Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0004792

Physical Location & Seq

Genomic Coordinates Forward (+)

31702066 .. 31704832

Gene Structure 2767 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG159100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 831 bp

ATGAAATCTGTAGTGGAGAAAGCTTCTCGGGTGAAGCGAGACATGGATGAAAGTGAAAATGAACTAGATGTGCAGGACACATCACCATTTATCTCTACAATTGAAGGTATGGGGAAGAAGAAGAAAGCAAATGCCATGAGTCGTGGAGGGAGACTTTCGAATCCTTCCAACTCACATGAGTTTAGGGACGCATTGCGTAAGAAGGAACCAACAGATTACAAGGACAATTCTAGAGTAACTACGAAAGATTTTTTTGAGCCACTCCCTGAGAGTCGGCATAAACCATATATGCGTCAGAAGCCTAACACCATCGTAGACAGACAAAAGGTTTCAGTTTCAAGAAAAGGATGGGGTAGTGGAGGGTCCGTAAGCGATTCATCGGAGTATCCAGACCTAGACCAACGAAGGAAAGTGTCCAATGATGGTGGCTTTTTCAGTCGAAAATCCTTTAGGGATGCGGGATGCAGTGAGTATCTGATTGAATGTCTAAGGAAGCAGCTTTTCCAGCGTCCATCACATATTCAGGCCATGGCGTTTGCTCCAGTTGTGGCTGGAAAAACCTCTATTATAGCTGACCAAAGTGGATCTGGCAAAACATTGGCTTATCTTGCTCCTGTCATTCAGCAATTGGCTTCTCAGGTTTTGGGTAATTGCCGATCAATATCAAAATTTGGAGTTCCTGTCAGGTCTATGGTTGTAACAGGCGGTCATCGACAGAAAACTCAGCTGGAAAGTTTGCAAGAAGGTGTTGATGTTCTAATTGCAACCCCAGGTCGATTTATATATCTAATTAAGGAGGGCTTCTTGCAATTGTCAAATTTAAGATGGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001101 GO:0002376 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:0006950 GO:0006952 GO:0006955 GO:0006968 GO:0008026 GO:0008150 GO:0008152 GO:0008186 GO:0009507 GO:0009536 GO:0009605 GO:0009607 GO:0009620 GO:0009719 GO:0009723 GO:0009725 GO:0009751 GO:0009753 GO:0009814 GO:0009817 GO:0009987 GO:0010033 GO:0010501 GO:0014070 GO:0016070 GO:0016462 GO:0016787 GO:0016817 GO:0016818 GO:0016887 GO:0017111 GO:0031974 GO:0031981 GO:0032870 GO:0034641 GO:0035690 GO:0042221 GO:0042493 GO:0042623 GO:0043170 GO:0043207 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:0044444 GO:0044446 GO:0044464 GO:0045087 GO:0046483 GO:0046677 GO:0050832 GO:0050896 GO:0051704 GO:0051707 GO:0051716 GO:0070013 GO:0070035 GO:0070887 GO:0071229 GO:0071236 GO:0071310 GO:0071369 GO:0071395 GO:0071407 GO:0071446 GO:0071495 GO:0071704 GO:0090304 GO:0098542 GO:0140098 GO:1901360 GO:1901700 GO:1901701

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DEAD Helicase_C

Protein Analysis

276

Amino Acids

30.87

Weight (kDa)

9.74

Isoelectric Point (pI)

57.15

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DEAD	PF00270	173 - 274	1.6e-11	DEAD/DEAH box helicase

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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0004792)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G06980
fragaria_vesca	FvH4_4g21860 FvH4_4g21860 FvH4_4g21860 FvH4_4g21860 FvH4_4g21860 FvH4_4g21860 FvH4_4g21860 FvH4_4g21860 FvH4_4g21860
malus_domestica	MD16G1131600.v1.1
prunus_persica	Prupe.1G209200_v2.0.a1
pyrus_communis	pycom16g11600
rosa_chinensis	RchiOBHm_Chr4g0410871 RchiOBHm_Chr4g0428121
rosa_laevigata	RLG00000007180 RLG00000008393
rosa_multiflora	Rmu_sc0004940.1_g000014 Rmu_sc0007108.1_g000006 Rmu_sc0009599.1_g000014
rosa_roxburghii	Rroxscaffold_5G00369830
rosa_rugosa	Rorug04G0222400
rosa_samantha	Rh4AG163400 Rh4AG279700 Rh4BG285100 Rh4CG176300 Rh4CG300700 Rh4DG159100 Rh4DG282200
rosa_wichuraiana	Rw0G005430 Rw4G024300

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	315
AciI	CCGC	2 cut(s)	458, 705
AclWI	GGATC	1 cut(s)	592
AcsI	RAATTY	2 cut(s)	668, 817
AgsI	TTSAA	3 cut(s)	104, 339, 482
AjnI	CCWGG	1 cut(s)	769
AluBI	AGCT	4 cut(s)	23, 499, 572, 727
AluI	AGCT	4 cut(s)	23, 499, 572, 727
Alw26I	GTCTC	2 cut(s)	33, 145
AlwI	GGATC	1 cut(s)	592
Ama87I	CYCGRG	1 cut(s)	27
AoxI	GGCC	1 cut(s)	525
ApeKI	GCWGC	1 cut(s)	496
ApoI	RAATTY	2 cut(s)	668, 817
AspS9I	GGNCC	1 cut(s)	363
AsuHPI	GGTGA	2 cut(s)	43, 75
AsuII	TTCGAA	1 cut(s)	158
AvaI	CYCGRG	1 cut(s)	27
AvaII	GGWCC	1 cut(s)	363
BbvI	GCAGC	1 cut(s)	508
BccI	CCATC	5 cut(s)	317, 342, 416, 520, 819
BciT130I	CCWGG	1 cut(s)	771
BciVI	GTATCC	1 cut(s)	396
BcoDI	GTCTC	2 cut(s)	33, 145
BfaI	CTAG	3 cut(s)	65, 231, 395
BfmI	CTRYAG	1 cut(s)	9
BfuI	GTATCC	1 cut(s)	396
BisI	GCNGC	1 cut(s)	497
BlsI	GCNGC	1 cut(s)	498
Bme1390I	CCNGG	1 cut(s)	771
Bme18I	GGWCC	1 cut(s)	363
BmeT110I	CYCGRG	1 cut(s)	27
BmgT120I	GGNCC	1 cut(s)	363
BmiI	GGNNCC	2 cut(s)	207, 364
BmrFI	CCNGG	1 cut(s)	771
BmsI	GCATC	2 cut(s)	445, 452
BpmI	CTGGAG	1 cut(s)	525
Bpu14I	TTCGAA	1 cut(s)	158
BsaBI	GATNNNNATC	1 cut(s)	661
BsaJI	CCNNGG	2 cut(s)	528, 769
BsaXI	ACNNNNNCTCC	4 cut(s)	351, 381, 666, 696
Bse1I	ACTGG	1 cut(s)	542
Bse3DI	GCAATG	1 cut(s)	191
Bse8I	GATNNNNATC	1 cut(s)	661
BseBI	CCWGG	1 cut(s)	771
BseDI	CCNNGG	2 cut(s)	528, 769
BseGI	GGATG	4 cut(s)	52, 353, 460, 467
BseJI	GATNNNNATC	1 cut(s)	661
BseMI	GCAATG	1 cut(s)	191
BseMII	CTCAG	3 cut(s)	258, 650, 737
BseNI	ACTGG	1 cut(s)	542
BseXI	GCAGC	1 cut(s)	508
BsgI	GTGCAG	1 cut(s)	92
BshFI	GGCC	1 cut(s)	527
BsiHKCI	CYCGRG	1 cut(s)	27
BslFI	GGGAC	1 cut(s)	200
BsmAI	GTCTC	2 cut(s)	33, 145
BsmFI	GGGAC	1 cut(s)	200
BsnI	GGCC	1 cut(s)	527
BsoBI	CYCGRG	1 cut(s)	27
Bsp119I	TTCGAA	1 cut(s)	158
Bsp143I	GATC	2 cut(s)	584, 656
Bsp19I	CCATGG	1 cut(s)	528
BspACI	CCGC	2 cut(s)	458, 705
BspANI	GGCC	1 cut(s)	527
BspCNI	CTCAG	3 cut(s)	259, 649, 736
BspLI	GGNNCC	2 cut(s)	207, 364
BspPI	GGATC	1 cut(s)	592
BspT104I	TTCGAA	1 cut(s)	158
BsrDI	GCAATG	1 cut(s)	191
BsrI	ACTGG	1 cut(s)	542
BssECI	CCNNGG	2 cut(s)	528, 769
BssMI	GATC	2 cut(s)	584, 656
BssT1I	CCWWGG	1 cut(s)	528
Bst2UI	CCWGG	1 cut(s)	771
BstBI	TTCGAA	1 cut(s)	158
BstDEI	CTNAG	4 cut(s)	267, 488, 636, 723
BstDSI	CCRYGG	1 cut(s)	528
BstF5I	GGATG	4 cut(s)	52, 353, 460, 467
BstKTI	GATC	2 cut(s)	587, 659
BstMAI	GTCTC	2 cut(s)	33, 145
BstMBI	GATC	2 cut(s)	584, 656
BstMWI	GCNNNNNNNGC	3 cut(s)	298, 505, 608
BstNI	CCWGG	1 cut(s)	771
BstSCI	CCNGG	1 cut(s)	769
BstSFI	CTRYAG	1 cut(s)	9
BstV1I	GCAGC	1 cut(s)	508
BstX2I	RGATCY	1 cut(s)	584
BstYI	RGATCY	1 cut(s)	584
BsuI	GTATCC	1 cut(s)	396
BsuRI	GGCC	1 cut(s)	527
BtgI	CCRYGG	1 cut(s)	528
BtsCI	GGATG	4 cut(s)	52, 353, 460, 467
BtsI	GCAGTG	1 cut(s)	472
BtsIMutI	CAGTG	1 cut(s)	472
Cfr13I	GGNCC	1 cut(s)	363
CseI	GACGC	3 cut(s)	197, 281, 497
CspCI	CAANNNNNGTGG	2 cut(s)	406, 441
CviAII	CATG	4 cut(s)	43, 136, 176, 529
DdeI	CTNAG	4 cut(s)	267, 488, 636, 723
DpnI	GATC	2 cut(s)	586, 658
DpnII	GATC	2 cut(s)	584, 656
Eco130I	CCWWGG	1 cut(s)	528
Eco47I	GGWCC	1 cut(s)	363
Eco88I	CYCGRG	1 cut(s)	27
EcoRII	CCWGG	1 cut(s)	769
EcoT14I	CCWWGG	1 cut(s)	528
ErhI	CCWWGG	1 cut(s)	528
FaeI	CATG	4 cut(s)	46, 139, 179, 532
FalI	AAGNNNNNCTT	2 cut(s)	785, 817
FaqI	GGGAC	1 cut(s)	200
FatI	CATG	4 cut(s)	42, 135, 175, 528
FauI	CCCGC	1 cut(s)	451
FblI	GTMKAC	1 cut(s)	315
Fnu4HI	GCNGC	1 cut(s)	497
FokI	GGATG	4 cut(s)	59, 360, 467, 474
Fsp4HI	GCNGC	1 cut(s)	497
FspBI	CTAG	3 cut(s)	65, 231, 395
GluI	GCNGC	1 cut(s)	497
GsuI	CTGGAG	1 cut(s)	525
HaeIII	GGCC	1 cut(s)	527
HgaI	GACGC	3 cut(s)	197, 281, 497
Hin1II	CATG	4 cut(s)	46, 139, 179, 532
HindIII	AAGCTT	1 cut(s)	21
HinfI	GANTC	4 cut(s)	139, 160, 271, 374
HphI	GGTGA	2 cut(s)	43, 75
Hpy166II	GTNNAC	1 cut(s)	316
Hpy188I	TCNGA	3 cut(s)	297, 382, 477
Hpy188III	TCNNGA	3 cut(s)	231, 339, 389
Hpy8I	GTNNAC	1 cut(s)	316
HpyAV	CCTTC	5 cut(s)	98, 174, 196, 399, 737
HpyCH4V	TGCA	5 cut(s)	73, 465, 739, 764, 808
HpyF10VI	GCNNNNNNNGC	3 cut(s)	298, 505, 608
HpyF3I	CTNAG	4 cut(s)	267, 488, 636, 723
Hsp92II	CATG	4 cut(s)	46, 139, 179, 532
Kzo9I	GATC	2 cut(s)	584, 656
LmnI	GCTCC	2 cut(s)	544, 616
Lsp1109I	GCAGC	1 cut(s)	508
LweI	GCATC	2 cut(s)	445, 452
MaeI	CTAG	3 cut(s)	65, 231, 395
MaeIII	GTNAC	2 cut(s)	235, 697
MalI	GATC	2 cut(s)	586, 658
MboI	GATC	2 cut(s)	584, 656
MboII	GAAGA	3 cut(s)	127, 130, 133
MfeI	CAATTG	3 cut(s)	99, 626, 809
MflI	RGATCY	1 cut(s)	584
MluCI	AATT	9 cut(s)	99, 226, 626, 649, 668, 759, 789, 809, 817
MlyI	GAGTC	2 cut(s)	148, 280
MmeI	TCCRAC	1 cut(s)	192
MnlI	CCTC	4 cut(s)	140, 353, 571, 790
MseI	TTAA	2 cut(s)	792, 821
MspA1I	CMGCKG	1 cut(s)	727
MspR9I	CCNGG	1 cut(s)	771
MunI	CAATTG	3 cut(s)	99, 626, 809
MvaI	CCWGG	1 cut(s)	771
MwoI	GCNNNNNNNGC	3 cut(s)	298, 505, 608
NcoI	CCATGG	1 cut(s)	528
NdeII	GATC	2 cut(s)	584, 656
NlaIII	CATG	4 cut(s)	46, 139, 179, 532
NlaIV	GGNNCC	2 cut(s)	207, 364
NspV	TTCGAA	1 cut(s)	158
PcsI	WCGNNNNNNNCGW	1 cut(s)	34
PfeI	GAWTC	2 cut(s)	160, 374
PkrI	GCNGC	1 cut(s)	498
PleI	GAGTC	2 cut(s)	147, 279
PpsI	GAGTC	2 cut(s)	147, 279
Psp6I	CCWGG	1 cut(s)	769
PspGI	CCWGG	1 cut(s)	769
PspN4I	GGNNCC	2 cut(s)	207, 364
PspPI	GGNCC	1 cut(s)	363
PsuI	RGATCY	1 cut(s)	584
PvuII	CAGCTG	1 cut(s)	727
SaqAI	TTAA	2 cut(s)	792, 821
SatI	GCNGC	1 cut(s)	497
Sau3AI	GATC	2 cut(s)	584, 656
Sau96I	GGNCC	1 cut(s)	363
SchI	GAGTC	2 cut(s)	148, 280
ScrFI	CCNGG	1 cut(s)	771
SfaNI	GCATC	2 cut(s)	445, 452
SfcI	CTRYAG	1 cut(s)	9
SfuI	TTCGAA	1 cut(s)	158
SinI	GGWCC	1 cut(s)	363
Sse9I	AATT	9 cut(s)	99, 226, 626, 649, 668, 759, 789, 809, 817
SsiI	CCGC	2 cut(s)	458, 705
SspMI	CTAG	3 cut(s)	65, 231, 395
StyD4I	CCNGG	1 cut(s)	769
StyI	CCWWGG	1 cut(s)	528
TaqI	TCGA	4 cut(s)	158, 439, 712, 775
TasI	AATT	9 cut(s)	99, 226, 626, 649, 668, 759, 789, 809, 817
TfiI	GAWTC	2 cut(s)	160, 374
Tru1I	TTAA	2 cut(s)	792, 821
Tru9I	TTAA	2 cut(s)	792, 821
TscAI	CASTG	1 cut(s)	472
TseI	GCWGC	1 cut(s)	496
TspDTI	ATGAA	4 cut(s)	17, 63, 75, 366
TspGWI	ACGGA	1 cut(s)	355
TspRI	CASTG	1 cut(s)	472
VpaK11BI	GGWCC	1 cut(s)	363
XapI	RAATTY	2 cut(s)	668, 817
XbaI	TCTAGA	1 cut(s)	230
XcmI	CCANNNNNNNNNTGG	1 cut(s)	584
XmiI	GTMKAC	1 cut(s)	315
XspI	CTAG	3 cut(s)	65, 231, 395

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