Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2D

Orthogroup ID

OG0004622

Physical Location & Seq

Genomic Coordinates Forward (+)

39528357 .. 39528878

Gene Structure 522 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2DG318000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 522 bp

ATGGAGTTGGCTAAGCATTTTATTCGAACAAATATAGAACCAGAATGGATGGTTTTATGTCTATTACCAGTTCTTCCGCCCGAGTTGAGACCAATCATTCAGATAGATGGGGGTAAACTAATGAGCTCGGATATTAATGAACTCTATAGAAGAGTTATTTATCGGAACAAAACTCTTATCGATCTCTTAACAACAAGTAGATCTACGCCAGGAGAATTAGTAATGTGTCAGGAGAAATTGGTACAAGAAGCTGTGGATACACTTCTTGATATTGGAATCGGTGGACAACCAATGAGGGACGGTCATAATAAGGTTTACAAGTCGTTTTCAGACGTAATTGAAGGAAAAGAGGGAAGATTTCGTGAGACTCTGCTTGGCAAACGGGTCGATTATTCGGGGCGTTCTATCATTGTTGCAAGTCCTTCACTTTCATTACATCAATGTGGATTGCCTCGCGAAGTAGCAATAGAGCTTTTCCAGATATTTGTAATTTGTGGTTTAATTAGACAGCATTTTGCCTAG

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

173

Amino Acids

19.6

Weight (kDa)

6.9

Isoelectric Point (pI)

48.42

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_1	PF04997	8 - 124	2.3e-29	RNA polymerase Rpb1, domain 1
RNA_pol_Rpb1_2	PF00623	126 - 170	4.3e-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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Align Labels (Cladogram)

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Publication-ready

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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)	456
AciI	CCGC	1 cut(s)	77
AfaI	GTAC	1 cut(s)	243
AgsI	TTSAA	1 cut(s)	341
AjnI	CCWGG	1 cut(s)	208
AluBI	AGCT	3 cut(s)	126, 251, 472
AluI	AGCT	3 cut(s)	126, 251, 472
Alw21I	GWGCWC	1 cut(s)	128
Alw26I	GTCTC	2 cut(s)	82, 359
Ama87I	CYCGRG	1 cut(s)	80
AseI	ATTAAT	1 cut(s)	135
AsuII	TTCGAA	1 cut(s)	25
AvaI	CYCGRG	1 cut(s)	80
BanII	GRGCYC	1 cut(s)	128
Bbv12I	GWGCWC	1 cut(s)	128
BccI	CCATC	2 cut(s)	43, 101
BcgI	CGANNNNNNTGC	4 cut(s)	5, 39, 367, 401
BciT130I	CCWGG	1 cut(s)	210
BciVI	GTATCC	1 cut(s)	250
BcoDI	GTCTC	2 cut(s)	82, 359
BfaI	CTAG	1 cut(s)	520
BfmI	CTRYAG	1 cut(s)	145
BfuI	GTATCC	1 cut(s)	250
BglII	AGATCT	1 cut(s)	200
BlpI	GCTNAGC	1 cut(s)	12
Bme1390I	CCNGG	1 cut(s)	210
BmeT110I	CYCGRG	1 cut(s)	80
BmrFI	CCNGG	1 cut(s)	210
Bpu1102I	GCTNAGC	1 cut(s)	12
Bpu14I	TTCGAA	1 cut(s)	25
Bsa29I	ATCGAT	1 cut(s)	180
BsaI	GGTCTC	1 cut(s)	82
BsaXI	ACNNNNNCTCC	2 cut(s)	204, 234
Bse1I	ACTGG	1 cut(s)	68
BseBI	CCWGG	1 cut(s)	210
BseCI	ATCGAT	1 cut(s)	180
BseGI	GGATG	1 cut(s)	54
BseNI	ACTGG	1 cut(s)	68
Bsh1236I	CGCG	1 cut(s)	456
BshVI	ATCGAT	1 cut(s)	180
BsiHKAI	GWGCWC	1 cut(s)	128
BsiHKCI	CYCGRG	1 cut(s)	80
BslFI	GGGAC	1 cut(s)	311
BsmAI	GTCTC	2 cut(s)	82, 359
BsmFI	GGGAC	1 cut(s)	311
Bso31I	GGTCTC	1 cut(s)	82
BsoBI	CYCGRG	1 cut(s)	80
Bsp119I	TTCGAA	1 cut(s)	25
Bsp1286I	GDGCHC	1 cut(s)	128
Bsp143I	GATC	2 cut(s)	181, 200
Bsp1720I	GCTNAGC	1 cut(s)	12
Bsp68I	TCGCGA	1 cut(s)	456
BspACI	CCGC	1 cut(s)	77
BspDI	ATCGAT	1 cut(s)	180
BspFNI	CGCG	1 cut(s)	456
BspT104I	TTCGAA	1 cut(s)	25
BspTNI	GGTCTC	1 cut(s)	82
BsrI	ACTGG	1 cut(s)	68
BssMI	GATC	2 cut(s)	181, 200
Bst2UI	CCWGG	1 cut(s)	210
Bst4CI	ACNGT	1 cut(s)	302
Bst6I	CTCTTC	1 cut(s)	145
BstBI	TTCGAA	1 cut(s)	25
BstDEI	CTNAG	1 cut(s)	12
BstF5I	GGATG	1 cut(s)	54
BstFNI	CGCG	1 cut(s)	456
BstKTI	GATC	2 cut(s)	184, 203
BstMAI	GTCTC	2 cut(s)	82, 359
BstMBI	GATC	2 cut(s)	181, 200
BstNI	CCWGG	1 cut(s)	210
BstSCI	CCNGG	1 cut(s)	208
BstSFI	CTRYAG	1 cut(s)	145
BstUI	CGCG	1 cut(s)	456
BstX2I	RGATCY	1 cut(s)	200
BstYI	RGATCY	1 cut(s)	200
Bsu15I	ATCGAT	1 cut(s)	180
BsuI	GTATCC	1 cut(s)	250
BsuTUI	ATCGAT	1 cut(s)	180
BtsCI	GGATG	1 cut(s)	54
BtuMI	TCGCGA	1 cut(s)	456
ClaI	ATCGAT	1 cut(s)	180
Csp6I	GTAC	1 cut(s)	242
CviJI	RGCY	4 cut(s)	11, 126, 251, 472
CviKI_1	RGCY	4 cut(s)	11, 126, 251, 472
CviQI	GTAC	1 cut(s)	242
DdeI	CTNAG	1 cut(s)	12
DpnI	GATC	2 cut(s)	183, 202
DpnII	GATC	2 cut(s)	181, 200
Eam1104I	CTCTTC	1 cut(s)	145
EarI	CTCTTC	1 cut(s)	145
EciI	GGCGGA	1 cut(s)	66
Ecl136II	GAGCTC	1 cut(s)	126
Eco24I	GRGCYC	1 cut(s)	128
Eco31I	GGTCTC	1 cut(s)	82
Eco53kI	GAGCTC	1 cut(s)	126
Eco88I	CYCGRG	1 cut(s)	80
EcoICRI	GAGCTC	1 cut(s)	126
EcoRII	CCWGG	1 cut(s)	208
EcoT38I	GRGCYC	1 cut(s)	128
FaiI	YATR	4 cut(s)	35, 58, 147, 306
FaqI	GGGAC	1 cut(s)	311
FokI	GGATG	1 cut(s)	61
FriOI	GRGCYC	1 cut(s)	128
FspBI	CTAG	1 cut(s)	520
HinfI	GANTC	2 cut(s)	276, 367
Hpy166II	GTNNAC	3 cut(s)	116, 284, 316
Hpy188I	TCNGA	4 cut(s)	102, 130, 165, 331
Hpy188III	TCNNGA	5 cut(s)	230, 266, 362, 455, 478
Hpy8I	GTNNAC	3 cut(s)	116, 284, 316
HpyAV	CCTTC	2 cut(s)	335, 432
HpyCH4III	ACNGT	1 cut(s)	302
HpyCH4IV	ACGT	1 cut(s)	333
HpyCH4V	TGCA	1 cut(s)	416
HpyF3I	CTNAG	1 cut(s)	12
HpySE526I	ACGT	1 cut(s)	333
Kzo9I	GATC	2 cut(s)	181, 200
LpnPI	CCDG	6 cut(s)	54, 81, 195, 215, 222, 491
MaeI	CTAG	1 cut(s)	520
MaeII	ACGT	1 cut(s)	333
MalI	GATC	2 cut(s)	183, 202
MboI	GATC	2 cut(s)	181, 200
MboII	GAAGA	3 cut(s)	65, 162, 366
MflI	RGATCY	1 cut(s)	200
MhlI	GDGCHC	1 cut(s)	128
MluCI	AATT	5 cut(s)	215, 236, 336, 489, 501
MlyI	GAGTC	1 cut(s)	361
MnlI	CCTC	3 cut(s)	288, 343, 462
MseI	TTAA	3 cut(s)	135, 188, 500
MslI	CAYNNNNRTG	1 cut(s)	441
MspR9I	CCNGG	1 cut(s)	210
MvaI	CCWGG	1 cut(s)	210
MvnI	CGCG	1 cut(s)	456
NdeII	GATC	2 cut(s)	181, 200
NruI	TCGCGA	1 cut(s)	456
NspV	TTCGAA	1 cut(s)	25
PfeI	GAWTC	1 cut(s)	276
PleI	GAGTC	1 cut(s)	361
PpsI	GAGTC	1 cut(s)	361
PshBI	ATTAAT	1 cut(s)	135
Psp124BI	GAGCTC	1 cut(s)	128
Psp6I	CCWGG	1 cut(s)	208
PspGI	CCWGG	1 cut(s)	208
PsuI	RGATCY	1 cut(s)	200
RruI	TCGCGA	1 cut(s)	456
RsaI	GTAC	1 cut(s)	243
RsaNI	GTAC	1 cut(s)	242
RseI	CAYNNNNRTG	1 cut(s)	441
SacI	GAGCTC	1 cut(s)	128
SaqAI	TTAA	3 cut(s)	135, 188, 500
Sau3AI	GATC	2 cut(s)	181, 200
SchI	GAGTC	1 cut(s)	361
ScrFI	CCNGG	1 cut(s)	210
SduI	GDGCHC	1 cut(s)	128
SetI	ASST	5 cut(s)	128, 253, 315, 336, 474
SfcI	CTRYAG	1 cut(s)	145
SfuI	TTCGAA	1 cut(s)	25
SmiMI	CAYNNNNRTG	1 cut(s)	441
Sse9I	AATT	5 cut(s)	215, 236, 336, 489, 501
SsiI	CCGC	1 cut(s)	77
SspMI	CTAG	1 cut(s)	520
SstI	GAGCTC	1 cut(s)	128
StyD4I	CCNGG	1 cut(s)	208
TaaI	ACNGT	1 cut(s)	302
TaiI	ACGT	1 cut(s)	336
TaqI	TCGA	3 cut(s)	25, 180, 387
TasI	AATT	5 cut(s)	215, 236, 336, 489, 501
TfiI	GAWTC	1 cut(s)	276
Tru1I	TTAA	3 cut(s)	135, 188, 500
Tru9I	TTAA	3 cut(s)	135, 188, 500
TspDTI	ATGAA	2 cut(s)	153, 420
VspI	ATTAAT	1 cut(s)	135
XspI	CTAG	1 cut(s)	520

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