksp22I	TGATCA	1 cut(s)	259
KspAI	GTTAAC	1 cut(s)	327
Kzo9I	GATC	4 cut(s)	43, 259, 316, 406
LmnI	GCTCC	1 cut(s)	502
MaeI	CTAG	2 cut(s)	273, 302
MaeIII	GTNAC	1 cut(s)	612
MalI	GATC	4 cut(s)	45, 261, 318, 408
MboI	GATC	4 cut(s)	43, 259, 316, 406
MboII	GAAGA	6 cut(s)	178, 431, 436, 460, 527, 532
MflI	RGATCY	1 cut(s)	406
MhlI	GDGCHC	1 cut(s)	159
MluCI	AATT	3 cut(s)	134, 278, 574
MlyI	GAGTC	2 cut(s)	336, 496
MnlI	CCTC	7 cut(s)	112, 134, 142, 193, 356, 454, 581
MroI	TCCGGA	1 cut(s)	126
MseI	TTAA	2 cut(s)	105, 326
MspI	CCGG	3 cut(s)	58, 83, 127
MvnI	CGCG	1 cut(s)	598
MwoI	GCNNNNNNNGC	3 cut(s)	71, 593, 597
NdeII	GATC	4 cut(s)	43, 259, 316, 406
NlaIII	CATG	1 cut(s)	228
NlaIV	GGNNCC	1 cut(s)	178
NmuCI	GTSAC	1 cut(s)	612
NspI	RCATGY	1 cut(s)	228
PauI	GCGCGC	1 cut(s)	596
PinAI	ACCGGT	1 cut(s)	57
PleI	GAGTC	2 cut(s)	336, 495
PpsI	GAGTC	2 cut(s)	336, 495
PpuMI	RGGWCCY	1 cut(s)	121
Psp5II	RGGWCCY	1 cut(s)	121
PspFI	CCCAGC	1 cut(s)	350
PspN4I	GGNNCC	1 cut(s)	178
PspPI	GGNCC	4 cut(s)	72, 121, 143, 177
PspPPI	RGGWCCY	1 cut(s)	121
PsuI	RGATCY	1 cut(s)	406
PteI	GCGCGC	1 cut(s)	596
RsaI	GTAC	1 cut(s)	606
RsaNI	GTAC	1 cut(s)	605
SaqAI	TTAA	2 cut(s)	105, 326
Sau3AI	GATC	4 cut(s)	43, 259, 316, 406
Sau96I	GGNCC	4 cut(s)	72, 121, 143, 177
SchI	GAGTC	2 cut(s)	336, 496
SduI	GDGCHC	1 cut(s)	159
SetI	ASST	5 cut(s)	123, 153, 395, 507, 589
SgrAI	CRCCGGYG	1 cut(s)	57
SinI	GGWCC	2 cut(s)	121, 177
SmlI	CTYRAG	2 cut(s)	266, 531
SmoI	CTYRAG	2 cut(s)	266, 531
Sse9I	AATT	3 cut(s)	134, 278, 574
SsiI	CCGC	2 cut(s)	65, 173
SspMI	CTAG	2 cut(s)	273, 302
TaaI	ACNGT	3 cut(s)	112, 169, 604
TaqI	TCGA	2 cut(s)	153, 456
TasI	AATT	3 cut(s)	134, 278, 574
TatI	WGTACW	1 cut(s)	604
Tru1I	TTAA	2 cut(s)	105, 326
Tru9I	TTAA	2 cut(s)	105, 326
TscAI	CASTG	2 cut(s)	31, 607
TseFI	GTSAC	1 cut(s)	612
Tsp45I	GTSAC	1 cut(s)	612
TspDTI	ATGAA	2 cut(s)	205, 528
TspRI	CASTG	2 cut(s)	31, 607
VpaK11BI	GGWCC	2 cut(s)	121, 177
XagI	CCTNNNNNAGG	1 cut(s)	128
XapI	RAATTY	2 cut(s)	134, 278
XceI	RCATGY	1 cut(s)	228
XspI	CTAG	2 cut(s)	273, 302

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