Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0007390

Physical Location & Seq

Genomic Coordinates Reverse (-)

6786297 .. 6789544

Gene Structure 3248 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG031300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 531 bp

ATGTTTCTCAAAACTGAGTTGCAGTGGAATGTTGTAATCCCTGCTGAAAGCTTGGATGCGAAGGGATTGATGCTCCAAAAGGCAATTGTTATCCGGCTGCTGGATGATTTTTCTAAGAGAAAGGCCACAAAGGATCTCGGATACCTTCTTGCTCTCACAACTGTGGAGAAAATAGGAGAGGGAAAAGTCAGGCAGCATACTGGGGATGTGCTTTTTCCAGTCACCTTTAGCGCCATCTCCTTTAAGCTTTTCAGAGGAGAGATCTTAGAGGGAGTAGTGCACAAGGTGCTGAAGCAGGGAGTTATATTGAGATGCGGTCCCATTGAGAATGTATATCTCTCTTCTTCGAAAATGCCCGATTACAACTATGTTCCAGGGGAGAATCCTATCTTCTTGAATGACAAGATGTCTAAGATTGAAAAAGGTGTCACGCTGCGTTTCATTGTCATTGGAGCTAAGTGGCTTGAGGCAGAAAGGGAATTTCAGGCATTGGTTGGCTTACATGCTGATTATCTAGGTCCAGTTTCTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000419 GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0003723 GO:0003727 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0030880 GO:0031974 GO:0031981 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0055029 GO:0061695 GO:0070013 GO:0097159 GO:1901363 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

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

Pfam Domains

Protein Families

SHS2_Rpb7-N

Protein Analysis

176

Amino Acids

19.72

Weight (kDa)

8.91

Isoelectric Point (pI)

36.09

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	10 - 68	3.2e-06	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0007390)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G14660 AT4G14660 AT4G14660
fragaria_vesca	FvH4_4g12050 FvH4_4g12050
malus_domestica	MD16G1207700.v1.1
prunus_persica	Prupe.1G030000_v2.0.a1 Prupe.1G030000_v2.0.a1 Prupe.1G030000_v2.0.a1 Prupe.1G030000_v2.0.a1
pyrus_communis	pycom13g17890 pycom16g17510
rosa_chinensis	RchiOBHm_Chr4g0390271 RchiOBHm_Chr4g0390761
rosa_laevigata	RLG00000009929
rosa_multiflora	Rmu_sc0004432.1_g000009 Rmu_sc0014620.1_g000003
rosa_roxburghii	Rroxscaffold_5G00336390
rosa_rugosa	Rorug03G0328900
rosa_samantha	Rh4AG031300 Rh4AG033100 Rh4BG025300 Rh4CG034300 Rh4DG026500
rosa_wichuraiana	Rw4G002490

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	315
AclWI	GGATC	1 cut(s)	141
AcsI	RAATTY	1 cut(s)	479
AcuI	CTGAAG	1 cut(s)	311
AdeI	CACNNNGTG	1 cut(s)	286
AfiI	CCNNNNNNNGG	1 cut(s)	100
AgsI	TTSAA	2 cut(s)	397, 419
AhdI	GACNNNNNGTC	1 cut(s)	406
AjnI	CCWGG	1 cut(s)	373
AleI	CACNNNNGTG	1 cut(s)	161
AluBI	AGCT	3 cut(s)	51, 247, 455
AluI	AGCT	3 cut(s)	51, 247, 455
Alw21I	GWGCWC	1 cut(s)	282
Alw44I	GTGCAC	1 cut(s)	278
AlwI	GGATC	1 cut(s)	141
AoxI	GGCC	1 cut(s)	123
ApaLI	GTGCAC	1 cut(s)	278
ApeKI	GCWGC	3 cut(s)	97, 193, 433
ApoI	RAATTY	1 cut(s)	479
AspLEI	GCGC	1 cut(s)	233
AspS9I	GGNCC	2 cut(s)	317, 518
AsuHPI	GGTGA	1 cut(s)	214
AsuII	TTCGAA	1 cut(s)	347
AvaII	GGWCC	2 cut(s)	317, 518
BaeGI	GKGCMC	1 cut(s)	282
Bbv12I	GWGCWC	1 cut(s)	282
BbvI	GCAGC	3 cut(s)	84, 205, 420
BccI	CCATC	1 cut(s)	242
BciT130I	CCWGG	1 cut(s)	375
BciVI	GTATCC	1 cut(s)	134
BfaI	CTAG	1 cut(s)	515
BfoI	RGCGCY	1 cut(s)	234
BfuI	GTATCC	1 cut(s)	134
BglII	AGATCT	1 cut(s)	261
BisI	GCNGC	3 cut(s)	98, 194, 434
BlsI	GCNGC	3 cut(s)	99, 195, 435
Bme1390I	CCNGG	1 cut(s)	375
Bme18I	GGWCC	2 cut(s)	317, 518
BmeRI	GACNNNNNGTC	1 cut(s)	406
BmgT120I	GGNCC	2 cut(s)	317, 518
BmiI	GGNNCC	1 cut(s)	319
BmrFI	CCNGG	1 cut(s)	375
BmrI	ACTGGG	1 cut(s)	210
BmsI	GCATC	3 cut(s)	46, 60, 302
BmuI	ACTGGG	1 cut(s)	210
Bpu14I	TTCGAA	1 cut(s)	347
BpuEI	CTTGAG	1 cut(s)	485
BsaJI	CCNNGG	1 cut(s)	374
Bsc4I	CCNNNNNNNGG	1 cut(s)	100
Bse1I	ACTGG	3 cut(s)	205, 218, 521
BseBI	CCWGG	1 cut(s)	375
BseDI	CCNNGG	1 cut(s)	374
BseGI	GGATG	3 cut(s)	61, 109, 211
BseLI	CCNNNNNNNGG	1 cut(s)	100
BseMII	CTCAG	1 cut(s)	6
BseNI	ACTGG	3 cut(s)	205, 218, 521
BseRI	GAGGAG	1 cut(s)	270
BseSI	GKGCMC	1 cut(s)	282
BseXI	GCAGC	3 cut(s)	84, 205, 420
BshFI	GGCC	1 cut(s)	125
BsiHKAI	GWGCWC	1 cut(s)	282
BsiSI	CCGG	1 cut(s)	94
BslFI	GGGAC	1 cut(s)	303
BslI	CCNNNNNNNGG	1 cut(s)	100
BsmFI	GGGAC	1 cut(s)	303
BsnI	GGCC	1 cut(s)	125
Bsp119I	TTCGAA	1 cut(s)	347
Bsp1286I	GDGCHC	1 cut(s)	282
Bsp143I	GATC	2 cut(s)	133, 261
BspACI	CCGC	1 cut(s)	315
BspANI	GGCC	1 cut(s)	125
BspCNI	CTCAG	1 cut(s)	7
BspLI	GGNNCC	1 cut(s)	319
BspPI	GGATC	1 cut(s)	141
BspT104I	TTCGAA	1 cut(s)	347
BsrI	ACTGG	3 cut(s)	205, 218, 521
BssECI	CCNNGG	1 cut(s)	374
BssMI	GATC	2 cut(s)	133, 261
Bst2UI	CCWGG	1 cut(s)	375
Bst4CI	ACNGT	1 cut(s)	163
Bst6I	CTCTTC	1 cut(s)	346
BstAPI	GCANNNNNTGC	1 cut(s)	286
BstBI	TTCGAA	1 cut(s)	347
BstDEI	CTNAG	6 cut(s)	15, 114, 265, 411, 456, 528
BstF5I	GGATG	3 cut(s)	61, 109, 211
BstH2I	RGCGCY	1 cut(s)	234
BstHHI	GCGC	1 cut(s)	233
BstKTI	GATC	2 cut(s)	136, 264
BstMBI	GATC	2 cut(s)	133, 261
BstMWI	GCNNNNNNNGC	1 cut(s)	286
BstNI	CCWGG	1 cut(s)	375
BstNSI	RCATGY	1 cut(s)	506
BstSCI	CCNGG	1 cut(s)	373
BstSLI	GKGCMC	1 cut(s)	282
BstV1I	GCAGC	3 cut(s)	84, 205, 420
BstX2I	RGATCY	2 cut(s)	133, 261
BstYI	RGATCY	2 cut(s)	133, 261
BsuI	GTATCC	1 cut(s)	134
BsuRI	GGCC	1 cut(s)	125
BtsCI	GGATG	3 cut(s)	61, 109, 211
BtsI	GCAGTG	1 cut(s)	29
BtsIMutI	CAGTG	1 cut(s)	29
CfoI	GCGC	1 cut(s)	233
Cfr13I	GGNCC	2 cut(s)	317, 518
CviAII	CATG	1 cut(s)	503
CviJI	RGCY	7 cut(s)	51, 97, 125, 247, 455, 463, 498
CviKI_1	RGCY	7 cut(s)	51, 97, 125, 247, 455, 463, 498
DdeI	CTNAG	6 cut(s)	15, 114, 265, 411, 456, 528
DpnI	GATC	2 cut(s)	135, 263
DpnII	GATC	2 cut(s)	133, 261
DraIII	CACNNNGTG	1 cut(s)	286
DriI	GACNNNNNGTC	1 cut(s)	406
Eam1104I	CTCTTC	1 cut(s)	346
Eam1105I	GACNNNNNGTC	1 cut(s)	406
EarI	CTCTTC	1 cut(s)	346
Eco47I	GGWCC	2 cut(s)	317, 518
Eco57I	CTGAAG	1 cut(s)	311
EcoRII	CCWGG	1 cut(s)	373
FaeI	CATG	1 cut(s)	506
FaiI	YATR	5 cut(s)	198, 305, 334, 369, 504
FaqI	GGGAC	1 cut(s)	303
FatI	CATG	1 cut(s)	502
Fnu4HI	GCNGC	3 cut(s)	98, 194, 434
FokI	GGATG	3 cut(s)	68, 116, 218
Fsp4HI	GCNGC	3 cut(s)	98, 194, 434
FspBI	CTAG	1 cut(s)	515
GlaI	GCGC	1 cut(s)	232
GluI	GCNGC	3 cut(s)	98, 194, 434
HaeII	RGCGCY	1 cut(s)	234
HaeIII	GGCC	1 cut(s)	125
HapII	CCGG	1 cut(s)	94
HhaI	GCGC	1 cut(s)	233
Hin1II	CATG	1 cut(s)	506
Hin6I	GCGC	1 cut(s)	231
HinP1I	GCGC	1 cut(s)	231
HindIII	AAGCTT	2 cut(s)	49, 245
HinfI	GANTC	1 cut(s)	382
HpaII	CCGG	1 cut(s)	94
HphI	GGTGA	1 cut(s)	214
Hpy166II	GTNNAC	1 cut(s)	280
Hpy188I	TCNGA	2 cut(s)	140, 254
Hpy188III	TCNNGA	1 cut(s)	394
Hpy8I	GTNNAC	1 cut(s)	280
HpyAV	CCTTC	2 cut(s)	55, 155
HpyCH4III	ACNGT	1 cut(s)	163
HpyCH4V	TGCA	2 cut(s)	22, 280
HpyF10VI	GCNNNNNNNGC	1 cut(s)	286
HpyF3I	CTNAG	6 cut(s)	15, 114, 265, 411, 456, 528
Hsp92II	CATG	1 cut(s)	506
HspAI	GCGC	1 cut(s)	231
Kzo9I	GATC	2 cut(s)	133, 261
LmnI	GCTCC	2 cut(s)	78, 452
Lsp1109I	GCAGC	3 cut(s)	84, 205, 420
LweI	GCATC	3 cut(s)	46, 60, 302
MaeI	CTAG	1 cut(s)	515
MaeIII	GTNAC	2 cut(s)	220, 427
MalI	GATC	2 cut(s)	135, 263
MboI	GATC	2 cut(s)	133, 261
MboII	GAAGA	3 cut(s)	333, 336, 382
MfeI	CAATTG	1 cut(s)	84
MflI	RGATCY	2 cut(s)	133, 261
MhlI	GDGCHC	1 cut(s)	282
MluCI	AATT	2 cut(s)	84, 479
MnlI	CCTC	4 cut(s)	172, 248, 262, 460
MseI	TTAA	1 cut(s)	243
MslI	CAYNNNNRTG	1 cut(s)	161
MspI	CCGG	1 cut(s)	94
MspR9I	CCNGG	1 cut(s)	375
MunI	CAATTG	1 cut(s)	84
MvaI	CCWGG	1 cut(s)	375
MwoI	GCNNNNNNNGC	1 cut(s)	286
NdeII	GATC	2 cut(s)	133, 261
NlaIII	CATG	1 cut(s)	506
NlaIV	GGNNCC	1 cut(s)	319
NmuCI	GTSAC	2 cut(s)	220, 427
NspI	RCATGY	1 cut(s)	506
NspV	TTCGAA	1 cut(s)	347
OliI	CACNNNNGTG	1 cut(s)	161
PfeI	GAWTC	1 cut(s)	382
PkrI	GCNGC	3 cut(s)	99, 195, 435
Psp6I	CCWGG	1 cut(s)	373
PspGI	CCWGG	1 cut(s)	373
PspN4I	GGNNCC	1 cut(s)	319
PspPI	GGNCC	2 cut(s)	317, 518
PsuI	RGATCY	2 cut(s)	133, 261
RseI	CAYNNNNRTG	1 cut(s)	161
SaqAI	TTAA	1 cut(s)	243
SatI	GCNGC	3 cut(s)	98, 194, 434
Sau3AI	GATC	2 cut(s)	133, 261
Sau96I	GGNCC	2 cut(s)	317, 518
ScrFI	CCNGG	1 cut(s)	375
SduI	GDGCHC	1 cut(s)	282
SetI	ASST	8 cut(s)	53, 147, 227, 249, 288, 427, 457, 520
SfaNI	GCATC	3 cut(s)	46, 60, 302
SfuI	TTCGAA	1 cut(s)	347
SinI	GGWCC	2 cut(s)	317, 518
SmiMI	CAYNNNNRTG	1 cut(s)	161
SmlI	CTYRAG	1 cut(s)	464
SmoI	CTYRAG	1 cut(s)	464
Sse9I	AATT	2 cut(s)	84, 479
SsiI	CCGC	1 cut(s)	315
SspMI	CTAG	1 cut(s)	515
StyD4I	CCNGG	1 cut(s)	373
TaaI	ACNGT	1 cut(s)	163
TaqI	TCGA	1 cut(s)	347
TasI	AATT	2 cut(s)	84, 479
TfiI	GAWTC	1 cut(s)	382
Tru1I	TTAA	1 cut(s)	243
Tru9I	TTAA	1 cut(s)	243
TscAI	CASTG	1 cut(s)	29
TseFI	GTSAC	2 cut(s)	220, 427
TseI	GCWGC	3 cut(s)	97, 193, 433
Tsp45I	GTSAC	2 cut(s)	220, 427
TspDTI	ATGAA	1 cut(s)	430
TspRI	CASTG	1 cut(s)	29
VneI	GTGCAC	1 cut(s)	278
VpaK11BI	GGWCC	2 cut(s)	317, 518
XapI	RAATTY	1 cut(s)	479
XceI	RCATGY	1 cut(s)	506
XspI	CTAG	1 cut(s)	515

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