Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0002873

Physical Location & Seq

Genomic Coordinates Forward (+)

21833645 .. 21836952

Gene Structure 3308 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00235080.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 474 bp

ATGGGAGTTCCAGCTTTCTACAGGTGGCTAGCGGAGAAGTATCCACTCGTCGTCGTCGATGTGGTGGAAGAAGAACCGGTTGTAATCGATGATGTTTCGATTCCGGTCCACACCAAGAAGCCAAATCCTAACAGCGAGTATGACAATCAGTACCTCGATATGAATGGGATTATTCTCAACATCATCAAAAAACCATCAATCTCTCATCAAAACACCATGGGTCTCTCATCAAAACACCATCTCGATCAAGGAACAGAAGCTAGGTTGGTTAGTTTGGTTATGGCTATTTGTCAATGCCTTGACTGGAATGGAAGAATTTATGAGGAAGCTAGTACCAAGCATTTGAATGAATATGGAGAAGCTGGGTTGCGTACGTTGACGCTTGCTTATAAAAAGCTTGAGGAGTCTGAGTATTCTGCTTGGAACAATGAATTTCAAAAGCAAAATCATCTATCGGGGCTGATAGGGAGGTGA

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 zf-CCHC

Protein Analysis

157

Amino Acids

17.89

Weight (kDa)

5.48

Isoelectric Point (pI)

39.0

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
XRN_N	PF03159	1 - 72	4.8e-13	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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Publication-ready

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Orthologous Genes (Group: OG0002873)

Species	Orthologous Gene IDs
malus_domestica	MD15G1369000.v1.1
rosa_chinensis	RchiOBHm_Chr2g0158691 RchiOBHm_Chr3g0461771 RchiOBHm_Chr3g0477511 RchiOBHm_Chr4g0391611 RchiOBHm_Chr5g0060841 RchiOBHm_Chr5g0074511 RchiOBHm_Chr5g0074521 RchiOBHm_Chr6g0248211
rosa_laevigata	RLG00000001875 RLG00000032521
rosa_multiflora	Rmu_sc0001803.1_g000035 Rmu_sc0002942.1_g000044 Rmu_sc0005455.1_g000008 Rmu_sc0006619.1_g000001 Rmu_sc0015767.1_g000001 Rmu_sc0034909.1_g000001
rosa_roxburghii	Rroxscaffold_2G00094060 Rroxscaffold_2G00116020 Rroxscaffold_3G00235080 Rroxscaffold_5G00358150 Rroxscaffold_5G00359750
rosa_rugosa	Rorug05G0328100 Rorug05G0352400 Rorug07G0018800 Rorug07G0018900
rosa_samantha	Rh2AG426900 Rh2BG244900 Rh2BG245000 Rh2BG415100 Rh3BG245300 Rh3CG117000 Rh3CG370200 Rh3CG370300 Rh4DG044300 Rh5DG334900 Rh5DG403500 Rh6CG125700 Rh7CG192300

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	390
AciI	CCGC	1 cut(s)	32
AcsI	RAATTY	2 cut(s)	315, 431
AfaI	GTAC	3 cut(s)	152, 334, 373
AgeI	ACCGGT	1 cut(s)	76
AgsI	TTSAA	2 cut(s)	346, 437
AluBI	AGCT	5 cut(s)	14, 260, 329, 362, 397
AluI	AGCT	5 cut(s)	14, 260, 329, 362, 397
Alw26I	GTCTC	1 cut(s)	227
ApoI	RAATTY	2 cut(s)	315, 431
AsiGI	ACCGGT	1 cut(s)	76
AspS9I	GGNCC	1 cut(s)	106
AsuNHI	GCTAGC	1 cut(s)	28
AvaII	GGWCC	1 cut(s)	106
BccI	CCATC	2 cut(s)	202, 246
BciVI	GTATCC	1 cut(s)	51
BcoDI	GTCTC	1 cut(s)	227
BfaI	CTAG	3 cut(s)	29, 261, 330
BfmI	CTRYAG	1 cut(s)	19
BfuI	GTATCC	1 cut(s)	51
Bme18I	GGWCC	1 cut(s)	106
BmgT120I	GGNCC	1 cut(s)	106
BmtI	GCTAGC	1 cut(s)	32
BpuEI	CTTGAG	1 cut(s)	419
Bsa29I	ATCGAT	1 cut(s)	87
BsaI	GGTCTC	1 cut(s)	227
BsaJI	CCNNGG	1 cut(s)	216
BsaWI	WCCGGW	2 cut(s)	76, 103
BsaXI	ACNNNNNCTCC	2 cut(s)	395, 425
Bse118I	RCCGGY	1 cut(s)	76
Bse1I	ACTGG	1 cut(s)	308
BseCI	ATCGAT	1 cut(s)	87
BseDI	CCNNGG	1 cut(s)	216
BseMII	CTCAG	1 cut(s)	399
BseNI	ACTGG	1 cut(s)	308
BseRI	GAGGAG	1 cut(s)	416
BseYI	CCCAGC	1 cut(s)	362
BshTI	ACCGGT	1 cut(s)	76
BshVI	ATCGAT	1 cut(s)	87
BsiSI	CCGG	2 cut(s)	77, 104
BsiWI	CGTACG	1 cut(s)	371
BsmAI	GTCTC	1 cut(s)	227
Bso31I	GGTCTC	1 cut(s)	227
Bsp143I	GATC	1 cut(s)	244
Bsp19I	CCATGG	1 cut(s)	216
BspACI	CCGC	1 cut(s)	32
BspCNI	CTCAG	1 cut(s)	400
BspDI	ATCGAT	1 cut(s)	87
BspOI	GCTAGC	1 cut(s)	32
BspTNI	GGTCTC	1 cut(s)	227
BsrFI	RCCGGY	1 cut(s)	76
BsrI	ACTGG	1 cut(s)	308
BssAI	RCCGGY	1 cut(s)	76
BssECI	CCNNGG	1 cut(s)	216
BssMI	GATC	1 cut(s)	244
BssT1I	CCWWGG	1 cut(s)	216
BstC8I	GCNNGC	2 cut(s)	30, 384
BstDEI	CTNAG	1 cut(s)	408
BstDSI	CCRYGG	1 cut(s)	216
BstKTI	GATC	1 cut(s)	247
BstMAI	GTCTC	1 cut(s)	227
BstMBI	GATC	1 cut(s)	244
BstSFI	CTRYAG	1 cut(s)	19
Bsu15I	ATCGAT	1 cut(s)	87
BsuI	GTATCC	1 cut(s)	51
BsuTUI	ATCGAT	1 cut(s)	87
BtgI	CCRYGG	1 cut(s)	216
Cac8I	GCNNGC	2 cut(s)	30, 384
Cfr10I	RCCGGY	1 cut(s)	76
Cfr13I	GGNCC	1 cut(s)	106
ClaI	ATCGAT	1 cut(s)	87
CseI	GACGC	1 cut(s)	388
Csp6I	GTAC	3 cut(s)	151, 333, 372
CspAI	ACCGGT	1 cut(s)	76
CviAII	CATG	1 cut(s)	217
CviJI	RGCY	9 cut(s)	14, 28, 121, 260, 284, 329, 362, 397, 460
CviKI_1	RGCY	9 cut(s)	14, 28, 121, 260, 284, 329, 362, 397, 460
CviQI	GTAC	3 cut(s)	151, 333, 372
DdeI	CTNAG	1 cut(s)	408
DpnI	GATC	1 cut(s)	246
DpnII	GATC	1 cut(s)	244
Eco130I	CCWWGG	1 cut(s)	216
Eco31I	GGTCTC	1 cut(s)	227
Eco47I	GGWCC	1 cut(s)	106
EcoT14I	CCWWGG	1 cut(s)	216
ErhI	CCWWGG	1 cut(s)	216
FaeI	CATG	1 cut(s)	220
FaiI	YATR	7 cut(s)	141, 161, 218, 281, 321, 354, 390
FatI	CATG	1 cut(s)	216
FspBI	CTAG	3 cut(s)	29, 261, 330
GsaI	CCCAGC	1 cut(s)	366
HapII	CCGG	2 cut(s)	77, 104
HgaI	GACGC	1 cut(s)	388
Hin1II	CATG	1 cut(s)	220
HincII	GTYRAC	1 cut(s)	378
HindII	GTYRAC	1 cut(s)	378
HindIII	AAGCTT	1 cut(s)	395
HinfI	GANTC	2 cut(s)	100, 404
HpaII	CCGG	2 cut(s)	77, 104
Hpy166II	GTNNAC	2 cut(s)	109, 378
Hpy188I	TCNGA	1 cut(s)	409
Hpy188III	TCNNGA	1 cut(s)	242
Hpy8I	GTNNAC	2 cut(s)	109, 378
Hpy99I	CGWCG	3 cut(s)	53, 56, 59
HpyCH4IV	ACGT	1 cut(s)	374
HpyF3I	CTNAG	1 cut(s)	408
HpySE526I	ACGT	1 cut(s)	374
Hsp92II	CATG	1 cut(s)	220
Kzo9I	GATC	1 cut(s)	244
LpnPI	CCDG	6 cut(s)	7, 24, 90, 117, 289, 348
MaeI	CTAG	3 cut(s)	29, 261, 330
MaeII	ACGT	1 cut(s)	374
MalI	GATC	1 cut(s)	246
MboI	GATC	1 cut(s)	244
MboII	GAAGA	3 cut(s)	80, 83, 324
MluCI	AATT	2 cut(s)	315, 431
MlyI	GAGTC	1 cut(s)	413
MnlI	CCTC	4 cut(s)	164, 316, 394, 462
MslI	CAYNNNNRTG	1 cut(s)	345
MspI	CCGG	2 cut(s)	77, 104
NcoI	CCATGG	1 cut(s)	216
NdeII	GATC	1 cut(s)	244
NheI	GCTAGC	1 cut(s)	28
NlaIII	CATG	1 cut(s)	220
PcsI	WCGNNNNNNNCGW	1 cut(s)	54
PfeI	GAWTC	1 cut(s)	100
Pfl23II	CGTACG	1 cut(s)	371
PinAI	ACCGGT	1 cut(s)	76
PleI	GAGTC	1 cut(s)	412
PpsI	GAGTC	1 cut(s)	412
PsiI	TTATAA	1 cut(s)	390
PspFI	CCCAGC	1 cut(s)	362
PspLI	CGTACG	1 cut(s)	371
PspPI	GGNCC	1 cut(s)	106
RsaI	GTAC	3 cut(s)	152, 334, 373
RsaNI	GTAC	3 cut(s)	151, 333, 372
RseI	CAYNNNNRTG	1 cut(s)	345
Sau3AI	GATC	1 cut(s)	244
Sau96I	GGNCC	1 cut(s)	106
SchI	GAGTC	1 cut(s)	413
SfcI	CTRYAG	1 cut(s)	19
SinI	GGWCC	1 cut(s)	106
SmiMI	CAYNNNNRTG	1 cut(s)	345
SmlI	CTYRAG	1 cut(s)	398
SmoI	CTYRAG	1 cut(s)	398
Sse9I	AATT	2 cut(s)	315, 431
SsiI	CCGC	1 cut(s)	32
SspMI	CTAG	3 cut(s)	29, 261, 330
StyI	CCWWGG	1 cut(s)	216
TaiI	ACGT	1 cut(s)	377
TaqI	TCGA	5 cut(s)	57, 87, 98, 156, 243
TasI	AATT	2 cut(s)	315, 431
TfiI	GAWTC	1 cut(s)	100
TspDTI	ATGAA	3 cut(s)	176, 363, 444
VpaK11BI	GGWCC	1 cut(s)	106
XapI	RAATTY	2 cut(s)	315, 431
XspI	CTAG	3 cut(s)	29, 261, 330

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