Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0011573

Physical Location & Seq

Genomic Coordinates Reverse (-)

6177308 .. 6178498

Gene Structure 1191 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG079400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 582 bp

ATGGCAAACCAATCTGAACCAAGCACTGCTACCAGCACAGATGATCTGAAGTTGCACCGGTGGGCGGTATGGGCCATCCCACCGGATAGCATTTGTAAGAGAGTTAAAACGGTGATGGAGGCCCTCCGGAAAGAATTTGGTGGGTCTGAGGTCGAGCCCCACATCACCGTTGCGGGGTCCATTCTCTTCAATCGCTCAGAGGCCATTGAGAAGTTCATCGGTGCATGTAATGAGATAAACCCCTATGTTTGTCAAGTCGATCAACTTGAGACTAGCAAATTCTACTTCCAATGTGTTTCCCTAGTCTTTCAGACAGATCATCAGTTAACACAGGAAACTGGACTCCTCGCTGGGCGTATGTATTGCAATAGTGCTAATATGCCACATTTGAGCTTGTTCTATGGGGATCTTACAGATGAAGAGAAGAAAAGAGCAGTAGAAATAGTGAAGAGTGTCGATGAGGGACTTTGTACCATTAGCTTCACCATATATCGGATGCAATTGTACAGGGTTAACTTCGAAGATAAAACTCAAAAATCTTGGGAGATGGTTTCTGAATGCAACCTTCGACCCAAAATCTAG

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

193

Amino Acids

22.05

Weight (kDa)

5.44

Isoelectric Point (pI)

45.18

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CPDase	PF07823	22 - 182	3.9e-09	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)

Image

Tree File

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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)
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	2 cut(s)	472, 506
AfiI	CCNNNNNNNGG	3 cut(s)	64, 174, 492
AgeI	ACCGGT	1 cut(s)	57
AgsI	TTSAA	1 cut(s)	190
AluBI	AGCT	2 cut(s)	393, 480
AluI	AGCT	2 cut(s)	393, 480
Alw26I	GTCTC	1 cut(s)	263
AlwI	GGATC	1 cut(s)	414
Aor13HI	TCCGGA	1 cut(s)	126
AoxI	GGCC	3 cut(s)	72, 120, 201
ApoI	RAATTY	2 cut(s)	134, 278
AsiGI	ACCGGT	1 cut(s)	57
AspS9I	GGNCC	3 cut(s)	72, 121, 177
AsuHPI	GGTGA	3 cut(s)	124, 157, 475
AsuII	TTCGAA	1 cut(s)	519
AvaII	GGWCC	1 cut(s)	177
BanII	GRGCYC	1 cut(s)	159
BccI	CCATC	3 cut(s)	83, 109, 541
BcoDI	GTCTC	1 cut(s)	263
BfaI	CTAG	3 cut(s)	273, 302, 580
Bme18I	GGWCC	1 cut(s)	177
BmgT120I	GGNCC	3 cut(s)	72, 121, 177
BmiI	GGNNCC	1 cut(s)	178
BmsI	GCATC	1 cut(s)	486
Bpu14I	TTCGAA	1 cut(s)	519
BpuEI	CTTGAG	1 cut(s)	287
BsaWI	WCCGGW	3 cut(s)	57, 82, 126
Bsc4I	CCNNNNNNNGG	3 cut(s)	64, 174, 492
Bse118I	RCCGGY	1 cut(s)	57
Bse1I	ACTGG	1 cut(s)	343
BseAI	TCCGGA	1 cut(s)	126
BseGI	GGATG	2 cut(s)	75, 501
BseLI	CCNNNNNNNGG	3 cut(s)	64, 174, 492
BseMII	CTCAG	2 cut(s)	138, 210
BseNI	ACTGG	1 cut(s)	343
BseRI	GAGGAG	1 cut(s)	335
BseYI	CCCAGC	1 cut(s)	350
BshFI	GGCC	3 cut(s)	74, 122, 203
BshTI	ACCGGT	1 cut(s)	57
BsiSI	CCGG	3 cut(s)	58, 83, 127
BslFI	GGGAC	1 cut(s)	477
BslI	CCNNNNNNNGG	3 cut(s)	64, 174, 492
BsmAI	GTCTC	1 cut(s)	263
BsmFI	GGGAC	1 cut(s)	477
BsmI	GAATGC	1 cut(s)	563
BsnI	GGCC	3 cut(s)	74, 122, 203
Bsp119I	TTCGAA	1 cut(s)	519
Bsp1286I	GDGCHC	1 cut(s)	159
Bsp13I	TCCGGA	1 cut(s)	126
Bsp1407I	TGTACA	1 cut(s)	504
Bsp143I	GATC	4 cut(s)	43, 259, 316, 406
BspACI	CCGC	2 cut(s)	65, 173
BspANI	GGCC	3 cut(s)	74, 122, 203
BspCNI	CTCAG	2 cut(s)	139, 209
BspEI	TCCGGA	1 cut(s)	126
BspLI	GGNNCC	1 cut(s)	178
BspPI	GGATC	1 cut(s)	414
BspT104I	TTCGAA	1 cut(s)	519
BsrFI	RCCGGY	1 cut(s)	57
BsrGI	TGTACA	1 cut(s)	504
BsrI	ACTGG	1 cut(s)	343
BssAI	RCCGGY	1 cut(s)	57
BssMI	GATC	4 cut(s)	43, 259, 316, 406
Bst4CI	ACNGT	2 cut(s)	112, 169
Bst6I	CTCTTC	3 cut(s)	191, 414, 443
BstAUI	TGTACA	1 cut(s)	504
BstBI	TTCGAA	1 cut(s)	519
BstDEI	CTNAG	2 cut(s)	147, 196
BstF5I	GGATG	2 cut(s)	75, 501
BstKTI	GATC	4 cut(s)	46, 262, 319, 409
BstMAI	GTCTC	1 cut(s)	263
BstMBI	GATC	4 cut(s)	43, 259, 316, 406
BstMWI	GCNNNNNNNGC	1 cut(s)	71
BstNSI	RCATGY	1 cut(s)	228
BstX2I	RGATCY	1 cut(s)	406
BstYI	RGATCY	1 cut(s)	406
BsuRI	GGCC	3 cut(s)	74, 122, 203
BtsCI	GGATG	2 cut(s)	75, 501
BtsI	GCAGTG	1 cut(s)	24
BtsIMutI	CAGTG	1 cut(s)	24
Cfr10I	RCCGGY	1 cut(s)	57
Cfr13I	GGNCC	3 cut(s)	72, 121, 177
Csp6I	GTAC	2 cut(s)	471, 505
CspAI	ACCGGT	1 cut(s)	57
CviAII	CATG	1 cut(s)	225
CviJI	RGCY	6 cut(s)	74, 122, 157, 203, 393, 480
CviKI_1	RGCY	6 cut(s)	74, 122, 157, 203, 393, 480
CviQI	GTAC	2 cut(s)	471, 505
DdeI	CTNAG	2 cut(s)	147, 196
DpnI	GATC	4 cut(s)	45, 261, 318, 408
DpnII	GATC	4 cut(s)	43, 259, 316, 406
Eam1104I	CTCTTC	3 cut(s)	191, 414, 443
EarI	CTCTTC	3 cut(s)	191, 414, 443
Eco24I	GRGCYC	1 cut(s)	159
Eco47I	GGWCC	1 cut(s)	177
Eco57I	CTGAAG	1 cut(s)	68
EcoO109I	RGGNCCY	1 cut(s)	121
EcoT38I	GRGCYC	1 cut(s)	159
FaeI	CATG	1 cut(s)	228
FaiI	YATR	8 cut(s)	70, 226, 246, 359, 380, 402, 488, 490
FaqI	GGGAC	1 cut(s)	477
FatI	CATG	1 cut(s)	224
FauI	CCCGC	1 cut(s)	166
FokI	GGATG	2 cut(s)	62, 508
FriOI	GRGCYC	1 cut(s)	159
FspBI	CTAG	3 cut(s)	273, 302, 580
GsaI	CCCAGC	1 cut(s)	354
HaeIII	GGCC	3 cut(s)	74, 122, 203
HapII	CCGG	3 cut(s)	58, 83, 127
Hin1II	CATG	1 cut(s)	228
HincII	GTYRAC	2 cut(s)	327, 514
HindII	GTYRAC	2 cut(s)	327, 514
HinfI	GANTC	1 cut(s)	342
HpaI	GTTAAC	2 cut(s)	327, 514
HpaII	CCGG	3 cut(s)	58, 83, 127
HphI	GGTGA	3 cut(s)	124, 157, 475
Hpy166II	GTNNAC	2 cut(s)	327, 514
Hpy188I	TCNGA	7 cut(s)	16, 48, 148, 199, 312, 495, 556
Hpy188III	TCNNGA	1 cut(s)	127
Hpy8I	GTNNAC	2 cut(s)	327, 514
HpyAV	CCTTC	1 cut(s)	575
HpyCH4III	ACNGT	2 cut(s)	112, 169
HpyCH4V	TGCA	5 cut(s)	55, 224, 366, 499, 561
HpyF10VI	GCNNNNNNNGC	1 cut(s)	71
HpyF3I	CTNAG	2 cut(s)	147, 196
Hsp92II	CATG	1 cut(s)	228
Kpn2I	TCCGGA	1 cut(s)	126
KspAI	GTTAAC	2 cut(s)	327, 514
Kzo9I	GATC	4 cut(s)	43, 259, 316, 406
LpnPI	CCDG	8 cut(s)	46, 71, 96, 140, 317, 324, 336, 493
LweI	GCATC	1 cut(s)	486
MaeI	CTAG	3 cut(s)	273, 302, 580
MalI	GATC	4 cut(s)	45, 261, 318, 408
MboI	GATC	4 cut(s)	43, 259, 316, 406
MboII	GAAGA	5 cut(s)	178, 431, 436, 460, 533
MfeI	CAATTG	1 cut(s)	500
MflI	RGATCY	1 cut(s)	406
MhlI	GDGCHC	1 cut(s)	159
MluCI	AATT	3 cut(s)	134, 278, 500
MlyI	GAGTC	1 cut(s)	336
MnlI	CCTC	6 cut(s)	112, 134, 142, 193, 356, 454
MroI	TCCGGA	1 cut(s)	126
MseI	TTAA	3 cut(s)	105, 326, 513
MspI	CCGG	3 cut(s)	58, 83, 127
MunI	CAATTG	1 cut(s)	500
Mva1269I	GAATGC	1 cut(s)	563
MwoI	GCNNNNNNNGC	1 cut(s)	71
NdeII	GATC	4 cut(s)	43, 259, 316, 406
NlaIII	CATG	1 cut(s)	228
NlaIV	GGNNCC	1 cut(s)	178
NspI	RCATGY	1 cut(s)	228
NspV	TTCGAA	1 cut(s)	519
PctI	GAATGC	1 cut(s)	563
PinAI	ACCGGT	1 cut(s)	57
PleI	GAGTC	1 cut(s)	336
PpsI	GAGTC	1 cut(s)	336
PspFI	CCCAGC	1 cut(s)	350
PspN4I	GGNNCC	1 cut(s)	178
PspPI	GGNCC	3 cut(s)	72, 121, 177
PsuI	RGATCY	1 cut(s)	406
RsaI	GTAC	2 cut(s)	472, 506
RsaNI	GTAC	2 cut(s)	471, 505
SaqAI	TTAA	3 cut(s)	105, 326, 513
Sau3AI	GATC	4 cut(s)	43, 259, 316, 406
Sau96I	GGNCC	3 cut(s)	72, 121, 177
SchI	GAGTC	1 cut(s)	336
SduI	GDGCHC	1 cut(s)	159
SetI	ASST	4 cut(s)	153, 395, 482, 567
SfaNI	GCATC	1 cut(s)	486
SfuI	TTCGAA	1 cut(s)	519
SgrAI	CRCCGGYG	1 cut(s)	57
SinI	GGWCC	1 cut(s)	177
SmlI	CTYRAG	1 cut(s)	266
SmoI	CTYRAG	1 cut(s)	266
Sse9I	AATT	3 cut(s)	134, 278, 500
SsiI	CCGC	2 cut(s)	65, 173
SspMI	CTAG	3 cut(s)	273, 302, 580
TaaI	ACNGT	2 cut(s)	112, 169
TaqI	TCGA	5 cut(s)	153, 258, 456, 519, 568
TasI	AATT	3 cut(s)	134, 278, 500
TatI	WGTACW	1 cut(s)	504
Tru1I	TTAA	3 cut(s)	105, 326, 513
Tru9I	TTAA	3 cut(s)	105, 326, 513
TscAI	CASTG	1 cut(s)	31
TspDTI	ATGAA	2 cut(s)	205, 432
TspRI	CASTG	1 cut(s)	31
VpaK11BI	GGWCC	1 cut(s)	177
XapI	RAATTY	2 cut(s)	134, 278
XceI	RCATGY	1 cut(s)	228
XspI	CTAG	3 cut(s)	273, 302, 580

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