Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0001198

Physical Location & Seq

Genomic Coordinates Forward (+)

20456662 .. 20458650

Gene Structure 1989 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG184600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 381 bp

ATGTCTGCCAAGTTCCCCTCCAAGCCTCTCCCTCCTGCTCAAGCTGGTTGTTTACCAACTTTGGCCACAACACCAGTCTGGATAGGTCTATACCAAGCTCTTTCGAATGTGGTAAATGAGATGGGAGACTCACTTACAAATGAGCAACATATGTCTCATGGCATTGTCAATGTTGATTACAAGGGTCTTCTTCAAGTGAAAAAGACTTTGCAGAAAGATTTGGGGAGAGAACCAAATAAGGGTGAACTAGCTGAGGCAACAAGTATGAGTGTGGTTCAAGTGAAAAAACACTTGGAGGTCGGTCGAGCTGCCATAAACAAAGTCATCAAGCATACGTTCCATGACACTATCAAGCTTTACTCGTGTCGCCTTTGGCATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000988 GO:0000990 GO:0003674 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0006091 GO:0006139 GO:0006351 GO:0006352 GO:0006355 GO:0006725 GO:0006807 GO:0006950 GO:0006970 GO:0006996 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009314 GO:0009416 GO:0009507 GO:0009536 GO:0009553 GO:0009628 GO:0009637 GO:0009639 GO:0009651 GO:0009657 GO:0009658 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010114 GO:0010207 GO:0010218 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010628 GO:0015979 GO:0016043 GO:0016070 GO:0016987 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0019684 GO:0022607 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0032501 GO:0032502 GO:0032774 GO:0033554 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043254 GO:0043933 GO:0044085 GO:0044087 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044424 GO:0044444 GO:0044464 GO:0045893 GO:0045935 GO:0046483 GO:0048229 GO:0048518 GO:0048522 GO:0048856 GO:0050789 GO:0050794 GO:0050896 GO:0051128 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0051716 GO:0060255 GO:0065003 GO:0065007 GO:0071214 GO:0071470 GO:0071472 GO:0071478 GO:0071482 GO:0071483 GO:0071704 GO:0071840 GO:0080090 GO:0090304 GO:0097659 GO:0104004 GO:0140110 GO:1901360 GO:1901362 GO:1901576 GO:1902680 GO:1903506 GO:1903508 GO:2000112 GO:2000142 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Sigma70_r2 Sigma70_r3 Sigma70_r4

Protein Analysis

126

Amino Acids

13.95

Weight (kDa)

9.33

Isoelectric Point (pI)

39.54

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Sigma70_r3	PF04539	64 - 104	9e-07	Sigma-70 region 3

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: OG0001198)

Species	Orthologous Gene IDs
malus_domestica	MD01G1215400.v1.1
rosa_chinensis	RchiOBHm_Chr2g0159861 RchiOBHm_Chr3g0459421 RchiOBHm_Chr3g0487861 RchiOBHm_Chr3g0492051 RchiOBHm_Chr5g0035771 RchiOBHm_Chr6g0246661 RchiOBHm_Chr7g0202831
rosa_laevigata	RLG00000001369 RLG00000011478 RLG00000020137 RLG00000020475 RLG00000032827 RLG00000034363 RLG00000035497
rosa_multiflora	Rmu_co7998598.1_g000001 Rmu_sc0001163.1_g000040 Rmu_sc0002839.1_g000004 Rmu_sc0002942.1_g000020 Rmu_sc0028697.1_g000001
rosa_roxburghii	Rroxscaffold_3G00225820 Rroxscaffold_5G00370220 Rroxscaffold_7G00168140
rosa_rugosa	Rorug01G0101200 Rorug02G0305900
rosa_samantha	Rh1AG016700 Rh1BG026700 Rh1BG034000 Rh1BG041100 Rh1DG451700 Rh2AG266600 Rh2AG315500 Rh2AG432100 Rh2AG442100 Rh2BG273300 Rh2BG470100 Rh2CG429400 Rh3BG376000 Rh3CG334900 Rh3DG337000 Rh4CG134700 Rh4CG188500 Rh5AG186100 Rh5DG184600 Rh5DG184700 Rh6AG270600 Rh7AG267600 Rh7AG285300 Rh7CG286400 Rh7CG304400 Rh7CG304500 Rh7CG509000 Rh7DG208100 Rh7DG248900 Rh7DG476600
rosa_wichuraiana	Rw1G012800 Rw6G006910

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AcoI	YGGCCR	1 cut(s)	63
AfiI	CCNNNNNNNGG	1 cut(s)	239
AgsI	TTSAA	2 cut(s)	194, 278
AjuI	GAANNNNNNNTTGG	2 cut(s)	275, 307
AluBI	AGCT	5 cut(s)	44, 98, 251, 308, 355
AluI	AGCT	5 cut(s)	44, 98, 251, 308, 355
Alw26I	GTCTC	2 cut(s)	120, 159
AoxI	GGCC	1 cut(s)	63
ApeKI	GCWGC	1 cut(s)	308
AsuHPI	GGTGA	1 cut(s)	254
AsuII	TTCGAA	1 cut(s)	104
BalI	TGGCCA	1 cut(s)	65
BauI	CACGAG	1 cut(s)	361
BbsI	GAAGAC	1 cut(s)	179
BbvCI	CCTCAGC	1 cut(s)	252
BbvI	GCAGC	1 cut(s)	295
BccI	CCATC	1 cut(s)	115
BcoDI	GTCTC	2 cut(s)	120, 159
BfaI	CTAG	1 cut(s)	248
BisI	GCNGC	1 cut(s)	309
BlsI	GCNGC	1 cut(s)	310
BpiI	GAAGAC	1 cut(s)	179
Bpu10I	CCTNAGC	1 cut(s)	252
Bpu14I	TTCGAA	1 cut(s)	104
BpuEI	CTTGAG	1 cut(s)	24
Bsc4I	CCNNNNNNNGG	1 cut(s)	239
Bse1I	ACTGG	1 cut(s)	74
BseLI	CCNNNNNNNGG	1 cut(s)	239
BseMII	CTCAG	1 cut(s)	243
BseNI	ACTGG	1 cut(s)	74
BseXI	GCAGC	1 cut(s)	295
Bsh1285I	CGRYCG	1 cut(s)	304
BshFI	GGCC	1 cut(s)	65
BsiEI	CGRYCG	1 cut(s)	304
BslI	CCNNNNNNNGG	1 cut(s)	239
BsmAI	GTCTC	2 cut(s)	120, 159
BsnI	GGCC	1 cut(s)	65
Bsp119I	TTCGAA	1 cut(s)	104
BspANI	GGCC	1 cut(s)	65
BspCNI	CTCAG	1 cut(s)	244
BspT104I	TTCGAA	1 cut(s)	104
BsrI	ACTGG	1 cut(s)	74
BssSI	CACGAG	1 cut(s)	361
Bst2BI	CACGAG	1 cut(s)	361
BstBI	TTCGAA	1 cut(s)	104
BstDEI	CTNAG	1 cut(s)	252
BstMAI	GTCTC	2 cut(s)	120, 159
BstMCI	CGRYCG	1 cut(s)	304
BstV1I	GCAGC	1 cut(s)	295
BstV2I	GAAGAC	1 cut(s)	179
BsuRI	GGCC	1 cut(s)	65
CviAII	CATG	2 cut(s)	158, 341
CviJI	RGCY	7 cut(s)	25, 44, 65, 98, 251, 308, 355
CviKI_1	RGCY	7 cut(s)	25, 44, 65, 98, 251, 308, 355
DdeI	CTNAG	1 cut(s)	252
EaeI	YGGCCR	1 cut(s)	63
FaeI	CATG	2 cut(s)	161, 344
FaiI	YATR	8 cut(s)	91, 150, 152, 159, 266, 314, 333, 342
FatI	CATG	2 cut(s)	157, 340
FauNDI	CATATG	1 cut(s)	150
Fnu4HI	GCNGC	1 cut(s)	309
Fsp4HI	GCNGC	1 cut(s)	309
FspBI	CTAG	1 cut(s)	248
GluI	GCNGC	1 cut(s)	309
HaeIII	GGCC	1 cut(s)	65
Hin1II	CATG	2 cut(s)	161, 344
HindIII	AAGCTT	1 cut(s)	353
HinfI	GANTC	1 cut(s)	128
HphI	GGTGA	1 cut(s)	254
Hpy166II	GTNNAC	2 cut(s)	53, 245
Hpy188III	TCNNGA	1 cut(s)	79
Hpy8I	GTNNAC	2 cut(s)	53, 245
HpyCH4IV	ACGT	1 cut(s)	335
HpyCH4V	TGCA	1 cut(s)	211
HpyF3I	CTNAG	1 cut(s)	252
HpySE526I	ACGT	1 cut(s)	335
Hsp92II	CATG	2 cut(s)	161, 344
LpnPI	CCDG	4 cut(s)	30, 48, 64, 87
Lsp1109I	GCAGC	1 cut(s)	295
MaeI	CTAG	1 cut(s)	248
MaeII	ACGT	1 cut(s)	335
MboII	GAAGA	2 cut(s)	179, 182
MlsI	TGGCCA	1 cut(s)	65
MluNI	TGGCCA	1 cut(s)	65
MlyI	GAGTC	1 cut(s)	122
MnlI	CCTC	5 cut(s)	28, 36, 42, 247, 289
Mox20I	TGGCCA	1 cut(s)	65
MscI	TGGCCA	1 cut(s)	65
Msp20I	TGGCCA	1 cut(s)	65
NdeI	CATATG	1 cut(s)	150
NlaIII	CATG	2 cut(s)	161, 344
NspV	TTCGAA	1 cut(s)	104
PkrI	GCNGC	1 cut(s)	310
PleI	GAGTC	1 cut(s)	122
PpsI	GAGTC	1 cut(s)	122
SatI	GCNGC	1 cut(s)	309
SchI	GAGTC	1 cut(s)	122
SetI	ASST	8 cut(s)	46, 88, 100, 253, 300, 310, 338, 357
SfuI	TTCGAA	1 cut(s)	104
SmlI	CTYRAG	1 cut(s)	39
SmoI	CTYRAG	1 cut(s)	39
SspMI	CTAG	1 cut(s)	248
TaiI	ACGT	1 cut(s)	338
TaqI	TCGA	2 cut(s)	104, 304
TaqII	GACCGA	1 cut(s)	290
TseI	GCWGC	1 cut(s)	308
XspI	CTAG	1 cut(s)	248

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