Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0011573

Physical Location & Seq

Genomic Coordinates Forward (+)

6429673 .. 6430422

Gene Structure 750 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG080300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 468 bp

ATGGAGGCCCTCCGGAAGGAATTTGGTGGGCCTGAGGTTGAGCCCCACATTACTGTTGCAGGGTGCATTCTCTTCAATCGCTCAGAGGCCATTGAAAAGTTCATCGGTGCATGTAATGAGATAAACCCCTATGTTTGTCAAGTCGATCAACTTGAGACTAGCAAATTCTATTTCCAATGTGTTTCCCTTGTCTTTCAGACAGATCATCAGTTGACACAGGAAACTGGACTCTTGGCTGCGCGTATGTATTGCAATAGTGCTAATATGCCACATTTGAGCTTGTTCTATGGGGATCTTACAGATGAAGAGAAGAAAAGAGCAGTAGAAATAGTGAAGAGTGTCGATGAGGGACTTTGTACCATTAGCTTCACCATAAATCGGATGCAATTGTATAGGGTTAACTTCGAAGATAAAACTCAAAAATCTTGGGAGATGGTTTCTGAATGCAACCTTCGACCTAAAATCTAA

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

155

Amino Acids

17.8

Weight (kDa)

5.11

Isoelectric Point (pI)

43.51

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CPDase	PF07823	11 - 144	4.3e-06	Cyclic phosphodiesterase-like protein

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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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)	241
AccIII	TCCGGA	1 cut(s)	12
AclWI	GGATC	1 cut(s)	300
AcsI	RAATTY	2 cut(s)	20, 164
AfaI	GTAC	1 cut(s)	358
AfiI	CCNNNNNNNGG	2 cut(s)	16, 378
AgsI	TTSAA	2 cut(s)	76, 95
AluBI	AGCT	2 cut(s)	279, 366
AluI	AGCT	2 cut(s)	279, 366
Alw26I	GTCTC	1 cut(s)	149
AlwI	GGATC	1 cut(s)	300
Aor13HI	TCCGGA	1 cut(s)	12
AoxI	GGCC	3 cut(s)	6, 29, 87
ApeKI	GCWGC	1 cut(s)	236
ApoI	RAATTY	2 cut(s)	20, 164
AspLEI	GCGC	1 cut(s)	241
AspS9I	GGNCC	2 cut(s)	7, 29
AsuHPI	GGTGA	1 cut(s)	361
AsuII	TTCGAA	1 cut(s)	405
AxyI	CCTNAGG	1 cut(s)	33
BanII	GRGCYC	1 cut(s)	45
BbvI	GCAGC	1 cut(s)	223
BccI	CCATC	1 cut(s)	427
BcoDI	GTCTC	1 cut(s)	149
BfaI	CTAG	1 cut(s)	159
BisI	GCNGC	1 cut(s)	237
BlsI	GCNGC	1 cut(s)	238
BmgT120I	GGNCC	2 cut(s)	7, 29
BmsI	GCATC	1 cut(s)	372
Bpu14I	TTCGAA	1 cut(s)	405
BpuEI	CTTGAG	1 cut(s)	173
BsaWI	WCCGGW	1 cut(s)	12
Bsc4I	CCNNNNNNNGG	2 cut(s)	16, 378
Bse1I	ACTGG	1 cut(s)	229
Bse21I	CCTNAGG	1 cut(s)	33
BseAI	TCCGGA	1 cut(s)	12
BseGI	GGATG	1 cut(s)	387
BseLI	CCNNNNNNNGG	2 cut(s)	16, 378
BseMII	CTCAG	2 cut(s)	24, 96
BseNI	ACTGG	1 cut(s)	229
BseXI	GCAGC	1 cut(s)	223
Bsh1236I	CGCG	1 cut(s)	241
BshFI	GGCC	3 cut(s)	8, 31, 89
BsiSI	CCGG	1 cut(s)	13
BslFI	GGGAC	1 cut(s)	363
BslI	CCNNNNNNNGG	2 cut(s)	16, 378
BsmAI	GTCTC	1 cut(s)	149
BsmFI	GGGAC	1 cut(s)	363
BsmI	GAATGC	2 cut(s)	66, 449
BsnI	GGCC	3 cut(s)	8, 31, 89
Bsp119I	TTCGAA	1 cut(s)	405
Bsp1286I	GDGCHC	1 cut(s)	45
Bsp13I	TCCGGA	1 cut(s)	12
Bsp143I	GATC	3 cut(s)	145, 202, 292
BspANI	GGCC	3 cut(s)	8, 31, 89
BspCNI	CTCAG	2 cut(s)	25, 95
BspEI	TCCGGA	1 cut(s)	12
BspFNI	CGCG	1 cut(s)	241
BspPI	GGATC	1 cut(s)	300
BspT104I	TTCGAA	1 cut(s)	405
BsrI	ACTGG	1 cut(s)	229
BssMI	GATC	3 cut(s)	145, 202, 292
Bst4CI	ACNGT	1 cut(s)	55
Bst6I	CTCTTC	3 cut(s)	77, 300, 329
BstBI	TTCGAA	1 cut(s)	405
BstDEI	CTNAG	2 cut(s)	33, 82
BstENI	CCTNNNNNAGG	1 cut(s)	14
BstF5I	GGATG	1 cut(s)	387
BstFNI	CGCG	1 cut(s)	241
BstHHI	GCGC	1 cut(s)	241
BstKTI	GATC	3 cut(s)	148, 205, 295
BstMAI	GTCTC	1 cut(s)	149
BstMBI	GATC	3 cut(s)	145, 202, 292
BstNSI	RCATGY	1 cut(s)	114
BstUI	CGCG	1 cut(s)	241
BstV1I	GCAGC	1 cut(s)	223
BstX2I	RGATCY	1 cut(s)	292
BstYI	RGATCY	1 cut(s)	292
Bsu36I	CCTNAGG	1 cut(s)	33
BsuRI	GGCC	3 cut(s)	8, 31, 89
BtsCI	GGATG	1 cut(s)	387
CfoI	GCGC	1 cut(s)	241
Cfr13I	GGNCC	2 cut(s)	7, 29
Csp6I	GTAC	1 cut(s)	357
CviAII	CATG	1 cut(s)	111
CviJI	RGCY	7 cut(s)	8, 31, 43, 89, 236, 279, 366
CviKI_1	RGCY	7 cut(s)	8, 31, 43, 89, 236, 279, 366
CviQI	GTAC	1 cut(s)	357
DdeI	CTNAG	2 cut(s)	33, 82
DpnI	GATC	3 cut(s)	147, 204, 294
DpnII	GATC	3 cut(s)	145, 202, 292
Eam1104I	CTCTTC	3 cut(s)	77, 300, 329
EarI	CTCTTC	3 cut(s)	77, 300, 329
Eco24I	GRGCYC	1 cut(s)	45
Eco81I	CCTNAGG	1 cut(s)	33
EcoNI	CCTNNNNNAGG	1 cut(s)	14
EcoO109I	RGGNCCY	1 cut(s)	7
EcoT38I	GRGCYC	1 cut(s)	45
FaeI	CATG	1 cut(s)	114
FaiI	YATR	7 cut(s)	112, 132, 245, 266, 288, 374, 393
FaqI	GGGAC	1 cut(s)	363
FatI	CATG	1 cut(s)	110
Fnu4HI	GCNGC	1 cut(s)	237
FokI	GGATG	1 cut(s)	394
FriOI	GRGCYC	1 cut(s)	45
Fsp4HI	GCNGC	1 cut(s)	237
FspBI	CTAG	1 cut(s)	159
GlaI	GCGC	1 cut(s)	240
GluI	GCNGC	1 cut(s)	237
HaeIII	GGCC	3 cut(s)	8, 31, 89
HapII	CCGG	1 cut(s)	13
HhaI	GCGC	1 cut(s)	241
Hin1II	CATG	1 cut(s)	114
Hin6I	GCGC	1 cut(s)	239
HinP1I	GCGC	1 cut(s)	239
HincII	GTYRAC	2 cut(s)	213, 400
HindII	GTYRAC	2 cut(s)	213, 400
HinfI	GANTC	1 cut(s)	228
HpaI	GTTAAC	1 cut(s)	400
HpaII	CCGG	1 cut(s)	13
HphI	GGTGA	1 cut(s)	361
Hpy166II	GTNNAC	2 cut(s)	213, 400
Hpy188I	TCNGA	4 cut(s)	85, 198, 381, 442
Hpy188III	TCNNGA	1 cut(s)	13
Hpy8I	GTNNAC	2 cut(s)	213, 400
HpyAV	CCTTC	2 cut(s)	10, 461
HpyCH4III	ACNGT	1 cut(s)	55
HpyCH4V	TGCA	6 cut(s)	59, 66, 110, 252, 385, 447
HpyF3I	CTNAG	2 cut(s)	33, 82
Hsp92II	CATG	1 cut(s)	114
HspAI	GCGC	1 cut(s)	239
Kpn2I	TCCGGA	1 cut(s)	12
KspAI	GTTAAC	1 cut(s)	400
Kzo9I	GATC	3 cut(s)	145, 202, 292
LpnPI	CCDG	5 cut(s)	26, 45, 45, 203, 210
Lsp1109I	GCAGC	1 cut(s)	223
LweI	GCATC	1 cut(s)	372
MaeI	CTAG	1 cut(s)	159
MalI	GATC	3 cut(s)	147, 204, 294
MboI	GATC	3 cut(s)	145, 202, 292
MboII	GAAGA	5 cut(s)	64, 317, 322, 346, 419
MfeI	CAATTG	1 cut(s)	386
MflI	RGATCY	1 cut(s)	292
MhlI	GDGCHC	1 cut(s)	45
MluCI	AATT	3 cut(s)	20, 164, 386
MlyI	GAGTC	1 cut(s)	222
MnlI	CCTC	4 cut(s)	20, 28, 79, 340
MroI	TCCGGA	1 cut(s)	12
MseI	TTAA	1 cut(s)	399
MspI	CCGG	1 cut(s)	13
MunI	CAATTG	1 cut(s)	386
Mva1269I	GAATGC	2 cut(s)	66, 449
MvnI	CGCG	1 cut(s)	241
NdeII	GATC	3 cut(s)	145, 202, 292
NlaIII	CATG	1 cut(s)	114
NspI	RCATGY	1 cut(s)	114
NspV	TTCGAA	1 cut(s)	405
PctI	GAATGC	2 cut(s)	66, 449
PkrI	GCNGC	1 cut(s)	238
PleI	GAGTC	1 cut(s)	222
PpsI	GAGTC	1 cut(s)	222
PspPI	GGNCC	2 cut(s)	7, 29
PsuI	RGATCY	1 cut(s)	292
RsaI	GTAC	1 cut(s)	358
RsaNI	GTAC	1 cut(s)	357
SaqAI	TTAA	1 cut(s)	399
SatI	GCNGC	1 cut(s)	237
Sau3AI	GATC	3 cut(s)	145, 202, 292
Sau96I	GGNCC	2 cut(s)	7, 29
SchI	GAGTC	1 cut(s)	222
SduI	GDGCHC	1 cut(s)	45
SetI	ASST	5 cut(s)	39, 281, 368, 453, 460
SfaNI	GCATC	1 cut(s)	372
SfuI	TTCGAA	1 cut(s)	405
SmlI	CTYRAG	1 cut(s)	152
SmoI	CTYRAG	1 cut(s)	152
Sse9I	AATT	3 cut(s)	20, 164, 386
SspMI	CTAG	1 cut(s)	159
TaaI	ACNGT	1 cut(s)	55
TaqI	TCGA	4 cut(s)	144, 342, 405, 454
TasI	AATT	3 cut(s)	20, 164, 386
Tru1I	TTAA	1 cut(s)	399
Tru9I	TTAA	1 cut(s)	399
TseI	GCWGC	1 cut(s)	236
TspDTI	ATGAA	2 cut(s)	91, 318
XagI	CCTNNNNNAGG	1 cut(s)	14
XapI	RAATTY	2 cut(s)	20, 164
XceI	RCATGY	1 cut(s)	114
XspI	CTAG	1 cut(s)	159

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