Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr7

Orthogroup ID

OG0001141

Physical Location & Seq

Genomic Coordinates Forward (+)

35358569 .. 35360421

Gene Structure 1853 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000034014

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1032 bp

ATGAAACAAGCCGTGGCAGCCGTGGAGATGATCGTAAGCTACGCATTCAAGAACAAGAGGCTTCTAGAGGAGGCTCTCACCCACCCCTCCCATTCCGACGCTGTGTCGTATCAGCGGCTCGAGTTCGTCGGCGATGCCGTTCTTAGCCTCGCTGTAAGCAACTACCTTTTTCTTGCTTACCCCAGAATTGACCAAGGCAACCTCTCTATGCTACGCGCCGCTAACGTCAGTACCGAGAAGCTCGCACGTGTTGCCGTACGACACGGGCTTTTTCGCTTCCTTCGCCACTCTGCACCTGTTCTCGATGATAAGGTCAATCCTGTTAGGGAGTTTACTGAAGTTGTCAGTGGAGAAGAAGAGATGCCACTTGTATATAGAGGGTCTGTAAAAGCCCCAAAAGTTCTTGCAGATATTGTGGAGTCTGTGGCTGCTGCTATCTATGTTGATTTGAATTTTGATCTGGAAAAACTTTGGATGATCTTTAGGCATGTTTTGGAGCCTATAGTGACGCTCGAAGACTTGCAGCAACAACCTCAACCCGTGACAAAGTTGTTTGAGGTTTGCCAAAAGCATGGGAAACATGTCGACATCAAGTATTGGAGGGATGAGACGAAAAGTATTGCGAGTGTGTATGTTGATGGCAAGTTTGTTGCCTCGGGTTCTTCTGAACAGAAAGAAGTTGCCAAGGTCAATGCTGCTGAGATAGCTCTATATAAGTTGTCAAAATTGATGCGCATGGATGATGCGTCGATTGAAGTTATTGCTGGAATTGATGGGTCATTTCATATTGAAGGAGCAAAACATAAGTTGCATGAGCTATGTGGAAAGAAGAAGTGGCCTAAACCAATCTACAACATCAAGCAAGACAAAGGTTCTTCACATGATGAGAAGAAGTTTGTATCGACAGTTCAAATTGCAACTATTGATGGTGTGCTTTGTATGACGGGAGATGAAATGTCGAGAGTAAAGGATGCAGAGAATTCTGCAGCTTCTTTAATGATCCGTGCTTTGCAAGAGTCTGATTATGTATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0004521 GO:0004525 GO:0004540 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016246 GO:0016441 GO:0016442 GO:0016458 GO:0016787 GO:0016788 GO:0016891 GO:0016893 GO:0019222 GO:0030422 GO:0031047 GO:0031050 GO:0031332 GO:0032296 GO:0032991 GO:0034641 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043331 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0060255 GO:0065007 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:0090305 GO:0090501 GO:0090502 GO:0097159 GO:0140098 GO:1901360 GO:1901363 GO:1901698 GO:1901699 GO:1990904

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DND1_DSRM Ribonuclease_3 dsrm

Protein Analysis

344

Amino Acids

38.41

Weight (kDa)

6.43

Isoelectric Point (pI)

33.98

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ribonucleas_3_3	PF14622	18 - 152	7.9e-18	Ribonuclease-III-like
Ribonuclease_3	PF00636	38 - 149	1.1e-21	Ribonuclease III domain
dsrm	PF00035	180 - 240	1.3e-08	Double-stranded RNA binding motif
DND1_DSRM	PF14709	265 - 338	1.6e-12	double strand RNA binding domain from DEAD END PROTEIN 1
dsrm	PF00035	266 - 337	9.1e-13	Double-stranded RNA binding motif

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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Orthologous Genes (Group: OG0001141)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G20420
fragaria_vesca	FvH4_3g23250
malus_domestica	MD03G1196200.v1.1 MD11G1212500.v1.1
prunus_persica	Prupe.4G219200_v2.0.a1 Prupe.4G219200_v2.0.a1 Prupe.4G219400_v2.0.a1 Prupe.4G219400_v2.0.a1
pyrus_communis	pycom03g14830 pycom11g18750
rosa_chinensis	RchiOBHm_Chr5g0040511 RchiOBHm_Chr5g0040931 RchiOBHm_Chr5g0040941
rosa_laevigata	RLG00000033986 RLG00000034014 RLG00000034016 RLG00000034026
rosa_multiflora	Rmu_co8051550.1_g000001 Rmu_co8392905.1_g000001 Rmu_sc0002475.1_g000019 Rmu_sc0002848.1_g000007 Rmu_sc0006651.1_g000007 Rmu_sc0006651.1_g000008 Rmu_sc0008620.1_g000001
rosa_roxburghii	Rroxscaffold_1G00039580 Rroxscaffold_1G00039750 Rroxscaffold_1G00039760 Rroxscaffold_1G00040130 Rroxscaffold_1G00040850
rosa_rugosa	Rorug02G0350900 Rorug02G0350900 Rorug02G0351000 Rorug05G0185500 Rorug05G0188700 Rorug05G0188900 Rorug05G0188900
rosa_samantha	Rh2AG398700 Rh2BG409100 Rh2CG385500 Rh2CG540800 Rh2DG418900 Rh5AG272400 Rh5AG274300 Rh5AG274400 Rh5AG344200 Rh5BG276400 Rh5BG279300 Rh5BG279400 Rh5CG308900 Rh5CG311400 Rh5CG311600 Rh5DG284900 Rh5DG287500
rosa_wichuraiana	Rw2G032480 Rw5G025510 Rw5G025770 Rw5G025780 Rw5G025790

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	734
AccI	GTMKAC	1 cut(s)	585
AccII	CGCG	1 cut(s)	216
AciI	CCGC	2 cut(s)	115, 219
AclWI	GGATC	1 cut(s)	994
AcsI	RAATTY	2 cut(s)	451, 979
AcuI	CTGAAG	1 cut(s)	357
AcvI	CACGTG	1 cut(s)	248
AfaI	GTAC	2 cut(s)	232, 258
AflIII	ACRYGT	2 cut(s)	247, 580
AgsI	TTSAA	5 cut(s)	49, 451, 755, 791, 911
AhdI	GACNNNNNGTC	1 cut(s)	103
AluBI	AGCT	5 cut(s)	39, 241, 707, 817, 989
AluI	AGCT	5 cut(s)	39, 241, 707, 817, 989
Alw26I	GTCTC	1 cut(s)	602
AlwI	GGATC	1 cut(s)	994
Ama87I	CYCGRG	2 cut(s)	119, 655
AoxI	GGCC	1 cut(s)	836
ApeKI	GCWGC	6 cut(s)	17, 428, 431, 523, 695, 986
ApoI	RAATTY	2 cut(s)	451, 979
AspLEI	GCGC	2 cut(s)	218, 735
AsuHPI	GGTGA	1 cut(s)	70
AvaI	CYCGRG	2 cut(s)	119, 655
BaeI	ACNNNNGTAYC	2 cut(s)	214, 247
BbrPI	CACGTG	1 cut(s)	248
BbsI	GAAGAC	1 cut(s)	522
BbvI	GCAGC	6 cut(s)	29, 415, 418, 535, 682, 998
BccI	CCATC	3 cut(s)	632, 767, 920
BceAI	ACGGC	3 cut(s)	5, 122, 239
BcoDI	GTCTC	1 cut(s)	602
BfaI	CTAG	1 cut(s)	65
BfmI	CTRYAG	2 cut(s)	501, 984
BisI	GCNGC	8 cut(s)	18, 116, 219, 429, 432, 524, 696, 987
BlsI	GCNGC	8 cut(s)	19, 117, 220, 430, 433, 525, 697, 988
BmeRI	GACNNNNNGTC	1 cut(s)	103
BmeT110I	CYCGRG	2 cut(s)	119, 655
BmiI	GGNNCC	1 cut(s)	498
BmsI	GCATC	5 cut(s)	124, 351, 720, 733, 961
BpiI	GAAGAC	1 cut(s)	522
BsaAI	YACGTR	1 cut(s)	248
BsaJI	CCNNGG	5 cut(s)	12, 21, 193, 654, 684
BseDI	CCNNGG	5 cut(s)	12, 21, 193, 654, 684
BseGI	GGATG	4 cut(s)	480, 610, 745, 976
BseMII	CTCAG	1 cut(s)	690
BseRI	GAGGAG	1 cut(s)	83
BseXI	GCAGC	6 cut(s)	29, 415, 418, 535, 682, 998
BsgI	GTGCAG	1 cut(s)	276
Bsh1236I	CGCG	1 cut(s)	216
BshFI	GGCC	1 cut(s)	838
BsiHKCI	CYCGRG	2 cut(s)	119, 655
BsiWI	CGTACG	1 cut(s)	256
BsmAI	GTCTC	1 cut(s)	602
BsmBI	CGTCTC	1 cut(s)	602
BsmI	GAATGC	1 cut(s)	44
BsnI	GGCC	1 cut(s)	838
BsoBI	CYCGRG	2 cut(s)	119, 655
Bsp143I	GATC	4 cut(s)	30, 457, 477, 999
BspACI	CCGC	2 cut(s)	115, 219
BspANI	GGCC	1 cut(s)	838
BspCNI	CTCAG	1 cut(s)	691
BspFNI	CGCG	1 cut(s)	216
BspLI	GGNNCC	1 cut(s)	498
BspMAI	CTGCAG	1 cut(s)	988
BspPI	GGATC	1 cut(s)	994
BssECI	CCNNGG	5 cut(s)	12, 21, 193, 654, 684
BssMI	GATC	4 cut(s)	30, 457, 477, 999
BssT1I	CCWWGG	2 cut(s)	193, 684
Bst4CI	ACNGT	1 cut(s)	907
Bst6I	CTCTTC	1 cut(s)	351
BstAPI	GCANNNNNTGC	1 cut(s)	251
BstBAI	YACGTR	1 cut(s)	248
BstC8I	GCNNGC	1 cut(s)	243
BstDEI	CTNAG	2 cut(s)	143, 699
BstDSI	CCRYGG	2 cut(s)	12, 21
BstF5I	GGATG	4 cut(s)	480, 610, 745, 976
BstFNI	CGCG	1 cut(s)	216
BstHHI	GCGC	2 cut(s)	218, 735
BstKTI	GATC	4 cut(s)	33, 460, 480, 1002
BstMAI	GTCTC	1 cut(s)	602
BstMBI	GATC	4 cut(s)	30, 457, 477, 999
BstMWI	GCNNNNNNNGC	4 cut(s)	17, 251, 282, 704
BstNSI	RCATGY	2 cut(s)	491, 584
BstSFI	CTRYAG	2 cut(s)	501, 984
BstUI	CGCG	1 cut(s)	216
BstV1I	GCAGC	6 cut(s)	29, 415, 418, 535, 682, 998
BstV2I	GAAGAC	1 cut(s)	522
BstXI	CCANNNNNNTGG	1 cut(s)	572
BsuRI	GGCC	1 cut(s)	838
BtgI	CCRYGG	2 cut(s)	12, 21
BtgZI	GCGATG	1 cut(s)	147
BtsCI	GGATG	4 cut(s)	480, 610, 745, 976
BtsIMutI	CAGTG	1 cut(s)	352
Cac8I	GCNNGC	1 cut(s)	243
CfoI	GCGC	2 cut(s)	218, 735
CseI	GACGC	3 cut(s)	107, 517, 735
Csp6I	GTAC	2 cut(s)	231, 257
CviAII	CATG	6 cut(s)	488, 572, 581, 736, 812, 881
CviQI	GTAC	2 cut(s)	231, 257
DdeI	CTNAG	2 cut(s)	143, 699
DpnI	GATC	4 cut(s)	32, 459, 479, 1001
DpnII	GATC	4 cut(s)	30, 457, 477, 999
DriI	GACNNNNNGTC	1 cut(s)	103
Eam1104I	CTCTTC	1 cut(s)	351
Eam1105I	GACNNNNNGTC	1 cut(s)	103
EarI	CTCTTC	1 cut(s)	351
Eco130I	CCWWGG	2 cut(s)	193, 684
Eco57I	CTGAAG	1 cut(s)	357
Eco72I	CACGTG	1 cut(s)	248
Eco88I	CYCGRG	2 cut(s)	119, 655
EcoRI	GAATTC	1 cut(s)	979
EcoT14I	CCWWGG	2 cut(s)	193, 684
ErhI	CCWWGG	2 cut(s)	193, 684
Esp3I	CGTCTC	1 cut(s)	602
FaeI	CATG	6 cut(s)	491, 575, 584, 739, 815, 884
FatI	CATG	6 cut(s)	487, 571, 580, 735, 811, 880
FblI	GTMKAC	1 cut(s)	585
Fnu4HI	GCNGC	8 cut(s)	18, 116, 219, 429, 432, 524, 696, 987
FokI	GGATG	4 cut(s)	487, 617, 752, 983
Fsp4HI	GCNGC	8 cut(s)	18, 116, 219, 429, 432, 524, 696, 987
FspAI	RTGCGCAY	1 cut(s)	734
FspBI	CTAG	1 cut(s)	65
FspI	TGCGCA	1 cut(s)	734
GlaI	GCGC	2 cut(s)	217, 734
GluI	GCNGC	8 cut(s)	18, 116, 219, 429, 432, 524, 696, 987
HaeIII	GGCC	1 cut(s)	838
HgaI	GACGC	3 cut(s)	107, 517, 735
HhaI	GCGC	2 cut(s)	218, 735
Hin1II	CATG	6 cut(s)	491, 575, 584, 739, 815, 884
Hin6I	GCGC	2 cut(s)	216, 733
HinP1I	GCGC	2 cut(s)	216, 733
HincII	GTYRAC	1 cut(s)	586
HindII	GTYRAC	1 cut(s)	586
HinfI	GANTC	2 cut(s)	419, 1016
HphI	GGTGA	1 cut(s)	70
Hpy166II	GTNNAC	2 cut(s)	333, 586
Hpy188I	TCNGA	3 cut(s)	97, 667, 1021
Hpy188III	TCNNGA	5 cut(s)	49, 65, 302, 461, 960
Hpy8I	GTNNAC	2 cut(s)	333, 586
Hpy99I	CGWCG	3 cut(s)	101, 131, 751
HpyAV	CCTTC	2 cut(s)	290, 785
HpyCH4III	ACNGT	1 cut(s)	907
HpyCH4IV	ACGT	2 cut(s)	225, 247
HpyCH4V	TGCA	8 cut(s)	293, 407, 523, 811, 917, 974, 986, 1012
HpyF10VI	GCNNNNNNNGC	4 cut(s)	17, 251, 282, 704
HpyF3I	CTNAG	2 cut(s)	143, 699
HpySE526I	ACGT	2 cut(s)	225, 247
Hsp92II	CATG	6 cut(s)	491, 575, 584, 739, 815, 884
HspAI	GCGC	2 cut(s)	216, 733
Kzo9I	GATC	4 cut(s)	30, 457, 477, 999
LmnI	GCTCC	2 cut(s)	496, 794
LpnPI	CCDG	5 cut(s)	196, 309, 333, 446, 750
Lsp1109I	GCAGC	6 cut(s)	29, 415, 418, 535, 682, 998
LweI	GCATC	5 cut(s)	124, 351, 720, 733, 961
MaeI	CTAG	1 cut(s)	65
MaeII	ACGT	2 cut(s)	225, 247
MaeIII	GTNAC	2 cut(s)	505, 541
MalI	GATC	4 cut(s)	32, 459, 479, 1001
MboI	GATC	4 cut(s)	30, 457, 477, 999
MboII	GAAGA	7 cut(s)	365, 368, 527, 654, 841, 867, 901
MluCI	AATT	6 cut(s)	186, 451, 725, 768, 912, 979
MlyI	GAGTC	2 cut(s)	428, 1025
MmeI	TCCRAC	1 cut(s)	120
MseI	TTAA	1 cut(s)	995
MspA1I	CMGCKG	1 cut(s)	115
Mva1269I	GAATGC	1 cut(s)	44
MvnI	CGCG	1 cut(s)	216
MwoI	GCNNNNNNNGC	4 cut(s)	17, 251, 282, 704
NdeII	GATC	4 cut(s)	30, 457, 477, 999
NlaIII	CATG	6 cut(s)	491, 575, 584, 739, 815, 884
NlaIV	GGNNCC	1 cut(s)	498
NmuCI	GTSAC	2 cut(s)	505, 541
NsbI	TGCGCA	1 cut(s)	734
NspI	RCATGY	2 cut(s)	491, 584
PaeR7I	CTCGAG	1 cut(s)	119
PciI	ACATGT	1 cut(s)	580
PcsI	WCGNNNNNNNCGW	2 cut(s)	135, 231
PctI	GAATGC	1 cut(s)	44
Pfl23II	CGTACG	1 cut(s)	256
PkrI	GCNGC	8 cut(s)	19, 117, 220, 430, 433, 525, 697, 988
PleI	GAGTC	2 cut(s)	427, 1024
PmaCI	CACGTG	1 cut(s)	248
PmlI	CACGTG	1 cut(s)	248
PpsI	GAGTC	2 cut(s)	427, 1024
Ppu21I	YACGTR	1 cut(s)	248
PscI	ACATGT	1 cut(s)	580
PspCI	CACGTG	1 cut(s)	248
PspLI	CGTACG	1 cut(s)	256
PspN4I	GGNNCC	1 cut(s)	498
PspXI	VCTCGAGB	1 cut(s)	119
PsrI	GAACNNNNNNTAC	2 cut(s)	891, 923
PstI	CTGCAG	1 cut(s)	988
RsaI	GTAC	2 cut(s)	232, 258
RsaNI	GTAC	2 cut(s)	231, 257
SalI	GTCGAC	1 cut(s)	584
SaqAI	TTAA	1 cut(s)	995
SatI	GCNGC	8 cut(s)	18, 116, 219, 429, 432, 524, 696, 987
Sau3AI	GATC	4 cut(s)	30, 457, 477, 999
SchI	GAGTC	2 cut(s)	428, 1025
SfaNI	GCATC	5 cut(s)	124, 351, 720, 733, 961
SfcI	CTRYAG	2 cut(s)	501, 984
Sfr274I	CTCGAG	1 cut(s)	119
SlaI	CTCGAG	1 cut(s)	119
SmlI	CTYRAG	1 cut(s)	119
SmoI	CTYRAG	1 cut(s)	119
Sse9I	AATT	6 cut(s)	186, 451, 725, 768, 912, 979
SsiI	CCGC	2 cut(s)	115, 219
SspMI	CTAG	1 cut(s)	65
StyI	CCWWGG	2 cut(s)	193, 684
TaaI	ACNGT	1 cut(s)	907
TaiI	ACGT	2 cut(s)	228, 250
TaqI	TCGA	7 cut(s)	120, 303, 513, 585, 749, 902, 959
TasI	AATT	6 cut(s)	186, 451, 725, 768, 912, 979
TauI	GCSGC	2 cut(s)	118, 221
Tru1I	TTAA	1 cut(s)	995
Tru9I	TTAA	1 cut(s)	995
TscAI	CASTG	1 cut(s)	352
TseFI	GTSAC	2 cut(s)	505, 541
TseI	GCWGC	6 cut(s)	17, 428, 431, 523, 695, 986
Tsp45I	GTSAC	2 cut(s)	505, 541
TspDTI	ATGAA	3 cut(s)	17, 773, 966
TspGWI	ACGGA	1 cut(s)	992
TspRI	CASTG	1 cut(s)	352
XapI	RAATTY	2 cut(s)	451, 979
XbaI	TCTAGA	1 cut(s)	64
XceI	RCATGY	2 cut(s)	491, 584
XhoI	CTCGAG	1 cut(s)	119
XmiI	GTMKAC	1 cut(s)	585
XspI	CTAG	1 cut(s)	65

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