Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0002185

Physical Location & Seq

Genomic Coordinates Reverse (-)

45217523 .. 45219100

Gene Structure 1578 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG336700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 870 bp

ATGGGGGTTCCATCGTTTTTTCGTTGGTTGGTAAACAAGTACCCTAAAGTGGTGGTGAAAGCCATTGAAGCGGGAGAGGATCAGTTTCTAGATGCAAGCTTGCCAAACCCAAATGGCATAGAGTTCGATAACCTGTTTCTAGACATGAATGGGATTATCCATCCCTGCTTTCATCCGGAAGAAGATGATGATGATGACGGTTATGGACTTGCACCGCCAAGAACTTATGAAGATGTCTTCAACAATATTTTCGAATACATTGATCGGCTTTTCAATATTGTTAGACCAAGGAAACTACTCTACATAGCCATTGATGGAGTTGCTCCGAGGGCTAAAATGAATCAACAGCGCGCCAGGCGTTTTAAGTCGGCAATGGACAAGAATCTTGCTGAGGCTGAAGAAGAGAAACTAAGACAGCAATTTGCAAAGGAAGGGAAAAAAATCCTACTAGAACAGGAGTCTGAAGTTTCTGATTCTAATATAATCACCCCTGGAACGGATTTCATGTACAAGTTATCCAAGGCTCTTCAAAGCTACATCAATCTACGTTTAAGCCAAGATTCAGGCTGGAGGGACATCAAGGTAATACTTTCTGATGCCAATGTTCCTGGGGAAGGAGAACATAAAGTGATGTCGTTCATACGTCACCAGCGAACTGTTCCTTCTTATGATCCAAACACCCGCCATTGCTTGTATGGTCTGGATGCGGATCTTATAATGTTGTCTTTGGCAACACATGAAGTTCACCTTTCCATACTAAGAGAGGTTGAATTTGCAAACCTTTCAAGTTTTATCAATTTCCTTTCTCTCTCTCTTTTTTTTTTTTCGGTTTATTTTTTTACCATGTTACAGCTTGGAATTTGGTCTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000966 GO:0000967 GO:0003674 GO:0003824 GO:0004518 GO:0004527 GO:0004532 GO:0004534 GO:0004540 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006364 GO:0006396 GO:0006401 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0008409 GO:0009056 GO:0009057 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010586 GO:0010587 GO:0010604 GO:0010628 GO:0016070 GO:0016072 GO:0016075 GO:0016787 GO:0016788 GO:0016796 GO:0016896 GO:0019222 GO:0019439 GO:0022613 GO:0034470 GO:0034471 GO:0034641 GO:0034655 GO:0034660 GO:0034661 GO:0042254 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043632 GO:0043633 GO:0043634 GO:0044085 GO:0044237 GO:0044238 GO:0044248 GO:0044260 GO:0044265 GO:0044270 GO:0044424 GO:0044464 GO:0046483 GO:0046700 GO:0048518 GO:0048519 GO:0048523 GO:0050789 GO:0050794 GO:0060147 GO:0060149 GO:0060255 GO:0060968 GO:0060969 GO:0065007 GO:0071025 GO:0071027 GO:0071029 GO:0071035 GO:0071046 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0090501 GO:0090503 GO:0140098 GO:1901360 GO:1901361 GO:1901575

KEGG Pathways

Metabolic & Signaling

ko03008 ko03018 map03008 map03018

Pfam Domains

Protein Families

XRN_N

Protein Analysis

289

Amino Acids

33.3

Weight (kDa)

5.24

Isoelectric Point (pI)

47.75

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
XRN_N	PF03159	1 - 255	5.8e-103	XRN 5'-3' exonuclease N-terminus

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: OG0002185)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G75660 AT5G42540 AT5G42540
fragaria_vesca	FvH4_2g38700 FvH4_2g38700 FvH4_5g21470
malus_domestica	MD00G1128500.v1.1 MD08G1014700.v1.1 MD15G1014000.v1.1
prunus_persica	Prupe.1G367600_v2.0.a1 Prupe.1G367600_v2.0.a1 Prupe.1G367600_v2.0.a1 Prupe.1G367600_v2.0.a1 Prupe.1G367600_v2.0.a1 Prupe.1G367600_v2.0.a1 Prupe.1G367600_v2.0.a1 Prupe.1G367600_v2.0.a1
pyrus_communis	pycom08g01310 pycom15g01210
rosa_chinensis	RchiOBHm_Chr5g0009961 RchiOBHm_Chr6g0302611
rosa_laevigata	RLG00000011157 RLG00000031714
rosa_multiflora	Rmu_sc0027322.1_g000001 Rmu_sc0027323.1_g000001 Rmu_sc0039467.1_g000001 Rmu_sc0039989.1_g000001 Rmu_sc0041627.1_g000001
rosa_roxburghii	Rroxscaffold_1G00066230 Rroxscaffold_7G00165520
rosa_rugosa	Rorug04G0447300 Rorug06G0315300 Rorug06G0315400
rosa_samantha	Rh5AG078800 Rh5BG073500 Rh5CG086100 Rh5DG074200 Rh5DG336700 Rh6AG428700 Rh6BG473800 Rh6CG441000 Rh6DG427700
rosa_wichuraiana	Rw6G037100

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	716
AccII	CGCG	1 cut(s)	351
AccIII	TCCGGA	1 cut(s)	175
AciI	CCGC	4 cut(s)	71, 215, 682, 707
AclWI	GGATC	3 cut(s)	87, 665, 717
AcsI	RAATTY	2 cut(s)	770, 858
AcuI	CTGAAG	2 cut(s)	417, 483
AfaI	GTAC	2 cut(s)	41, 509
AfiI	CCNNNNNNNGG	3 cut(s)	49, 496, 614
AgsI	TTSAA	6 cut(s)	68, 241, 274, 530, 770, 786
AjnI	CCWGG	3 cut(s)	353, 490, 607
AluBI	AGCT	3 cut(s)	99, 534, 853
AluI	AGCT	3 cut(s)	99, 534, 853
AlwI	GGATC	3 cut(s)	87, 665, 717
Aor13HI	TCCGGA	1 cut(s)	175
ApoI	RAATTY	2 cut(s)	770, 858
AspLEI	GCGC	2 cut(s)	351, 353
AsuHPI	GGTGA	4 cut(s)	67, 478, 638, 737
AsuII	TTCGAA	1 cut(s)	252
BbsI	GAAGAC	1 cut(s)	229
BbvCI	CCTCAGC	1 cut(s)	390
BccI	CCATC	3 cut(s)	19, 168, 308
BcgI	CGANNNNNNTGC	2 cut(s)	106, 140
BciT130I	CCWGG	3 cut(s)	355, 492, 609
BfaI	CTAG	3 cut(s)	89, 140, 449
Bme1390I	CCNGG	3 cut(s)	355, 492, 609
BmiI	GGNNCC	1 cut(s)	9
BmrFI	CCNGG	3 cut(s)	355, 492, 609
BmsI	GCATC	3 cut(s)	82, 586, 694
BpiI	GAAGAC	1 cut(s)	229
BpmI	CTGGAG	1 cut(s)	589
Bpu10I	CCTNAGC	1 cut(s)	390
Bpu14I	TTCGAA	1 cut(s)	252
BsaBI	GATNNNNATC	1 cut(s)	708
BsaJI	CCNNGG	5 cut(s)	287, 326, 490, 519, 608
BsaWI	WCCGGW	1 cut(s)	175
Bsc4I	CCNNNNNNNGG	3 cut(s)	49, 496, 614
Bse3DI	GCAATG	2 cut(s)	378, 685
Bse8I	GATNNNNATC	1 cut(s)	708
BseAI	TCCGGA	1 cut(s)	175
BseBI	CCWGG	3 cut(s)	355, 492, 609
BseDI	CCNNGG	5 cut(s)	287, 326, 490, 519, 608
BseGI	GGATG	3 cut(s)	160, 172, 709
BseJI	GATNNNNATC	1 cut(s)	708
BseLI	CCNNNNNNNGG	3 cut(s)	49, 496, 614
BseMI	GCAATG	2 cut(s)	378, 685
BseMII	CTCAG	1 cut(s)	381
BsePI	GCGCGC	1 cut(s)	349
Bsh1236I	CGCG	1 cut(s)	351
BsiSI	CCGG	1 cut(s)	176
BslFI	GGGAC	1 cut(s)	587
BslI	CCNNNNNNNGG	3 cut(s)	49, 496, 614
BsmFI	GGGAC	1 cut(s)	587
Bsp119I	TTCGAA	1 cut(s)	252
Bsp13I	TCCGGA	1 cut(s)	175
Bsp1407I	TGTACA	1 cut(s)	507
Bsp143I	GATC	4 cut(s)	79, 262, 670, 709
BspACI	CCGC	4 cut(s)	71, 215, 682, 707
BspCNI	CTCAG	1 cut(s)	382
BspEI	TCCGGA	1 cut(s)	175
BspFNI	CGCG	1 cut(s)	351
BspLI	GGNNCC	1 cut(s)	9
BspPI	GGATC	3 cut(s)	87, 665, 717
BspQI	GCTCTTC	1 cut(s)	531
BspT104I	TTCGAA	1 cut(s)	252
BsrDI	GCAATG	2 cut(s)	378, 685
BsrGI	TGTACA	1 cut(s)	507
BssECI	CCNNGG	5 cut(s)	287, 326, 490, 519, 608
BssHII	GCGCGC	1 cut(s)	349
BssMI	GATC	4 cut(s)	79, 262, 670, 709
BssT1I	CCWWGG	2 cut(s)	287, 519
Bst2UI	CCWGG	3 cut(s)	355, 492, 609
Bst4CI	ACNGT	2 cut(s)	200, 658
Bst6I	CTCTTC	2 cut(s)	396, 531
BstAUI	TGTACA	1 cut(s)	507
BstBI	TTCGAA	1 cut(s)	252
BstC8I	GCNNGC	3 cut(s)	97, 101, 351
BstDEI	CTNAG	3 cut(s)	390, 410, 758
BstENI	CCTNNNNNAGG	1 cut(s)	612
BstF5I	GGATG	3 cut(s)	160, 172, 709
BstFNI	CGCG	1 cut(s)	351
BstHHI	GCGC	2 cut(s)	351, 353
BstKTI	GATC	4 cut(s)	82, 265, 673, 712
BstMBI	GATC	4 cut(s)	79, 262, 670, 709
BstMWI	GCNNNNNNNGC	3 cut(s)	68, 329, 355
BstNI	CCWGG	3 cut(s)	355, 492, 609
BstSCI	CCNGG	3 cut(s)	353, 490, 607
BstUI	CGCG	1 cut(s)	351
BstV2I	GAAGAC	1 cut(s)	229
BstX2I	RGATCY	1 cut(s)	709
BstYI	RGATCY	1 cut(s)	709
BtsCI	GGATG	3 cut(s)	160, 172, 709
Cac8I	GCNNGC	3 cut(s)	97, 101, 351
CfoI	GCGC	2 cut(s)	351, 353
Csp6I	GTAC	2 cut(s)	40, 508
CviAII	CATG	4 cut(s)	145, 505, 737, 844
CviQI	GTAC	2 cut(s)	40, 508
DdeI	CTNAG	3 cut(s)	390, 410, 758
DpnI	GATC	4 cut(s)	81, 264, 672, 711
DpnII	GATC	4 cut(s)	79, 262, 670, 709
Eam1104I	CTCTTC	2 cut(s)	396, 531
EarI	CTCTTC	2 cut(s)	396, 531
Eco130I	CCWWGG	2 cut(s)	287, 519
Eco57I	CTGAAG	2 cut(s)	417, 483
EcoNI	CCTNNNNNAGG	1 cut(s)	612
EcoRII	CCWGG	3 cut(s)	353, 490, 607
EcoT14I	CCWWGG	2 cut(s)	287, 519
ErhI	CCWWGG	2 cut(s)	287, 519
FaeI	CATG	4 cut(s)	148, 508, 740, 847
FalI	AAGNNNNNCTT	2 cut(s)	732, 764
FaqI	GGGAC	1 cut(s)	587
FatI	CATG	4 cut(s)	144, 504, 736, 843
FauI	CCCGC	2 cut(s)	64, 689
FokI	GGATG	3 cut(s)	147, 159, 716
FspBI	CTAG	3 cut(s)	89, 140, 449
GlaI	GCGC	2 cut(s)	350, 352
GsuI	CTGGAG	1 cut(s)	589
HapII	CCGG	1 cut(s)	176
HhaI	GCGC	2 cut(s)	351, 353
Hin1II	CATG	4 cut(s)	148, 508, 740, 847
Hin6I	GCGC	2 cut(s)	349, 351
HinP1I	GCGC	2 cut(s)	349, 351
HindIII	AAGCTT	1 cut(s)	97
HinfI	GANTC	5 cut(s)	340, 382, 458, 473, 560
HpaII	CCGG	1 cut(s)	176
HphI	GGTGA	4 cut(s)	67, 478, 638, 737
Hpy166II	GTNNAC	2 cut(s)	34, 745
Hpy188I	TCNGA	4 cut(s)	327, 463, 472, 595
Hpy188III	TCNNGA	5 cut(s)	89, 140, 176, 701, 867
Hpy8I	GTNNAC	2 cut(s)	34, 745
HpyAV	CCTTC	3 cut(s)	425, 608, 672
HpyCH4III	ACNGT	2 cut(s)	200, 658
HpyCH4IV	ACGT	2 cut(s)	547, 643
HpyCH4V	TGCA	4 cut(s)	95, 212, 425, 776
HpyF10VI	GCNNNNNNNGC	3 cut(s)	68, 329, 355
HpyF3I	CTNAG	3 cut(s)	390, 410, 758
HpySE526I	ACGT	2 cut(s)	547, 643
Hsp92II	CATG	4 cut(s)	148, 508, 740, 847
HspAI	GCGC	2 cut(s)	349, 351
Kpn2I	TCCGGA	1 cut(s)	175
Kzo9I	GATC	4 cut(s)	79, 262, 670, 709
LguI	GCTCTTC	1 cut(s)	531
LmnI	GCTCC	1 cut(s)	328
LweI	GCATC	3 cut(s)	82, 586, 694
MaeI	CTAG	3 cut(s)	89, 140, 449
MaeII	ACGT	2 cut(s)	547, 643
MaeIII	GTNAC	2 cut(s)	644, 846
MalI	GATC	4 cut(s)	81, 264, 672, 711
MboI	GATC	4 cut(s)	79, 262, 670, 709
MboII	GAAGA	7 cut(s)	191, 194, 229, 242, 410, 413, 518
MflI	RGATCY	1 cut(s)	709
MluCI	AATT	4 cut(s)	419, 770, 796, 858
MlyI	GAGTC	1 cut(s)	467
MnlI	CCTC	5 cut(s)	70, 321, 385, 564, 757
MroI	TCCGGA	1 cut(s)	175
MseI	TTAA	2 cut(s)	363, 551
MspI	CCGG	1 cut(s)	176
MspR9I	CCNGG	3 cut(s)	355, 492, 609
MvaI	CCWGG	3 cut(s)	355, 492, 609
MvnI	CGCG	1 cut(s)	351
MwoI	GCNNNNNNNGC	3 cut(s)	68, 329, 355
NdeII	GATC	4 cut(s)	79, 262, 670, 709
NlaIII	CATG	4 cut(s)	148, 508, 740, 847
NlaIV	GGNNCC	1 cut(s)	9
NmuCI	GTSAC	1 cut(s)	644
NspV	TTCGAA	1 cut(s)	252
PauI	GCGCGC	1 cut(s)	349
PciSI	GCTCTTC	1 cut(s)	531
PcsI	WCGNNNNNNNCGW	1 cut(s)	649
PfeI	GAWTC	4 cut(s)	340, 382, 473, 560
PleI	GAGTC	1 cut(s)	466
PpsI	GAGTC	1 cut(s)	466
PsiI	TTATAA	1 cut(s)	716
Psp6I	CCWGG	3 cut(s)	353, 490, 607
PspGI	CCWGG	3 cut(s)	353, 490, 607
PspN4I	GGNNCC	1 cut(s)	9
PsuI	RGATCY	1 cut(s)	709
PteI	GCGCGC	1 cut(s)	349
RsaI	GTAC	2 cut(s)	41, 509
RsaNI	GTAC	2 cut(s)	40, 508
SapI	GCTCTTC	1 cut(s)	531
SaqAI	TTAA	2 cut(s)	363, 551
Sau3AI	GATC	4 cut(s)	79, 262, 670, 709
SchI	GAGTC	1 cut(s)	467
ScrFI	CCNGG	3 cut(s)	355, 492, 609
SfaNI	GCATC	3 cut(s)	82, 586, 694
SfuI	TTCGAA	1 cut(s)	252
Sse9I	AATT	4 cut(s)	419, 770, 796, 858
SsiI	CCGC	4 cut(s)	71, 215, 682, 707
SspI	AATATT	2 cut(s)	247, 277
SspMI	CTAG	3 cut(s)	89, 140, 449
StyD4I	CCNGG	3 cut(s)	353, 490, 607
StyI	CCWWGG	2 cut(s)	287, 519
TaaI	ACNGT	2 cut(s)	200, 658
TaiI	ACGT	2 cut(s)	550, 646
TaqI	TCGA	2 cut(s)	126, 252
TasI	AATT	4 cut(s)	419, 770, 796, 858
TatI	WGTACW	1 cut(s)	507
TfiI	GAWTC	4 cut(s)	340, 382, 473, 560
Tru1I	TTAA	2 cut(s)	363, 551
Tru9I	TTAA	2 cut(s)	363, 551
TseFI	GTSAC	1 cut(s)	644
Tsp45I	GTSAC	1 cut(s)	644
TspDTI	ATGAA	7 cut(s)	161, 161, 243, 353, 493, 628, 753
TspGWI	ACGGA	1 cut(s)	512
XagI	CCTNNNNNAGG	1 cut(s)	612
XapI	RAATTY	2 cut(s)	770, 858
XbaI	TCTAGA	2 cut(s)	88, 139
XcmI	CCANNNNNNNNNTGG	1 cut(s)	692
XspI	CTAG	3 cut(s)	89, 140, 449

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