Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Reverse (-)

26582249 .. 26585856

Gene Structure 3608 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG121400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 327 bp

ATGTTCACGCACCTTGATGTGAATTCAGAGGTGTACCCCATCAAAGAAGCCGAGAAGTTCTCCATGGCTCTTACTTCTACACTCAATTTGGATGGAACACCTGACACTGGCTATTTCACCCCGGGCAATCGCAAGACTTTGGCTGATGAATATGAATATGTCATGCAAGGGAAGCTTTACAAAATTTCAGAAGGCTCTAAACGTGATCCTAAAGCGGAGGTAAATGCTTCATTTGGTGGGCTTTTAATGATGCTGAAGGGGGAATCCGCTCAATTCAAGAACTTTGAACTTGATCAGAGGTTGTTTCTCCTCATTAGGAAGTTGTGA

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

108

Amino Acids

12.28

Weight (kDa)

5.82

Isoelectric Point (pI)

3.64

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	3 - 107	1.2e-35	RNA polymerase Rpb8

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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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)
AccBSI	CCGCTC	1 cut(s)	269
AciI	CCGC	2 cut(s)	215, 267
AclWI	GGATC	1 cut(s)	200
AcsI	RAATTY	2 cut(s)	22, 183
AcuI	CTGAAG	1 cut(s)	275
AfaI	GTAC	1 cut(s)	35
AfiI	CCNNNNNNNGG	1 cut(s)	107
AgsI	TTSAA	2 cut(s)	277, 287
AluBI	AGCT	1 cut(s)	175
AluI	AGCT	1 cut(s)	175
AlwI	GGATC	1 cut(s)	200
Ama87I	CYCGRG	1 cut(s)	121
ApoI	RAATTY	2 cut(s)	22, 183
AsuC2I	CCSGG	2 cut(s)	122, 123
AsuHPI	GGTGA	1 cut(s)	109
AvaI	CYCGRG	1 cut(s)	121
BccI	CCATC	2 cut(s)	47, 86
BclI	TGATCA	1 cut(s)	292
BcnI	CCSGG	2 cut(s)	122, 123
Bme1390I	CCNGG	2 cut(s)	122, 123
BmeT110I	CYCGRG	1 cut(s)	121
BmrFI	CCNGG	2 cut(s)	122, 123
BmsI	GCATC	1 cut(s)	240
BplI	GAGNNNNNCTC	2 cut(s)	44, 76
BpuMI	CCSGG	2 cut(s)	122, 123
BsaJI	CCNNGG	3 cut(s)	63, 120, 121
Bsc4I	CCNNNNNNNGG	1 cut(s)	107
Bse1I	ACTGG	1 cut(s)	112
BseDI	CCNNGG	3 cut(s)	63, 120, 121
BseGI	GGATG	1 cut(s)	97
BseLI	CCNNNNNNNGG	1 cut(s)	107
BseNI	ACTGG	1 cut(s)	112
BseRI	GAGGAG	1 cut(s)	299
BsiHKCI	CYCGRG	1 cut(s)	121
BsiSI	CCGG	1 cut(s)	122
BslI	CCNNNNNNNGG	1 cut(s)	107
BsoBI	CYCGRG	1 cut(s)	121
Bsp143I	GATC	2 cut(s)	205, 292
Bsp19I	CCATGG	1 cut(s)	63
BspACI	CCGC	2 cut(s)	215, 267
BspPI	GGATC	1 cut(s)	200
BsrBI	CCGCTC	1 cut(s)	269
BsrI	ACTGG	1 cut(s)	112
BssECI	CCNNGG	3 cut(s)	63, 120, 121
BssMI	GATC	2 cut(s)	205, 292
BssT1I	CCWWGG	1 cut(s)	63
BstDSI	CCRYGG	1 cut(s)	63
BstF5I	GGATG	1 cut(s)	97
BstKTI	GATC	2 cut(s)	208, 295
BstMBI	GATC	2 cut(s)	205, 292
BstMWI	GCNNNNNNNGC	1 cut(s)	172
BstSCI	CCNGG	2 cut(s)	120, 121
BtgI	CCRYGG	1 cut(s)	63
BtsCI	GGATG	1 cut(s)	97
BtsIMutI	CAGTG	1 cut(s)	105
Cfr9I	CCCGGG	1 cut(s)	121
Csp6I	GTAC	1 cut(s)	34
CviAII	CATG	2 cut(s)	64, 163
CviJI	RGCY	7 cut(s)	50, 68, 111, 143, 175, 195, 241
CviKI_1	RGCY	7 cut(s)	50, 68, 111, 143, 175, 195, 241
CviQI	GTAC	1 cut(s)	34
DpnI	GATC	2 cut(s)	207, 294
DpnII	GATC	2 cut(s)	205, 292
Eco130I	CCWWGG	1 cut(s)	63
Eco57I	CTGAAG	1 cut(s)	275
Eco88I	CYCGRG	1 cut(s)	121
EcoRI	GAATTC	1 cut(s)	22
EcoT14I	CCWWGG	1 cut(s)	63
ErhI	CCWWGG	1 cut(s)	63
FaeI	CATG	2 cut(s)	67, 166
FaiI	YATR	4 cut(s)	65, 153, 159, 164
FalI	AAGNNNNNCTT	2 cut(s)	159, 191
FatI	CATG	2 cut(s)	63, 162
FbaI	TGATCA	1 cut(s)	292
FokI	GGATG	1 cut(s)	104
HapII	CCGG	1 cut(s)	122
Hin1II	CATG	2 cut(s)	67, 166
HindIII	AAGCTT	1 cut(s)	173
HinfI	GANTC	1 cut(s)	263
HpaII	CCGG	1 cut(s)	122
HphI	GGTGA	1 cut(s)	109
Hpy166II	GTNNAC	2 cut(s)	6, 34
Hpy188I	TCNGA	3 cut(s)	28, 190, 297
Hpy188III	TCNNGA	1 cut(s)	277
Hpy8I	GTNNAC	2 cut(s)	6, 34
HpyAV	CCTTC	2 cut(s)	185, 250
HpyCH4IV	ACGT	1 cut(s)	202
HpyCH4V	TGCA	1 cut(s)	166
HpyF10VI	GCNNNNNNNGC	1 cut(s)	172
HpySE526I	ACGT	1 cut(s)	202
Hsp92II	CATG	2 cut(s)	67, 166
Ksp22I	TGATCA	1 cut(s)	292
Kzo9I	GATC	2 cut(s)	205, 292
LpnPI	CCDG	3 cut(s)	93, 114, 135
LweI	GCATC	1 cut(s)	240
MaeII	ACGT	1 cut(s)	202
MalI	GATC	2 cut(s)	207, 294
MbiI	CCGCTC	1 cut(s)	269
MboI	GATC	2 cut(s)	205, 292
MluCI	AATT	4 cut(s)	22, 85, 183, 272
MnlI	CCTC	4 cut(s)	22, 211, 291, 320
MseI	TTAA	1 cut(s)	245
MslI	CAYNNNNRTG	1 cut(s)	15
MspI	CCGG	1 cut(s)	122
MspR9I	CCNGG	2 cut(s)	122, 123
MwoI	GCNNNNNNNGC	1 cut(s)	172
NciI	CCSGG	2 cut(s)	122, 123
NcoI	CCATGG	1 cut(s)	63
NdeII	GATC	2 cut(s)	205, 292
NlaIII	CATG	2 cut(s)	67, 166
NmeAIII	GCCGAG	1 cut(s)	76
PfeI	GAWTC	1 cut(s)	263
RsaI	GTAC	1 cut(s)	35
RsaNI	GTAC	1 cut(s)	34
RseI	CAYNNNNRTG	1 cut(s)	15
SaqAI	TTAA	1 cut(s)	245
Sau3AI	GATC	2 cut(s)	205, 292
ScrFI	CCNGG	2 cut(s)	122, 123
SetI	ASST	7 cut(s)	15, 33, 103, 177, 205, 222, 302
SfaNI	GCATC	1 cut(s)	240
SmaI	CCCGGG	1 cut(s)	123
SmiMI	CAYNNNNRTG	1 cut(s)	15
Sse9I	AATT	4 cut(s)	22, 85, 183, 272
SsiI	CCGC	2 cut(s)	215, 267
StyD4I	CCNGG	2 cut(s)	120, 121
StyI	CCWWGG	1 cut(s)	63
TaiI	ACGT	1 cut(s)	205
TasI	AATT	4 cut(s)	22, 85, 183, 272
TfiI	GAWTC	1 cut(s)	263
Tru1I	TTAA	1 cut(s)	245
Tru9I	TTAA	1 cut(s)	245
TscAI	CASTG	1 cut(s)	112
TspDTI	ATGAA	3 cut(s)	162, 168, 219
TspMI	CCCGGG	1 cut(s)	121
TspRI	CASTG	1 cut(s)	112
XapI	RAATTY	2 cut(s)	22, 183
XmaI	CCCGGG	1 cut(s)	121

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