Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0005055

Physical Location & Seq

Genomic Coordinates Forward (+)

8236725 .. 8238262

Gene Structure 1538 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG091000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 555 bp

ATGGCTTCCACCACCCCAGAAAAGCACGTCTATTCCGTGTGGGCGCTTCCACCGGACGACGTGACCCCCAGGCTCAAGAAGCTCATGGAGGGCCTCCGCGCCGAATTCAACGGGCCCTACTTCGACCCCCACATCACCGTCGTGGGGGCCATCACCTTGACCCCCGAAGACGCTCTCAACAAGTTTGAAACGGCCTCGCAGGCCGTGAAGGCCTACCAAGCCAAAGTTGAGAGCGTCGCCACTGGAACTTTCTTTTACCAGTGTGTGTTCCTCCTCATCAATCCCACTCCCCAGGTGGTGGAAGCTAGTGCAATCTGCTGTGGGCATTTTGGTTACAATAGCTCAACTCCTTACATGCCACATCTGAGTCTCCTGTACGCAGATCTGAGTGATGAAGATAAGAATAAAGCTCAAGAGAAAGCCAGCATTCTGGACGAGAGTATTGCTAGTCTGAGCTTCCCCGTTACTCGCCTTGCATTGTACAAAACTGACACTGAAGATAAAACTCTAAAATCTTGGGAGAAGATTGCTGAGTGCACACTCCAACCCAATTAG

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

184

Amino Acids

20.38

Weight (kDa)

5.07

Isoelectric Point (pI)

37.66

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CPDase	PF07823	12 - 145	7.4e-12	Cyclic phosphodiesterase-like protein
2_5_RNA_ligase2	PF13563	42 - 165	8.7e-09	2'-5' RNA ligase superfamily

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)

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Publication-ready

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Orthologous Genes (Group: OG0005055)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G18930
fragaria_vesca	FvH4_3g06750 FvH4_3g06750 FvH4_3g06750 FvH4_6g06860 FvH4_6g06860
malus_domestica	MD10G1271200.v1.1 MD10G1271300.v1.1
prunus_persica	Prupe.4G070300_v2.0.a1 Prupe.6G318900_v2.0.a1
pyrus_communis	pycom10g22700
rosa_chinensis	RchiOBHm_Chr3g0456341 RchiOBHm_Chr5g0012411
rosa_laevigata	RLG00000025311 RLG00000031911
rosa_multiflora	Rmu_co8444057.1_g000001 Rmu_sc0002607.1_g000022 Rmu_sc0018054.1_g000004
rosa_roxburghii	Rroxscaffold_1G00064260 Rroxscaffold_6G00422810
rosa_rugosa	Rorug05G0000900
rosa_samantha	Rh3AG072700 Rh3BG074800 Rh3CG074400 Rh5AG095400 Rh5AG499800 Rh5BG091600 Rh5DG091000
rosa_wichuraiana	Rw3G006240 Rw5G008340

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	298
AccII	CGCG	1 cut(s)	99
AciI	CCGC	1 cut(s)	97
AcsI	RAATTY	1 cut(s)	104
AcuI	CTGAAG	1 cut(s)	516
AfaI	GTAC	2 cut(s)	377, 482
AfiI	CCNNNNNNNGG	2 cut(s)	144, 298
AgsI	TTSAA	2 cut(s)	109, 188
AjiI	CACGTC	2 cut(s)	28, 61
AjnI	CCWGG	2 cut(s)	68, 291
AleI	CACNNNNGTG	1 cut(s)	140
AluBI	AGCT	5 cut(s)	82, 305, 342, 410, 456
AluI	AGCT	5 cut(s)	82, 305, 342, 410, 456
Alw21I	GWGCWC	1 cut(s)	539
Alw26I	GTCTC	1 cut(s)	374
Alw44I	GTGCAC	1 cut(s)	535
AoxI	GGCC	6 cut(s)	91, 113, 147, 192, 201, 210
ApaI	GGGCCC	1 cut(s)	117
ApaLI	GTGCAC	1 cut(s)	535
ApoI	RAATTY	1 cut(s)	104
AspLEI	GCGC	2 cut(s)	46, 101
AspS9I	GGNCC	4 cut(s)	91, 113, 114, 147
AsuHPI	GGTGA	2 cut(s)	127, 145
BaeGI	GKGCMC	2 cut(s)	117, 539
BanII	GRGCYC	1 cut(s)	117
BbsI	GAAGAC	1 cut(s)	174
Bbv12I	GWGCWC	1 cut(s)	539
BccI	CCATC	1 cut(s)	158
BceAI	ACGGC	2 cut(s)	188, 207
BcgI	CGANNNNNNTGC	2 cut(s)	425, 459
BciT130I	CCWGG	2 cut(s)	70, 293
BcoDI	GTCTC	1 cut(s)	374
BfaI	CTAG	2 cut(s)	306, 447
BfoI	RGCGCY	1 cut(s)	47
BglI	GCCNNNNNGGC	2 cut(s)	200, 209
BglII	AGATCT	1 cut(s)	382
Bme1390I	CCNGG	2 cut(s)	70, 293
BmgBI	CACGTC	2 cut(s)	28, 61
BmgT120I	GGNCC	4 cut(s)	91, 113, 114, 147
BmiI	GGNNCC	2 cut(s)	115, 148
BmrFI	CCNGG	2 cut(s)	70, 293
BpiI	GAAGAC	1 cut(s)	174
BpuEI	CTTGAG	2 cut(s)	59, 396
BsaJI	CCNNGG	2 cut(s)	68, 291
BsaWI	WCCGGW	1 cut(s)	52
Bsc4I	CCNNNNNNNGG	2 cut(s)	144, 298
Bse1I	ACTGG	2 cut(s)	247, 259
BseBI	CCWGG	2 cut(s)	70, 293
BseDI	CCNNGG	2 cut(s)	68, 291
BseLI	CCNNNNNNNGG	2 cut(s)	144, 298
BseMII	CTCAG	4 cut(s)	356, 377, 443, 522
BseNI	ACTGG	2 cut(s)	247, 259
BseRI	GAGGAG	1 cut(s)	263
BseSI	GKGCMC	2 cut(s)	117, 539
Bsh1236I	CGCG	1 cut(s)	99
BshFI	GGCC	6 cut(s)	93, 115, 149, 194, 203, 212
BsiHKAI	GWGCWC	1 cut(s)	539
BsiSI	CCGG	1 cut(s)	53
BslI	CCNNNNNNNGG	2 cut(s)	144, 298
BsmAI	GTCTC	1 cut(s)	374
BsmI	GAATGC	1 cut(s)	426
BsnI	GGCC	6 cut(s)	93, 115, 149, 194, 203, 212
Bsp120I	GGGCCC	1 cut(s)	113
Bsp1286I	GDGCHC	2 cut(s)	117, 539
Bsp1407I	TGTACA	1 cut(s)	480
Bsp143I	GATC	1 cut(s)	382
BspACI	CCGC	1 cut(s)	97
BspANI	GGCC	6 cut(s)	93, 115, 149, 194, 203, 212
BspCNI	CTCAG	4 cut(s)	357, 378, 444, 523
BspFNI	CGCG	1 cut(s)	99
BspLI	GGNNCC	2 cut(s)	115, 148
BsrGI	TGTACA	1 cut(s)	480
BsrI	ACTGG	2 cut(s)	247, 259
BssECI	CCNNGG	2 cut(s)	68, 291
BssMI	GATC	1 cut(s)	382
Bst2UI	CCWGG	2 cut(s)	70, 293
Bst4CI	ACNGT	1 cut(s)	139
BstAUI	TGTACA	1 cut(s)	480
BstC8I	GCNNGC	2 cut(s)	201, 424
BstDEI	CTNAG	4 cut(s)	365, 386, 452, 531
BstFNI	CGCG	1 cut(s)	99
BstH2I	RGCGCY	1 cut(s)	47
BstHHI	GCGC	2 cut(s)	46, 101
BstKTI	GATC	1 cut(s)	385
BstMAI	GTCTC	1 cut(s)	374
BstMBI	GATC	1 cut(s)	382
BstMWI	GCNNNNNNNGC	4 cut(s)	79, 200, 209, 218
BstNI	CCWGG	2 cut(s)	70, 293
BstNSI	RCATGY	1 cut(s)	358
BstSCI	CCNGG	2 cut(s)	68, 291
BstSLI	GKGCMC	2 cut(s)	117, 539
BstUI	CGCG	1 cut(s)	99
BstV2I	GAAGAC	1 cut(s)	174
BstX2I	RGATCY	1 cut(s)	382
BstXI	CCANNNNNNTGG	1 cut(s)	430
BstYI	RGATCY	1 cut(s)	382
BsuRI	GGCC	6 cut(s)	93, 115, 149, 194, 203, 212
BtrI	CACGTC	2 cut(s)	28, 61
BtsIMutI	CAGTG	3 cut(s)	240, 266, 492
Cac8I	GCNNGC	2 cut(s)	201, 424
CfoI	GCGC	2 cut(s)	46, 101
Cfr13I	GGNCC	4 cut(s)	91, 113, 114, 147
CseI	GACGC	2 cut(s)	179, 223
Csp6I	GTAC	2 cut(s)	376, 481
CviAII	CATG	2 cut(s)	85, 355
CviQI	GTAC	2 cut(s)	376, 481
DdeI	CTNAG	4 cut(s)	365, 386, 452, 531
DpnI	GATC	1 cut(s)	384
DpnII	GATC	1 cut(s)	382
Eco147I	AGGCCT	1 cut(s)	212
Eco24I	GRGCYC	1 cut(s)	117
Eco57I	CTGAAG	1 cut(s)	516
EcoO109I	RGGNCCY	2 cut(s)	91, 114
EcoRI	GAATTC	1 cut(s)	104
EcoRII	CCWGG	2 cut(s)	68, 291
EcoT38I	GRGCYC	1 cut(s)	117
FaeI	CATG	2 cut(s)	88, 358
FaiI	YATR	2 cut(s)	86, 356
FatI	CATG	2 cut(s)	84, 354
FriOI	GRGCYC	1 cut(s)	117
FspBI	CTAG	2 cut(s)	306, 447
GlaI	GCGC	2 cut(s)	45, 100
HaeII	RGCGCY	1 cut(s)	47
HaeIII	GGCC	6 cut(s)	93, 115, 149, 194, 203, 212
HapII	CCGG	1 cut(s)	53
HgaI	GACGC	2 cut(s)	179, 223
HhaI	GCGC	2 cut(s)	46, 101
Hin1II	CATG	2 cut(s)	88, 358
Hin6I	GCGC	2 cut(s)	44, 99
HinP1I	GCGC	2 cut(s)	44, 99
HinfI	GANTC	1 cut(s)	367
HpaII	CCGG	1 cut(s)	53
HphI	GGTGA	2 cut(s)	127, 145
Hpy166II	GTNNAC	1 cut(s)	537
Hpy188I	TCNGA	3 cut(s)	366, 387, 453
Hpy188III	TCNNGA	3 cut(s)	76, 413, 431
Hpy8I	GTNNAC	1 cut(s)	537
Hpy99I	CGWCG	3 cut(s)	62, 143, 239
HpyAV	CCTTC	1 cut(s)	202
HpyCH4III	ACNGT	1 cut(s)	139
HpyCH4IV	ACGT	2 cut(s)	27, 60
HpyCH4V	TGCA	3 cut(s)	311, 476, 537
HpyF10VI	GCNNNNNNNGC	4 cut(s)	79, 200, 209, 218
HpyF3I	CTNAG	4 cut(s)	365, 386, 452, 531
HpySE526I	ACGT	2 cut(s)	27, 60
Hsp92II	CATG	2 cut(s)	88, 358
HspAI	GCGC	2 cut(s)	44, 99
Kzo9I	GATC	1 cut(s)	382
MaeI	CTAG	2 cut(s)	306, 447
MaeII	ACGT	2 cut(s)	27, 60
MaeIII	GTNAC	3 cut(s)	61, 332, 463
MalI	GATC	1 cut(s)	384
MboI	GATC	1 cut(s)	382
MboII	GAAGA	4 cut(s)	179, 407, 509, 535
MflI	RGATCY	1 cut(s)	382
MhlI	GDGCHC	2 cut(s)	117, 539
MluCI	AATT	2 cut(s)	104, 550
MlyI	GAGTC	1 cut(s)	376
MnlI	CCTC	5 cut(s)	82, 104, 205, 281, 284
MslI	CAYNNNNRTG	1 cut(s)	140
MspI	CCGG	1 cut(s)	53
MspR9I	CCNGG	2 cut(s)	70, 293
Mva1269I	GAATGC	1 cut(s)	426
MvaI	CCWGG	2 cut(s)	70, 293
MvnI	CGCG	1 cut(s)	99
MwoI	GCNNNNNNNGC	4 cut(s)	79, 200, 209, 218
NdeII	GATC	1 cut(s)	382
NlaIII	CATG	2 cut(s)	88, 358
NlaIV	GGNNCC	2 cut(s)	115, 148
NmuCI	GTSAC	1 cut(s)	61
NspI	RCATGY	1 cut(s)	358
OliI	CACNNNNGTG	1 cut(s)	140
PceI	AGGCCT	1 cut(s)	212
PcsI	WCGNNNNNNNCGW	1 cut(s)	33
PctI	GAATGC	1 cut(s)	426
PflMI	CCANNNNNTGG	1 cut(s)	298
PleI	GAGTC	1 cut(s)	375
PpsI	GAGTC	1 cut(s)	375
Psp6I	CCWGG	2 cut(s)	68, 291
PspGI	CCWGG	2 cut(s)	68, 291
PspN4I	GGNNCC	2 cut(s)	115, 148
PspOMI	GGGCCC	1 cut(s)	113
PspPI	GGNCC	4 cut(s)	91, 113, 114, 147
PsuI	RGATCY	1 cut(s)	382
RsaI	GTAC	2 cut(s)	377, 482
RsaNI	GTAC	2 cut(s)	376, 481
RseI	CAYNNNNRTG	1 cut(s)	140
Sau3AI	GATC	1 cut(s)	382
Sau96I	GGNCC	4 cut(s)	91, 113, 114, 147
SchI	GAGTC	1 cut(s)	376
ScrFI	CCNGG	2 cut(s)	70, 293
SduI	GDGCHC	2 cut(s)	117, 539
SetI	ASST	9 cut(s)	30, 63, 84, 158, 297, 307, 344, 412, 458
SfiI	GGCCNNNNNGGCC	2 cut(s)	200, 209
SmiMI	CAYNNNNRTG	1 cut(s)	140
SmlI	CTYRAG	2 cut(s)	74, 411
SmoI	CTYRAG	2 cut(s)	74, 411
Sse9I	AATT	2 cut(s)	104, 550
SseBI	AGGCCT	1 cut(s)	212
SsiI	CCGC	1 cut(s)	97
SspMI	CTAG	2 cut(s)	306, 447
StuI	AGGCCT	1 cut(s)	212
StyD4I	CCNGG	2 cut(s)	68, 291
TaaI	ACNGT	1 cut(s)	139
TaiI	ACGT	2 cut(s)	30, 63
TaqI	TCGA	1 cut(s)	123
TasI	AATT	2 cut(s)	104, 550
TatI	WGTACW	1 cut(s)	480
TscAI	CASTG	3 cut(s)	247, 266, 499
TseFI	GTSAC	1 cut(s)	61
Tsp45I	GTSAC	1 cut(s)	61
TspDTI	ATGAA	1 cut(s)	408
TspGWI	ACGGA	1 cut(s)	25
TspRI	CASTG	3 cut(s)	247, 266, 499
Van91I	CCANNNNNTGG	1 cut(s)	298
VneI	GTGCAC	1 cut(s)	535
XapI	RAATTY	1 cut(s)	104
XceI	RCATGY	1 cut(s)	358
XcmI	CCANNNNNNNNNTGG	1 cut(s)	292
XspI	CTAG	2 cut(s)	306, 447

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