Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0004622

Physical Location & Seq

Genomic Coordinates Reverse (-)

49246111 .. 49246476

Gene Structure 366 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG244200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 366 bp

ATGGATGCACTTCTTGATAAGGGAATCCGTGGACAACCAATGAAGGATGGTCATAATAAGGTTTACAAGTCGTTTTTAGATGTAATTGAAGGAAAAGAGGGAAGATTTTGTGAGACTTTGCTTGGCAAACGAGTTGATTATTCGAGGCGTTCTGTCATTGTTGTAGGTCCTTCACTTTCATTACATCGATGTGGATTGCCTCGCGAAATAGCAATAGAGCTTTTTCAGACATTTTTAATTCGTGGTTTAATTAGACAGCATTTTGCCTCGAATATAGGAGTGGCTAAGAGTAAAATTCGGGAAAAAGAACCGGTTGTATGGGAAATACACTTTAGGAAGTTATGCAAGGGCATCCCGTATTGCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0009507 GO:0009536 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 map00230 map00240 map01100 map03020

Pfam Domains

Protein Families

RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3

Protein Analysis

121

Amino Acids

13.85

Weight (kDa)

9.69

Isoelectric Point (pI)

37.26

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_2	PF00623	42 - 90	1e-07	RNA polymerase Rpb1, domain 2

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: OG0004622)

Species	Orthologous Gene IDs
arabidopsis_thaliana	ATCG00170
malus_domestica	MD01G1014400.v1.1
pyrus_communis	pycom12397g00020 pycom12397g00340
rosa_chinensis	RchiOBHm_Chr4g0421201
rosa_laevigata	RLG00000000048 RLG00000000088 RLG00000000117 RLG00000000174 RLG00000000232 RLG00000000233 RLG00000000247 RLG00000000283 RLG00000000313 RLG00000000317 RLG00000000339
rosa_multiflora	Rmu_sc0001741.1_g000011
rosa_roxburghii	Rroxscaffold_2G00119090 Rroxscaffold_2G00119100
rosa_rugosa	RorugMtG0001800
rosa_samantha	Rh2AG294100 Rh2AG294200 Rh2DG057700 Rh2DG318000 Rh2DG318100 Rh4CG233400 Rh4CG244200 Rh7BG354800 Rh7CG382200
rosa_wichuraiana	Rw4G006960 Rw4G006970

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	204
AcsI	RAATTY	1 cut(s)	294
AgeI	ACCGGT	1 cut(s)	310
AgsI	TTSAA	1 cut(s)	89
AluBI	AGCT	1 cut(s)	220
AluI	AGCT	1 cut(s)	220
Alw26I	GTCTC	1 cut(s)	107
ApoI	RAATTY	1 cut(s)	294
AsiGI	ACCGGT	1 cut(s)	310
AspS9I	GGNCC	1 cut(s)	167
AvaII	GGWCC	1 cut(s)	167
BccI	CCATC	1 cut(s)	41
BcoDI	GTCTC	1 cut(s)	107
Bme18I	GGWCC	1 cut(s)	167
BmgT120I	GGNCC	1 cut(s)	167
BmsI	GCATC	1 cut(s)	360
Bsa29I	ATCGAT	1 cut(s)	187
BsaJI	CCNNGG	1 cut(s)	28
BsaWI	WCCGGW	1 cut(s)	310
Bse118I	RCCGGY	1 cut(s)	310
BseCI	ATCGAT	1 cut(s)	187
BseDI	CCNNGG	1 cut(s)	28
BseGI	GGATG	3 cut(s)	10, 52, 351
Bsh1236I	CGCG	1 cut(s)	204
BshTI	ACCGGT	1 cut(s)	310
BshVI	ATCGAT	1 cut(s)	187
BsiSI	CCGG	1 cut(s)	311
BsmAI	GTCTC	1 cut(s)	107
Bsp68I	TCGCGA	1 cut(s)	204
BspDI	ATCGAT	1 cut(s)	187
BspFNI	CGCG	1 cut(s)	204
BsrFI	RCCGGY	1 cut(s)	310
BssAI	RCCGGY	1 cut(s)	310
BssECI	CCNNGG	1 cut(s)	28
BstDEI	CTNAG	1 cut(s)	285
BstDSI	CCRYGG	1 cut(s)	28
BstF5I	GGATG	3 cut(s)	10, 52, 351
BstFNI	CGCG	1 cut(s)	204
BstMAI	GTCTC	1 cut(s)	107
BstUI	CGCG	1 cut(s)	204
Bsu15I	ATCGAT	1 cut(s)	187
BsuTUI	ATCGAT	1 cut(s)	187
BtgI	CCRYGG	1 cut(s)	28
BtsCI	GGATG	3 cut(s)	10, 52, 351
BtuMI	TCGCGA	1 cut(s)	204
Cfr10I	RCCGGY	1 cut(s)	310
Cfr13I	GGNCC	1 cut(s)	167
ClaI	ATCGAT	1 cut(s)	187
CspAI	ACCGGT	1 cut(s)	310
CviJI	RGCY	2 cut(s)	220, 284
CviKI_1	RGCY	2 cut(s)	220, 284
DdeI	CTNAG	1 cut(s)	285
Eco47I	GGWCC	1 cut(s)	167
EcoO109I	RGGNCCY	1 cut(s)	167
FaiI	YATR	4 cut(s)	54, 275, 319, 343
FokI	GGATG	3 cut(s)	17, 59, 338
HapII	CCGG	1 cut(s)	311
HinfI	GANTC	1 cut(s)	24
HpaII	CCGG	1 cut(s)	311
Hpy166II	GTNNAC	2 cut(s)	32, 64
Hpy188I	TCNGA	1 cut(s)	228
Hpy188III	TCNNGA	3 cut(s)	14, 203, 299
Hpy8I	GTNNAC	2 cut(s)	32, 64
HpyAV	CCTTC	3 cut(s)	37, 83, 180
HpyCH4V	TGCA	2 cut(s)	8, 345
HpyF3I	CTNAG	1 cut(s)	285
LpnPI	CCDG	1 cut(s)	324
LweI	GCATC	1 cut(s)	360
MboII	GAAGA	1 cut(s)	114
MluCI	AATT	4 cut(s)	84, 237, 249, 294
MnlI	CCTC	4 cut(s)	91, 138, 210, 277
MseI	TTAA	2 cut(s)	236, 248
MslI	CAYNNNNRTG	1 cut(s)	189
MspI	CCGG	1 cut(s)	311
MvnI	CGCG	1 cut(s)	204
NruI	TCGCGA	1 cut(s)	204
PfeI	GAWTC	1 cut(s)	24
PinAI	ACCGGT	1 cut(s)	310
PpuMI	RGGWCCY	1 cut(s)	167
Psp5II	RGGWCCY	1 cut(s)	167
PspPI	GGNCC	1 cut(s)	167
PspPPI	RGGWCCY	1 cut(s)	167
RruI	TCGCGA	1 cut(s)	204
RseI	CAYNNNNRTG	1 cut(s)	189
SaqAI	TTAA	2 cut(s)	236, 248
Sau96I	GGNCC	1 cut(s)	167
SetI	ASST	3 cut(s)	63, 169, 222
SfaNI	GCATC	1 cut(s)	360
SinI	GGWCC	1 cut(s)	167
SmiMI	CAYNNNNRTG	1 cut(s)	189
Sse9I	AATT	4 cut(s)	84, 237, 249, 294
TaqI	TCGA	3 cut(s)	143, 187, 269
TasI	AATT	4 cut(s)	84, 237, 249, 294
TfiI	GAWTC	1 cut(s)	24
Tru1I	TTAA	2 cut(s)	236, 248
Tru9I	TTAA	2 cut(s)	236, 248
TspDTI	ATGAA	2 cut(s)	56, 168
TspGWI	ACGGA	1 cut(s)	17
VpaK11BI	GGWCC	1 cut(s)	167
XapI	RAATTY	1 cut(s)	294

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