Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0003249

Physical Location & Seq

Genomic Coordinates Forward (+)

82774777 .. 82775284

Gene Structure 508 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG584000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 372 bp

ATGAAGGACATCTTTAATGTTCACTGGCTTGATCTCCAGGCTGTTGCTTCTTCATTTTGCTTTTCTAATCCACCTAAGGTAAATTTAAACTTAGACAGCAGTGCATCAATGTTCAGGAAGAACATGCACAGAGTGGATGGAATTCGACATGGAATCAATCCTAGAAATCCTTATGGAAGGCAAAACGGTGGAGATGATACAAGACAATTTGTGAGGCATCAGGATATAGAAGCCTCACCCTGCAGCTCTGCAGTAATTTTCTCCACAAGTTTTGTATTTTTTTTGGCTGATGGAACAAATCAAAATGAAACAAAGTTTTTCTGGGGTTTTCCTTCCTTTCACTCTGATCTTGTAACAATGGAGACACTGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003724 GO:0003824 GO:0004004 GO:0004386 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005730 GO:0005737 GO:0006139 GO:0006725 GO:0006807 GO:0008026 GO:0008150 GO:0008152 GO:0008186 GO:0009987 GO:0010501 GO:0016070 GO:0016462 GO:0016787 GO:0016817 GO:0016818 GO:0016887 GO:0017111 GO:0031974 GO:0031981 GO:0034641 GO:0042623 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0070013 GO:0070035 GO:0071704 GO:0090304 GO:0140098 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DEAD DUF4217 Helicase_C

Protein Analysis

123

Amino Acids

13.99

Weight (kDa)

6.49

Isoelectric Point (pI)

31.38

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CTE_SPB4	PF13959	2 - 27	9.9e-07	ATP-dependent rRNA helicase SPB4-like, C-terminal extension

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: OG0003249)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G18600
fragaria_vesca	FvH4_5g12870
malus_domestica	MD05G1177700.v1.1 MD06G1209500.v1.1 MD14G1220200.v1.1 MD15G1015500.v1.1
prunus_persica	Prupe.5G214700_v2.0.a1 Prupe.6G096100_v2.0.a1 Prupe.6G096400_v2.0.a1 Prupe.6G096400_v2.0.a1 Prupe.6G097300_v2.0.a1
pyrus_communis	pycom05g16360 pycom05g16400 pycom05g16410 pycom06g18710 pycom14g18230 pycom15g01320
rosa_chinensis	RchiOBHm_Chr5g0083351 RchiOBHm_Chr5g0083361 RchiOBHm_Chr7g0184361
rosa_laevigata	RLG00000004982 RLG00000037030
rosa_multiflora	Rmu_sc0001444.1_g000013 Rmu_sc0001557.1_g000022 Rmu_sc0002245.1_g000045
rosa_roxburghii	Rroxscaffold_1G00001130 Rroxscaffold_3G00269690
rosa_samantha	Rh5AG533800 Rh5BG561600 Rh5CG583900 Rh5CG584000 Rh7AG080700 Rh7BG066500 Rh7CG066800 Rh7DG066500
rosa_wichuraiana	Rw5G049900 Rw7G005460

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AcsI	RAATTY	2 cut(s)	82, 141
AdeI	CACNNNGTG	1 cut(s)	133
AjnI	CCWGG	1 cut(s)	36
AluBI	AGCT	1 cut(s)	246
AluI	AGCT	1 cut(s)	246
Alw26I	GTCTC	1 cut(s)	356
ApeKI	GCWGC	1 cut(s)	243
ApoI	RAATTY	2 cut(s)	82, 141
AsuHPI	GGTGA	1 cut(s)	228
AxyI	CCTNAGG	1 cut(s)	75
BbvI	GCAGC	1 cut(s)	255
BccI	CCATC	2 cut(s)	131, 284
BciT130I	CCWGG	1 cut(s)	38
BcoDI	GTCTC	1 cut(s)	356
BfaI	CTAG	1 cut(s)	162
BfmI	CTRYAG	2 cut(s)	241, 249
BisI	GCNGC	1 cut(s)	244
BlsI	GCNGC	1 cut(s)	245
Bme1390I	CCNGG	1 cut(s)	38
BmrFI	CCNGG	1 cut(s)	38
BmsI	GCATC	2 cut(s)	113, 226
BpmI	CTGGAG	1 cut(s)	20
BsaXI	ACNNNNNCTCC	1 cut(s)	353
Bse1I	ACTGG	1 cut(s)	29
Bse21I	CCTNAGG	1 cut(s)	75
BseBI	CCWGG	1 cut(s)	38
BseGI	GGATG	1 cut(s)	142
BseNI	ACTGG	1 cut(s)	29
BseXI	GCAGC	1 cut(s)	255
BsmAI	GTCTC	1 cut(s)	356
Bsp143I	GATC	2 cut(s)	31, 346
BspMAI	CTGCAG	2 cut(s)	245, 253
BsrI	ACTGG	1 cut(s)	29
BssMI	GATC	2 cut(s)	31, 346
Bst2UI	CCWGG	1 cut(s)	38
Bst4CI	ACNGT	2 cut(s)	188, 369
BstDEI	CTNAG	2 cut(s)	75, 91
BstF5I	GGATG	1 cut(s)	142
BstKTI	GATC	2 cut(s)	34, 349
BstMAI	GTCTC	1 cut(s)	356
BstMBI	GATC	2 cut(s)	31, 346
BstNI	CCWGG	1 cut(s)	38
BstNSI	RCATGY	1 cut(s)	127
BstSCI	CCNGG	1 cut(s)	36
BstSFI	CTRYAG	2 cut(s)	241, 249
BstV1I	GCAGC	1 cut(s)	255
Bsu36I	CCTNAGG	1 cut(s)	75
BtsCI	GGATG	1 cut(s)	142
BtsI	GCAGTG	1 cut(s)	106
BtsIMutI	CAGTG	3 cut(s)	22, 106, 365
CspCI	CAANNNNNGTGG	2 cut(s)	253, 288
CviAII	CATG	2 cut(s)	124, 149
CviJI	RGCY	5 cut(s)	28, 41, 233, 246, 287
CviKI_1	RGCY	5 cut(s)	28, 41, 233, 246, 287
DdeI	CTNAG	2 cut(s)	75, 91
DpnI	GATC	2 cut(s)	33, 348
DpnII	GATC	2 cut(s)	31, 346
DraI	TTTAAA	1 cut(s)	87
DraIII	CACNNNGTG	1 cut(s)	133
Eco81I	CCTNAGG	1 cut(s)	75
EcoRI	GAATTC	1 cut(s)	141
EcoRII	CCWGG	1 cut(s)	36
FaeI	CATG	2 cut(s)	127, 152
FaiI	YATR	4 cut(s)	125, 150, 174, 227
FalI	AAGNNNNNCTT	1 cut(s)	28
FatI	CATG	2 cut(s)	123, 148
Fnu4HI	GCNGC	1 cut(s)	244
FokI	GGATG	1 cut(s)	149
Fsp4HI	GCNGC	1 cut(s)	244
FspBI	CTAG	1 cut(s)	162
GluI	GCNGC	1 cut(s)	244
GsuI	CTGGAG	1 cut(s)	20
Hin1II	CATG	2 cut(s)	127, 152
HinfI	GANTC	1 cut(s)	153
HphI	GGTGA	1 cut(s)	228
Hpy166II	GTNNAC	1 cut(s)	22
Hpy188I	TCNGA	1 cut(s)	346
Hpy188III	TCNNGA	2 cut(s)	115, 221
Hpy8I	GTNNAC	1 cut(s)	22
HpyAV	CCTTC	2 cut(s)	171, 342
HpyCH4III	ACNGT	2 cut(s)	188, 369
HpyCH4V	TGCA	4 cut(s)	104, 127, 243, 251
HpyF3I	CTNAG	2 cut(s)	75, 91
Hsp92II	CATG	2 cut(s)	127, 152
Kzo9I	GATC	2 cut(s)	31, 346
LpnPI	CCDG	7 cut(s)	10, 23, 50, 100, 206, 253, 307
Lsp1109I	GCAGC	1 cut(s)	255
LweI	GCATC	2 cut(s)	113, 226
MaeI	CTAG	1 cut(s)	162
MaeIII	GTNAC	1 cut(s)	352
MalI	GATC	2 cut(s)	33, 348
MboI	GATC	2 cut(s)	31, 346
MboII	GAAGA	2 cut(s)	42, 130
MluCI	AATT	4 cut(s)	82, 141, 206, 255
MnlI	CCTC	2 cut(s)	207, 244
MseI	TTAA	2 cut(s)	15, 86
MspR9I	CCNGG	1 cut(s)	38
MvaI	CCWGG	1 cut(s)	38
NdeII	GATC	2 cut(s)	31, 346
NlaIII	CATG	2 cut(s)	127, 152
NspI	RCATGY	1 cut(s)	127
PfeI	GAWTC	1 cut(s)	153
PkrI	GCNGC	1 cut(s)	245
Psp6I	CCWGG	1 cut(s)	36
PspGI	CCWGG	1 cut(s)	36
PstI	CTGCAG	2 cut(s)	245, 253
SaqAI	TTAA	2 cut(s)	15, 86
SatI	GCNGC	1 cut(s)	244
Sau3AI	GATC	2 cut(s)	31, 346
ScrFI	CCNGG	1 cut(s)	38
SetI	ASST	3 cut(s)	76, 81, 248
SfaNI	GCATC	2 cut(s)	113, 226
SfcI	CTRYAG	2 cut(s)	241, 249
Sse9I	AATT	4 cut(s)	82, 141, 206, 255
SspMI	CTAG	1 cut(s)	162
StyD4I	CCNGG	1 cut(s)	36
TaaI	ACNGT	2 cut(s)	188, 369
TaqI	TCGA	1 cut(s)	145
TasI	AATT	4 cut(s)	82, 141, 206, 255
TfiI	GAWTC	1 cut(s)	153
Tru1I	TTAA	2 cut(s)	15, 86
Tru9I	TTAA	2 cut(s)	15, 86
TscAI	CASTG	3 cut(s)	29, 106, 372
TseI	GCWGC	1 cut(s)	243
TspDTI	ATGAA	3 cut(s)	17, 42, 321
TspRI	CASTG	3 cut(s)	29, 106, 372
XapI	RAATTY	2 cut(s)	82, 141
XceI	RCATGY	1 cut(s)	127
XspI	CTAG	1 cut(s)	162

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