Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0012090

Physical Location & Seq

Genomic Coordinates Forward (+)

56951416 .. 56953419

Gene Structure 2004 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG254800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 345 bp

ATGAGTACCATGAAGTTTTGCCGCGAATGCAACAACATTCTCTACCCCAAGGAGGACAAGGACCAGAAGATTCTCCTCTACGCGTGCCGCAATTGCGATCACCAGGAGGTTGCTGATAACAACTGTGTCTACAGAAATGAGATACACCACTCGGTTGGGGAACGCACTCAAATCTTGCAAGATGTAGCTGCAGATCCAACTCTACCTCGCACAAAAGCTGTGCGCTGTGCTCAGTGCAAGCATGGAGAAGCTGTCTTCTTTCAGGCAACTGCTAGAGGAGAGGAGGGGATGACTTTGTTCTTTGTTTGCTGCAACCCCAACTGTGGCTACAGGTGGAGGGACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000419 GO:0000428 GO:0001192 GO:0001193 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0006139 GO:0006259 GO:0006281 GO:0006283 GO:0006289 GO:0006304 GO:0006305 GO:0006306 GO:0006351 GO:0006352 GO:0006354 GO:0006366 GO:0006367 GO:0006368 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009892 GO:0009987 GO:0010467 GO:0010468 GO:0010605 GO:0010629 GO:0016070 GO:0016458 GO:0016591 GO:0018130 GO:0019222 GO:0019438 GO:0030880 GO:0031047 GO:0031974 GO:0031981 GO:0032259 GO:0032774 GO:0032991 GO:0033554 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043412 GO:0043414 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0044728 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0071704 GO:0080188 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

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

Pfam Domains

Protein Families

RNA_POL_M_15KD TFIIS_C

Protein Analysis

114

Amino Acids

13.18

Weight (kDa)

6.87

Isoelectric Point (pI)

42.04

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Zn_ribbon_RPB9	PF02150	4 - 36	2.3e-11	RNA polymerases M/15 Kd subunit
Zn_ribbon_TFIIS	PF01096	75 - 113	5e-10	Transcription factor S-II (TFIIS)

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0012090)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G16980 AT4G16265 AT4G16265
fragaria_vesca	FvH4_4g19480
malus_domestica	MD13G1156200.v1.1 MD16G1157100.v1.1
prunus_persica	Prupe.1G122000_v2.0.a1
pyrus_communis	pycom13g13360 pycom16g13210
rosa_chinensis	RchiOBHm_Chr4g0424591
rosa_laevigata	RLG00000007453
rosa_multiflora	Rmu_sc0002603.1_g000022 Rmu_sc0003942.1_g000007
rosa_roxburghii	Rroxscaffold_5G00366510
rosa_rugosa	Rorug04G0198000 Rorug04G0198000
rosa_samantha	Rh4AG254800 Rh4BG260300
rosa_wichuraiana	Rw4G022030

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	129
AccII	CGCG	2 cut(s)	24, 83
AciI	CCGC	2 cut(s)	22, 88
AclWI	GGATC	1 cut(s)	188
AfaI	GTAC	1 cut(s)	7
AfiI	CCNNNNNNNGG	2 cut(s)	52, 323
AflIII	ACRYGT	1 cut(s)	81
AjnI	CCWGG	1 cut(s)	102
AluBI	AGCT	3 cut(s)	188, 218, 251
AluI	AGCT	3 cut(s)	188, 218, 251
Alw21I	GWGCWC	1 cut(s)	232
AlwI	GGATC	1 cut(s)	188
ApeKI	GCWGC	2 cut(s)	188, 309
AspLEI	GCGC	1 cut(s)	225
AspS9I	GGNCC	1 cut(s)	61
AsuHPI	GGTGA	1 cut(s)	92
AvaII	GGWCC	1 cut(s)	61
BbsI	GAAGAC	1 cut(s)	247
Bbv12I	GWGCWC	1 cut(s)	232
BbvI	GCAGC	2 cut(s)	175, 296
BciT130I	CCWGG	1 cut(s)	104
BfaI	CTAG	1 cut(s)	273
BfmI	CTRYAG	3 cut(s)	130, 189, 328
BisI	GCNGC	4 cut(s)	22, 88, 189, 310
BlsI	GCNGC	4 cut(s)	23, 89, 190, 311
Bme1390I	CCNGG	1 cut(s)	104
Bme18I	GGWCC	1 cut(s)	61
BmgT120I	GGNCC	1 cut(s)	61
BmrFI	CCNGG	1 cut(s)	104
BpiI	GAAGAC	1 cut(s)	247
BsaJI	CCNNGG	1 cut(s)	48
BsaXI	ACNNNNNCTCC	2 cut(s)	237, 267
Bsc4I	CCNNNNNNNGG	2 cut(s)	52, 323
BseBI	CCWGG	1 cut(s)	104
BseDI	CCNNGG	1 cut(s)	48
BseGI	GGATG	1 cut(s)	294
BseLI	CCNNNNNNNGG	2 cut(s)	52, 323
BseMII	CTCAG	1 cut(s)	245
BseRI	GAGGAG	3 cut(s)	65, 291, 296
BseXI	GCAGC	2 cut(s)	175, 296
Bsh1236I	CGCG	2 cut(s)	24, 83
BsiHKAI	GWGCWC	1 cut(s)	232
BslI	CCNNNNNNNGG	2 cut(s)	52, 323
BsmI	GAATGC	1 cut(s)	32
Bsp1286I	GDGCHC	1 cut(s)	232
Bsp143I	GATC	2 cut(s)	97, 193
BspACI	CCGC	2 cut(s)	22, 88
BspCNI	CTCAG	1 cut(s)	244
BspFNI	CGCG	2 cut(s)	24, 83
BspMAI	CTGCAG	1 cut(s)	193
BspPI	GGATC	1 cut(s)	188
BssECI	CCNNGG	1 cut(s)	48
BssMI	GATC	2 cut(s)	97, 193
BssT1I	CCWWGG	1 cut(s)	48
Bst2UI	CCWGG	1 cut(s)	104
Bst4CI	ACNGT	2 cut(s)	125, 323
BstC8I	GCNNGC	2 cut(s)	85, 239
BstDEI	CTNAG	1 cut(s)	231
BstF5I	GGATG	1 cut(s)	294
BstFNI	CGCG	2 cut(s)	24, 83
BstHHI	GCGC	1 cut(s)	225
BstKTI	GATC	2 cut(s)	100, 196
BstMBI	GATC	2 cut(s)	97, 193
BstMWI	GCNNNNNNNGC	2 cut(s)	27, 93
BstNI	CCWGG	1 cut(s)	104
BstSCI	CCNGG	1 cut(s)	102
BstSFI	CTRYAG	3 cut(s)	130, 189, 328
BstUI	CGCG	2 cut(s)	24, 83
BstV1I	GCAGC	2 cut(s)	175, 296
BstV2I	GAAGAC	1 cut(s)	247
BstX2I	RGATCY	1 cut(s)	193
BstXI	CCANNNNNNTGG	1 cut(s)	155
BstYI	RGATCY	1 cut(s)	193
BtsCI	GGATG	1 cut(s)	294
BtsIMutI	CAGTG	1 cut(s)	239
Cac8I	GCNNGC	2 cut(s)	85, 239
CfoI	GCGC	1 cut(s)	225
Cfr13I	GGNCC	1 cut(s)	61
Csp6I	GTAC	1 cut(s)	6
CviAII	CATG	2 cut(s)	10, 242
CviJI	RGCY	4 cut(s)	188, 218, 251, 327
CviKI_1	RGCY	4 cut(s)	188, 218, 251, 327
CviQI	GTAC	1 cut(s)	6
DdeI	CTNAG	1 cut(s)	231
DpnI	GATC	2 cut(s)	99, 195
DpnII	GATC	2 cut(s)	97, 193
Eco130I	CCWWGG	1 cut(s)	48
Eco47I	GGWCC	1 cut(s)	61
EcoRII	CCWGG	1 cut(s)	102
EcoT14I	CCWWGG	1 cut(s)	48
ErhI	CCWWGG	1 cut(s)	48
FaeI	CATG	2 cut(s)	13, 245
FaiI	YATR	2 cut(s)	11, 243
FatI	CATG	2 cut(s)	9, 241
FblI	GTMKAC	1 cut(s)	129
Fnu4HI	GCNGC	4 cut(s)	22, 88, 189, 310
FokI	GGATG	1 cut(s)	301
Fsp4HI	GCNGC	4 cut(s)	22, 88, 189, 310
FspBI	CTAG	1 cut(s)	273
GlaI	GCGC	1 cut(s)	224
GluI	GCNGC	4 cut(s)	22, 88, 189, 310
HhaI	GCGC	1 cut(s)	225
Hin1II	CATG	2 cut(s)	13, 245
Hin6I	GCGC	1 cut(s)	223
HinP1I	GCGC	1 cut(s)	223
HinfI	GANTC	1 cut(s)	70
HphI	GGTGA	1 cut(s)	92
Hpy166II	GTNNAC	1 cut(s)	130
Hpy8I	GTNNAC	1 cut(s)	130
HpyCH4III	ACNGT	2 cut(s)	125, 323
HpyCH4V	TGCA	5 cut(s)	30, 178, 191, 237, 312
HpyF10VI	GCNNNNNNNGC	2 cut(s)	27, 93
HpyF3I	CTNAG	1 cut(s)	231
Hsp92II	CATG	2 cut(s)	13, 245
HspAI	GCGC	1 cut(s)	223
Kzo9I	GATC	2 cut(s)	97, 193
LpnPI	CCDG	5 cut(s)	77, 89, 116, 248, 316
Lsp1109I	GCAGC	2 cut(s)	175, 296
MaeI	CTAG	1 cut(s)	273
MalI	GATC	2 cut(s)	99, 195
MboI	GATC	2 cut(s)	97, 193
MboII	GAAGA	2 cut(s)	79, 247
MfeI	CAATTG	1 cut(s)	91
MflI	RGATCY	1 cut(s)	193
MhlI	GDGCHC	1 cut(s)	232
MluCI	AATT	1 cut(s)	91
MluI	ACGCGT	1 cut(s)	81
MmeI	TCCRAC	1 cut(s)	221
MnlI	CCTC	8 cut(s)	46, 86, 100, 216, 269, 274, 277, 330
MspR9I	CCNGG	1 cut(s)	104
MunI	CAATTG	1 cut(s)	91
Mva1269I	GAATGC	1 cut(s)	32
MvaI	CCWGG	1 cut(s)	104
MvnI	CGCG	2 cut(s)	24, 83
MwoI	GCNNNNNNNGC	2 cut(s)	27, 93
NdeII	GATC	2 cut(s)	97, 193
NlaIII	CATG	2 cut(s)	13, 245
PctI	GAATGC	1 cut(s)	32
PfeI	GAWTC	1 cut(s)	70
PkrI	GCNGC	4 cut(s)	23, 89, 190, 311
Psp6I	CCWGG	1 cut(s)	102
PspGI	CCWGG	1 cut(s)	102
PspPI	GGNCC	1 cut(s)	61
PstI	CTGCAG	1 cut(s)	193
PsuI	RGATCY	1 cut(s)	193
RsaI	GTAC	1 cut(s)	7
RsaNI	GTAC	1 cut(s)	6
SatI	GCNGC	4 cut(s)	22, 88, 189, 310
Sau3AI	GATC	2 cut(s)	97, 193
Sau96I	GGNCC	1 cut(s)	61
ScrFI	CCNGG	1 cut(s)	104
SduI	GDGCHC	1 cut(s)	232
SetI	ASST	6 cut(s)	111, 190, 208, 220, 253, 335
SfcI	CTRYAG	3 cut(s)	130, 189, 328
SinI	GGWCC	1 cut(s)	61
Sse9I	AATT	1 cut(s)	91
SsiI	CCGC	2 cut(s)	22, 88
SspMI	CTAG	1 cut(s)	273
StyD4I	CCNGG	1 cut(s)	102
StyI	CCWWGG	1 cut(s)	48
TaaI	ACNGT	2 cut(s)	125, 323
TasI	AATT	1 cut(s)	91
TauI	GCSGC	2 cut(s)	24, 90
TfiI	GAWTC	1 cut(s)	70
TscAI	CASTG	1 cut(s)	239
TseI	GCWGC	2 cut(s)	188, 309
TspDTI	ATGAA	1 cut(s)	26
TspRI	CASTG	1 cut(s)	239
VpaK11BI	GGWCC	1 cut(s)	61
XmiI	GTMKAC	1 cut(s)	129
XspI	CTAG	1 cut(s)	273

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