Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Forward (+)

17017149 .. 17017827

Gene Structure 679 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG097000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 270 bp

ATGGTTGATCGTCTTTCCGAGGATATATTTCAGGTGTTGCGACTGAACCCAGATGGAAAAAAGTTTGATAAAGTTACCCGAGTTGAAGCAAAGAGTGAGGCTTGCGAGACGTTCATGCACCTTGATGTGAATTCGGAGGTGTACCCCATCAAAGAAGGCGAGAAGTTCTCCATGGCTCTTACTTCTACACTCAATTTGGATGGAACACCTGACACTGGCTATTTCACCCCTGTAAAAAATTCCTTGTCTTTCTATATATCTCTTGTCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006366 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0032993 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097159 GO:0097659 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb8

Protein Analysis

89

Amino Acids

10.07

Weight (kDa)

4.84

Isoelectric Point (pI)

26.71

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	7 - 78	5.1e-23	RNA polymerase Rpb8

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

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Orthologous Genes (Group: OG0003142)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G54250 AT3G59600
fragaria_vesca	FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580
malus_domestica	MD03G1174900.v1.1 MD04G1053300.v1.1 MD05G1057600.v1.1 MD11G1193000.v1.1
prunus_persica	Prupe.4G249600_v2.0.a1 Prupe.4G249600_v2.0.a1
pyrus_communis	pycom03g13240 pycom11g16850
rosa_chinensis	RchiOBHm_Chr1g0332731 RchiOBHm_Chr5g0052071 RchiOBHm_Chr6g0273601
rosa_laevigata	RLG00000034845
rosa_multiflora	Rmu_sc0001587.1_g000001 Rmu_sc0032204.1_g000001 Rmu_ssc0000098.1_g000004
rosa_roxburghii	Rroxscaffold_1G00027860 Rroxscaffold_4G00318050
rosa_rugosa	Rorug01G0104600 Rorug05G0275000 Rorug05G0275100
rosa_samantha	Rh1AG127600 Rh1BG097000 Rh1CG121400 Rh5BG358000 Rh5CG383500 Rh5DG373400 Rh6CG194200
rosa_wichuraiana	Rw5G032800

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AcsI	RAATTY	2 cut(s)	130, 238
AfaI	GTAC	1 cut(s)	143
AfiI	CCNNNNNNNGG	1 cut(s)	215
AgsI	TTSAA	1 cut(s)	86
Alw26I	GTCTC	1 cut(s)	101
Ama87I	CYCGRG	1 cut(s)	78
ApoI	RAATTY	2 cut(s)	130, 238
AsuHPI	GGTGA	1 cut(s)	217
AvaI	CYCGRG	1 cut(s)	78
BccI	CCATC	3 cut(s)	47, 155, 194
BcoDI	GTCTC	1 cut(s)	101
BmeT110I	CYCGRG	1 cut(s)	78
BplI	GAGNNNNNCTC	2 cut(s)	152, 184
BsaJI	CCNNGG	2 cut(s)	18, 171
Bsc4I	CCNNNNNNNGG	1 cut(s)	215
Bse1I	ACTGG	1 cut(s)	220
BseDI	CCNNGG	2 cut(s)	18, 171
BseGI	GGATG	1 cut(s)	205
BseLI	CCNNNNNNNGG	1 cut(s)	215
BseNI	ACTGG	1 cut(s)	220
BsiHKCI	CYCGRG	1 cut(s)	78
BslI	CCNNNNNNNGG	1 cut(s)	215
BsmAI	GTCTC	1 cut(s)	101
BsmBI	CGTCTC	1 cut(s)	101
BsoBI	CYCGRG	1 cut(s)	78
Bsp143I	GATC	1 cut(s)	7
Bsp19I	CCATGG	1 cut(s)	171
BsrI	ACTGG	1 cut(s)	220
BssECI	CCNNGG	2 cut(s)	18, 171
BssMI	GATC	1 cut(s)	7
BssT1I	CCWWGG	1 cut(s)	171
BstC8I	GCNNGC	1 cut(s)	103
BstDSI	CCRYGG	1 cut(s)	171
BstF5I	GGATG	1 cut(s)	205
BstKTI	GATC	1 cut(s)	10
BstMAI	GTCTC	1 cut(s)	101
BstMBI	GATC	1 cut(s)	7
BtgI	CCRYGG	1 cut(s)	171
BtsCI	GGATG	1 cut(s)	205
BtsIMutI	CAGTG	1 cut(s)	213
Cac8I	GCNNGC	1 cut(s)	103
Csp6I	GTAC	1 cut(s)	142
CviAII	CATG	2 cut(s)	115, 172
CviJI	RGCY	3 cut(s)	101, 176, 219
CviKI_1	RGCY	3 cut(s)	101, 176, 219
CviQI	GTAC	1 cut(s)	142
DpnI	GATC	1 cut(s)	9
DpnII	GATC	1 cut(s)	7
Eco130I	CCWWGG	1 cut(s)	171
Eco88I	CYCGRG	1 cut(s)	78
EcoRI	GAATTC	1 cut(s)	130
EcoT14I	CCWWGG	1 cut(s)	171
ErhI	CCWWGG	1 cut(s)	171
Esp3I	CGTCTC	1 cut(s)	101
FaeI	CATG	2 cut(s)	118, 175
FaiI	YATR	5 cut(s)	26, 116, 173, 255, 257
FatI	CATG	2 cut(s)	114, 171
FokI	GGATG	1 cut(s)	212
Hin1II	CATG	2 cut(s)	118, 175
HphI	GGTGA	1 cut(s)	217
Hpy166II	GTNNAC	1 cut(s)	142
Hpy188I	TCNGA	2 cut(s)	19, 136
Hpy8I	GTNNAC	1 cut(s)	142
HpyAV	CCTTC	1 cut(s)	149
HpyCH4IV	ACGT	1 cut(s)	110
HpyCH4V	TGCA	1 cut(s)	118
HpySE526I	ACGT	1 cut(s)	110
Hsp92II	CATG	2 cut(s)	118, 175
Kzo9I	GATC	1 cut(s)	7
LpnPI	CCDG	5 cut(s)	17, 63, 201, 222, 243
MaeII	ACGT	1 cut(s)	110
MaeIII	GTNAC	1 cut(s)	73
MalI	GATC	1 cut(s)	9
MboI	GATC	1 cut(s)	7
MluCI	AATT	3 cut(s)	130, 193, 238
MnlI	CCTC	3 cut(s)	13, 91, 130
MslI	CAYNNNNRTG	1 cut(s)	123
NcoI	CCATGG	1 cut(s)	171
NdeII	GATC	1 cut(s)	7
NlaIII	CATG	2 cut(s)	118, 175
RsaI	GTAC	1 cut(s)	143
RsaNI	GTAC	1 cut(s)	142
RseI	CAYNNNNRTG	1 cut(s)	123
Sau3AI	GATC	1 cut(s)	7
SetI	ASST	5 cut(s)	36, 113, 123, 141, 211
SmiMI	CAYNNNNRTG	1 cut(s)	123
Sse9I	AATT	3 cut(s)	130, 193, 238
StyI	CCWWGG	1 cut(s)	171
TaiI	ACGT	1 cut(s)	113
TasI	AATT	3 cut(s)	130, 193, 238
TscAI	CASTG	1 cut(s)	220
TspDTI	ATGAA	1 cut(s)	103
TspRI	CASTG	1 cut(s)	220
XapI	RAATTY	2 cut(s)	130, 238

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