Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0004792

Physical Location & Seq

Genomic Coordinates Forward (+)

41334913 .. 41338930

Gene Structure 4018 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG163400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 864 bp

ATGATTGAATGTCTAAGGAAGCAGCTTTTCCAGCGTCCATCACATATTCAGGTTTTGGGTAATTGCCGATCAATATCAAAATTTGGAGTTCCTGTCAGGTCTATGGTTGTAACAGGCGGTCATCGACAGAAAACTCAGCTGGAAAGTTTGCAAGAAGGTGTTGATGTTCTAATTGCAACCCCAGGCCAATTTATATATCTAATTAAGGAGGGCTTCTTGCAATTGTCAAATTTAAGATGTGCTGTGCTGGATGAGGTAGATATAGTCTTTAATGATGAGGATTTTGAAGCAGCACTGCAAAGTTTAATCAATTCCGCACCTGCAACCACACAATATCTTTTTGTCACTGCAACTTTACCACTTGGCATTTACAACAAGTTAGTTGAAGATTTTCCTGATTGTCAAGTGGGCATGGCACCTGGAATGCACCGGATAAGCCCTGGCCTTGAAGAGGTTCTTGTAGATTGCCGTGGAGATGATCGGAGTGAAAAATCTCCAGAGATGACATTCACAAATAAGAAATCTGCTCTTCTACAGCTTGTGGAGGGAAGTCCAGTTCCCAAAACAATAGTCTTTTGTAACAAGATTGAGACATGCAGAAAAGTTGAGAATGTACTATCACGCTTTGACAGAAGTGGAACTCGTGTTCAAATTCTACCATTTCATTCTGCTCTGGCTCAAGAATCACGGCTTGCAAACATGAAGGAGTTCACCAATTCTCGTTCAGAGAAAGTAGCACAGTTTTTGGTCTGCACTGATAGAGCATCACGTGGAATCGACTTTCCTGGTGGGGATCATGTTATACTCTTCGACTTCCCTTGCGATCCAAGTGAGTACGTGCGGCGTGTAGGAAGAACTGCCTGA

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

287

Amino Acids

32.06

Weight (kDa)

6.24

Isoelectric Point (pI)

58.71

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DEAD	PF00270	17 - 120	1.1e-14	DEAD/DEAH box helicase
Helicase_C	PF00271	173 - 287	8.5e-22	Helicase conserved C-terminal domain

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)
AarI	CACCTGC	1 cut(s)	328
Acc36I	ACCTGC	1 cut(s)	328
AccB1I	GGYRCC	1 cut(s)	415
AciI	CCGC	3 cut(s)	117, 315, 841
AclWI	GGATC	2 cut(s)	801, 818
AcsI	RAATTY	3 cut(s)	80, 229, 651
AcvI	CACGTG	1 cut(s)	770
AfaI	GTAC	2 cut(s)	615, 836
AfiI	CCNNNNNNNGG	1 cut(s)	451
AgsI	TTSAA	5 cut(s)	8, 287, 386, 449, 650
AjnI	CCWGG	4 cut(s)	181, 418, 439, 784
AloI	GAACNNNNNNTCC	4 cut(s)	540, 572, 630, 662
AluBI	AGCT	3 cut(s)	25, 139, 538
AluI	AGCT	3 cut(s)	25, 139, 538
Alw26I	GTCTC	1 cut(s)	584
AlwI	GGATC	2 cut(s)	801, 818
AoxI	GGCC	2 cut(s)	184, 442
ApeKI	GCWGC	2 cut(s)	22, 290
ApoI	RAATTY	3 cut(s)	80, 229, 651
ArsI	GACNNNNNNTTYG	2 cut(s)	555, 587
Asp700I	GAANNNNTTC	3 cut(s)	390, 453, 707
AsuHPI	GGTGA	1 cut(s)	703
BanI	GGYRCC	1 cut(s)	415
BauI	CACGAG	1 cut(s)	642
BbrPI	CACGTG	1 cut(s)	770
BbvI	GCAGC	2 cut(s)	34, 302
BccI	CCATC	1 cut(s)	46
BceAI	ACGGC	2 cut(s)	453, 704
BciT130I	CCWGG	4 cut(s)	183, 420, 441, 786
BcoDI	GTCTC	1 cut(s)	584
BfmI	CTRYAG	1 cut(s)	533
BfuAI	ACCTGC	1 cut(s)	328
BisI	GCNGC	3 cut(s)	23, 291, 842
BlsI	GCNGC	3 cut(s)	24, 292, 843
Bme1390I	CCNGG	4 cut(s)	183, 420, 441, 786
BmiI	GGNNCC	1 cut(s)	417
BmrFI	CCNGG	4 cut(s)	183, 420, 441, 786
BmsI	GCATC	1 cut(s)	773
BpmI	CTGGAG	1 cut(s)	480
BpuEI	CTTGAG	1 cut(s)	663
BsaAI	YACGTR	2 cut(s)	770, 838
BsaBI	GATNNNNATC	1 cut(s)	73
BsaJI	CCNNGG	3 cut(s)	181, 439, 469
BsaWI	WCCGGW	1 cut(s)	429
BsaXI	ACNNNNNCTCC	2 cut(s)	78, 108
Bsc4I	CCNNNNNNNGG	1 cut(s)	451
Bse1I	ACTGG	1 cut(s)	554
Bse8I	GATNNNNATC	1 cut(s)	73
BseBI	CCWGG	4 cut(s)	183, 420, 441, 786
BseDI	CCNNGG	3 cut(s)	181, 439, 469
BseGI	GGATG	1 cut(s)	256
BseJI	GATNNNNATC	1 cut(s)	73
BseLI	CCNNNNNNNGG	1 cut(s)	451
BseMII	CTCAG	1 cut(s)	149
BseNI	ACTGG	1 cut(s)	554
BseXI	GCAGC	2 cut(s)	34, 302
BsgI	GTGCAG	1 cut(s)	736
BshFI	GGCC	2 cut(s)	186, 444
BshNI	GGYRCC	1 cut(s)	415
BsiSI	CCGG	1 cut(s)	430
BslI	CCNNNNNNNGG	1 cut(s)	451
BsmAI	GTCTC	1 cut(s)	584
BsmI	GAATGC	1 cut(s)	429
BsnI	GGCC	2 cut(s)	186, 444
Bsp143I	GATC	4 cut(s)	68, 478, 793, 823
BspACI	CCGC	3 cut(s)	117, 315, 841
BspANI	GGCC	2 cut(s)	186, 444
BspCNI	CTCAG	1 cut(s)	148
BspLI	GGNNCC	1 cut(s)	417
BspMI	ACCTGC	1 cut(s)	328
BspPI	GGATC	2 cut(s)	801, 818
BspQI	GCTCTTC	1 cut(s)	534
BspT107I	GGYRCC	1 cut(s)	415
BsrI	ACTGG	1 cut(s)	554
BssECI	CCNNGG	3 cut(s)	181, 439, 469
BssMI	GATC	4 cut(s)	68, 478, 793, 823
BssSI	CACGAG	1 cut(s)	642
Bst2BI	CACGAG	1 cut(s)	642
Bst2UI	CCWGG	4 cut(s)	183, 420, 441, 786
Bst4CI	ACNGT	1 cut(s)	741
Bst6I	CTCTTC	3 cut(s)	444, 534, 812
BstBAI	YACGTR	2 cut(s)	770, 838
BstC8I	GCNNGC	1 cut(s)	693
BstDEI	CTNAG	2 cut(s)	14, 135
BstDSI	CCRYGG	1 cut(s)	469
BstENI	CCTNNNNNAGG	1 cut(s)	449
BstF5I	GGATG	1 cut(s)	256
BstKTI	GATC	4 cut(s)	71, 481, 796, 826
BstMAI	GTCTC	1 cut(s)	584
BstMBI	GATC	4 cut(s)	68, 478, 793, 823
BstMWI	GCNNNNNNNGC	1 cut(s)	31
BstNI	CCWGG	4 cut(s)	183, 420, 441, 786
BstNSI	RCATGY	1 cut(s)	597
BstSCI	CCNGG	4 cut(s)	181, 418, 439, 784
BstSFI	CTRYAG	1 cut(s)	533
BstV1I	GCAGC	2 cut(s)	34, 302
BsuRI	GGCC	2 cut(s)	186, 444
BtgI	CCRYGG	1 cut(s)	469
BtsCI	GGATG	1 cut(s)	256
BtsI	GCAGTG	2 cut(s)	293, 345
BtsIMutI	CAGTG	3 cut(s)	293, 345, 753
BveI	ACCTGC	1 cut(s)	328
Cac8I	GCNNGC	1 cut(s)	693
CseI	GACGC	1 cut(s)	23
Csp6I	GTAC	2 cut(s)	614, 835
CviAII	CATG	4 cut(s)	412, 594, 700, 797
CviJI	RGCY	9 cut(s)	25, 139, 186, 213, 438, 444, 538, 677, 691
CviKI_1	RGCY	9 cut(s)	25, 139, 186, 213, 438, 444, 538, 677, 691
CviQI	GTAC	2 cut(s)	614, 835
DdeI	CTNAG	2 cut(s)	14, 135
DpnI	GATC	4 cut(s)	70, 480, 795, 825
DpnII	GATC	4 cut(s)	68, 478, 793, 823
Eam1104I	CTCTTC	3 cut(s)	444, 534, 812
EarI	CTCTTC	3 cut(s)	444, 534, 812
Eco72I	CACGTG	1 cut(s)	770
EcoNI	CCTNNNNNAGG	1 cut(s)	449
EcoRII	CCWGG	4 cut(s)	181, 418, 439, 784
FaeI	CATG	4 cut(s)	415, 597, 703, 800
FalI	AAGNNNNNCTT	4 cut(s)	197, 229, 441, 473
FatI	CATG	4 cut(s)	411, 593, 699, 796
Fnu4HI	GCNGC	3 cut(s)	23, 291, 842
FokI	GGATG	1 cut(s)	263
Fsp4HI	GCNGC	3 cut(s)	23, 291, 842
GluI	GCNGC	3 cut(s)	23, 291, 842
GsuI	CTGGAG	1 cut(s)	480
HaeIII	GGCC	2 cut(s)	186, 444
HapII	CCGG	1 cut(s)	430
HgaI	GACGC	1 cut(s)	23
Hin1II	CATG	4 cut(s)	415, 597, 703, 800
HinfI	GANTC	2 cut(s)	683, 774
HpaII	CCGG	1 cut(s)	430
HphI	GGTGA	1 cut(s)	703
Hpy166II	GTNNAC	1 cut(s)	711
Hpy188I	TCNGA	2 cut(s)	483, 727
Hpy188III	TCNNGA	3 cut(s)	395, 497, 680
Hpy8I	GTNNAC	1 cut(s)	711
HpyAV	CCTTC	2 cut(s)	149, 697
HpyCH4III	ACNGT	1 cut(s)	741
HpyCH4IV	ACGT	2 cut(s)	769, 837
HpyF10VI	GCNNNNNNNGC	1 cut(s)	31
HpyF3I	CTNAG	2 cut(s)	14, 135
HpySE526I	ACGT	2 cut(s)	769, 837
Hsp92II	CATG	4 cut(s)	415, 597, 703, 800
Kzo9I	GATC	4 cut(s)	68, 478, 793, 823
LguI	GCTCTTC	1 cut(s)	534
Lsp1109I	GCAGC	2 cut(s)	34, 302
LweI	GCATC	1 cut(s)	773
MaeII	ACGT	2 cut(s)	769, 837
MaeIII	GTNAC	3 cut(s)	109, 343, 578
MalI	GATC	4 cut(s)	70, 480, 795, 825
MboI	GATC	4 cut(s)	68, 478, 793, 823
MboII	GAAGA	5 cut(s)	398, 461, 521, 799, 864
MfeI	CAATTG	1 cut(s)	221
MnlI	CCTC	5 cut(s)	202, 247, 271, 445, 538
MroXI	GAANNNNTTC	3 cut(s)	390, 453, 707
MseI	TTAA	4 cut(s)	204, 233, 270, 305
MspA1I	CMGCKG	1 cut(s)	139
MspI	CCGG	1 cut(s)	430
MspR9I	CCNGG	4 cut(s)	183, 420, 441, 786
MunI	CAATTG	1 cut(s)	221
Mva1269I	GAATGC	1 cut(s)	429
MvaI	CCWGG	4 cut(s)	183, 420, 441, 786
MwoI	GCNNNNNNNGC	1 cut(s)	31
NdeII	GATC	4 cut(s)	68, 478, 793, 823
NlaIII	CATG	4 cut(s)	415, 597, 703, 800
NlaIV	GGNNCC	1 cut(s)	417
NmuCI	GTSAC	1 cut(s)	343
NspI	RCATGY	1 cut(s)	597
PaqCI	CACCTGC	1 cut(s)	328
PciSI	GCTCTTC	1 cut(s)	534
PctI	GAATGC	1 cut(s)	429
PdmI	GAANNNNTTC	3 cut(s)	390, 453, 707
PfeI	GAWTC	2 cut(s)	683, 774
PkrI	GCNGC	3 cut(s)	24, 292, 843
PmaCI	CACGTG	1 cut(s)	770
PmlI	CACGTG	1 cut(s)	770
Ppu21I	YACGTR	2 cut(s)	770, 838
Psp6I	CCWGG	4 cut(s)	181, 418, 439, 784
PspCI	CACGTG	1 cut(s)	770
PspGI	CCWGG	4 cut(s)	181, 418, 439, 784
PspN4I	GGNNCC	1 cut(s)	417
PvuII	CAGCTG	1 cut(s)	139
RsaI	GTAC	2 cut(s)	615, 836
RsaNI	GTAC	2 cut(s)	614, 835
SapI	GCTCTTC	1 cut(s)	534
SaqAI	TTAA	4 cut(s)	204, 233, 270, 305
SatI	GCNGC	3 cut(s)	23, 291, 842
Sau3AI	GATC	4 cut(s)	68, 478, 793, 823
ScrFI	CCNGG	4 cut(s)	183, 420, 441, 786
SfaNI	GCATC	1 cut(s)	773
SfcI	CTRYAG	1 cut(s)	533
SmlI	CTYRAG	1 cut(s)	678
SmoI	CTYRAG	1 cut(s)	678
SsiI	CCGC	3 cut(s)	117, 315, 841
StyD4I	CCNGG	4 cut(s)	181, 418, 439, 784
TaaI	ACNGT	1 cut(s)	741
TaiI	ACGT	2 cut(s)	772, 840
TaqI	TCGA	3 cut(s)	124, 777, 810
TatI	WGTACW	1 cut(s)	613
TauI	GCSGC	1 cut(s)	844
TfiI	GAWTC	2 cut(s)	683, 774
Tru1I	TTAA	4 cut(s)	204, 233, 270, 305
Tru9I	TTAA	4 cut(s)	204, 233, 270, 305
TscAI	CASTG	3 cut(s)	300, 352, 760
TseFI	GTSAC	1 cut(s)	343
TseI	GCWGC	2 cut(s)	22, 290
Tsp45I	GTSAC	1 cut(s)	343
TspDTI	ATGAA	2 cut(s)	653, 716
TspRI	CASTG	3 cut(s)	300, 352, 760
XagI	CCTNNNNNAGG	1 cut(s)	449
XapI	RAATTY	3 cut(s)	80, 229, 651
XceI	RCATGY	1 cut(s)	597
XmnI	GAANNNNTTC	3 cut(s)	390, 453, 707

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