Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0007016

Physical Location & Seq

Genomic Coordinates Reverse (-)

2766737 .. 2768632

Gene Structure 1896 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG043000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1125 bp

ATGCAGGAGGAAGAGAAAGCTCGAAATAGCGTGATGCTTGATTTGCTTTATGTCTATCCTTCTCATCCTTTGGCGTCGGATATTATTTTGTACTACCATTTATATTATCAGAGTCCCCCACATGAAAGATTTTTTTATACGATAAATACTAATCGTAGTGGTGGAATGAATGGATTCCTTTGGTTATCTGAGAGGAATGGCATTAGAAACGTAATCCCTTCCCCTGTGCATGGTTTTCCCAACATAGACTGTAACGAAGTCTTAAATGTTACATATGTTAGCCCTACAGCTCAAAAACACATCCCAGAACCTCCCGAGGGTGTGATCATGCCCAGAAAGGTTGTAAAACCTACGGATATCAAACCTCCCCCTGCGTTATGGCATGAAGACAATGGTCCCCGACGCTACCAAAACAGAGATAGGCCACAAATACCCGGAGCAATTGCTGGAACTGTGTTGGGAGAAGCAGCTCATCGACTTGTCAAGAACACACTAAATTTTAGACCTAGTAATCCATCCTCTGGATTTTGGGATCAATCGCAGCCTTTACGAACTTCTTCTGGAAACTACATTGGAAACTATCCAGTCAACAGACCAAGACCAGCTGGGCCATCTGGGTATGAAAGGGGTTTCCGTGAAGAACCAAATTATGGAAATTCCTTTAATCCTCAGGGCATCATGGCTAGGCCCAGAGCTCCTTACTCAAATGGTGTGCAGGGTGACAGACAGAGTTTTAGGACACAAGAAAGAACACAGTATCAAGAGCAGGGTTTTAGAGGACAAGAAAGAATACAATATCAAGAACAGTACCGCAACATGAGAACTGGGATGTCTGGTTTAACAATGGAAGGAAGTGTGAGAACCAGGTCTCCTGTAGTGGTGCAACCAGGGACGCCAAATTCAGGATACTCCACAAACCCACATCAGCAGTTTGTGCAGAACATGGGCGCTCTTCCACCGCCACCTACAAAGTGGATCAACAAAGAATTCGGTGCCAATGGTGGGATTTATGGTAGGCATCAGGAAACCGGATATGGCGGACCATATGAACAGCAGGTGAAAAAGGTTTATCAGGTAAAGACACGTCCTCCTCAGGACTTGCCAAACTCTGGAAACCAGGAGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000291 GO:0000902 GO:0000932 GO:0000956 GO:0003674 GO:0003676 GO:0003723 GO:0003729 GO:0003824 GO:0004518 GO:0004527 GO:0004532 GO:0004534 GO:0004540 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0005844 GO:0006139 GO:0006401 GO:0006402 GO:0006725 GO:0006807 GO:0006950 GO:0008150 GO:0008152 GO:0008409 GO:0009056 GO:0009057 GO:0009266 GO:0009408 GO:0009628 GO:0009653 GO:0009826 GO:0009888 GO:0009892 GO:0009987 GO:0010087 GO:0010286 GO:0010468 GO:0010494 GO:0010586 GO:0010587 GO:0010605 GO:0010629 GO:0016043 GO:0016049 GO:0016070 GO:0016071 GO:0016787 GO:0016788 GO:0016796 GO:0016896 GO:0019222 GO:0019439 GO:0031086 GO:0031087 GO:0032502 GO:0032989 GO:0032991 GO:0033554 GO:0034605 GO:0034641 GO:0034655 GO:0034660 GO:0034661 GO:0035770 GO:0036464 GO:0040007 GO:0040029 GO:0043170 GO:0043226 GO:0043228 GO:0043229 GO:0043232 GO:0044237 GO:0044238 GO:0044248 GO:0044260 GO:0044265 GO:0044270 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0046700 GO:0048519 GO:0048589 GO:0048856 GO:0048869 GO:0050789 GO:0050896 GO:0051301 GO:0051716 GO:0060255 GO:0060560 GO:0065007 GO:0070370 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0090501 GO:0090503 GO:0097159 GO:0140098 GO:1901360 GO:1901361 GO:1901363 GO:1901575 GO:1990904

KEGG Pathways

Metabolic & Signaling

ko03008 ko03018 ko04016 map03008 map03018 map04016

Pfam Domains

Protein Families

XRN_N zf-CCHC

Protein Analysis

374

Amino Acids

42.39

Weight (kDa)

9.52

Isoelectric Point (pI)

51.06

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
XRN_M	PF17846	2 - 120	7.9e-17	Xrn1 helical 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: OG0007016)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G54490 AT1G54490
fragaria_vesca	FvH4_6g03690 FvH4_6g03690
malus_domestica	MD04G1219200.v1.1 MD12G1236200.v1.1
prunus_persica	Prupe.6G338500_v2.0.a1 Prupe.6G338500_v2.0.a1
pyrus_communis	pycom04g19450 pycom12g21730
rosa_chinensis	RchiOBHm_Chr3g0452231
rosa_laevigata	RLG00000025615
rosa_multiflora	Rmu_sc0037132.1_g000001 Rmu_sc0041263.1_g000001
rosa_roxburghii	Rroxscaffold_164G00435930 Rroxscaffold_6G00429350
rosa_rugosa	Rorug02G0639400
rosa_samantha	Rh3AG041300 Rh3BG043000 Rh3BG043200 Rh3CG041400 Rh3CG041600 Rh3DG042300 Rh3DG042500
rosa_wichuraiana	Rw3G003160

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	1045
Acc36I	ACCTGC	1 cut(s)	1045
AccB1I	GGYRCC	1 cut(s)	992
AccB7I	CCANNNNNTGG	3 cut(s)	521, 650, 1109
AciI	CCGC	3 cut(s)	811, 959, 1038
AclWI	GGATC	2 cut(s)	540, 983
AcsI	RAATTY	4 cut(s)	496, 655, 898, 986
AcyI	GRCGYC	2 cut(s)	74, 893
AfaI	GTAC	2 cut(s)	92, 809
AfiI	CCNNNNNNNGG	7 cut(s)	230, 317, 521, 650, 902, 1002, 1109
AflIII	ACRYGT	1 cut(s)	1082
AjiI	CACGTC	1 cut(s)	1085
AjnI	CCWGG	3 cut(s)	863, 886, 1116
AloI	GAACNNNNNNTCC	2 cut(s)	853, 885
AluBI	AGCT	5 cut(s)	20, 290, 470, 605, 695
AluI	AGCT	5 cut(s)	20, 290, 470, 605, 695
Alw21I	GWGCWC	1 cut(s)	697
Alw26I	GTCTC	1 cut(s)	873
AlwI	GGATC	2 cut(s)	540, 983
Ama87I	CYCGRG	1 cut(s)	314
AoxI	GGCC	3 cut(s)	422, 608, 686
ApeKI	GCWGC	2 cut(s)	467, 541
ApoI	RAATTY	4 cut(s)	496, 655, 898, 986
Asp700I	GAANNNNTTC	2 cut(s)	173, 556
AspLEI	GCGC	1 cut(s)	950
AspS9I	GGNCC	4 cut(s)	395, 608, 687, 1040
AsuC2I	CCSGG	1 cut(s)	435
AsuHPI	GGTGA	2 cut(s)	731, 1069
AvaI	CYCGRG	1 cut(s)	314
AvaII	GGWCC	2 cut(s)	395, 1040
AxyI	CCTNAGG	2 cut(s)	669, 1092
BanI	GGYRCC	1 cut(s)	992
BanII	GRGCYC	1 cut(s)	697
BbsI	GAAGAC	1 cut(s)	393
Bbv12I	GWGCWC	1 cut(s)	697
BbvI	GCAGC	2 cut(s)	479, 553
BccI	CCATC	2 cut(s)	523, 619
BciT130I	CCWGG	3 cut(s)	865, 888, 1118
BciVI	GTATCC	1 cut(s)	899
BclI	TGATCA	1 cut(s)	324
BcnI	CCSGG	1 cut(s)	435
BcoDI	GTCTC	1 cut(s)	873
BfaI	CTAG	2 cut(s)	507, 684
BfmI	CTRYAG	2 cut(s)	285, 873
BfoI	RGCGCY	1 cut(s)	951
BfuAI	ACCTGC	1 cut(s)	1045
BfuI	GTATCC	1 cut(s)	899
BisI	GCNGC	2 cut(s)	468, 542
BlsI	GCNGC	2 cut(s)	469, 543
Bme1390I	CCNGG	4 cut(s)	435, 865, 888, 1118
Bme18I	GGWCC	2 cut(s)	395, 1040
BmeT110I	CYCGRG	1 cut(s)	314
BmgBI	CACGTC	1 cut(s)	1085
BmgT120I	GGNCC	4 cut(s)	395, 608, 687, 1040
BmiI	GGNNCC	2 cut(s)	397, 994
BmrFI	CCNGG	4 cut(s)	435, 865, 888, 1118
BmrI	ACTGGG	1 cut(s)	834
BmsI	GCATC	3 cut(s)	24, 684, 1027
BmuI	ACTGGG	1 cut(s)	834
BoxI	GACNNNNGTC	1 cut(s)	393
BpiI	GAAGAC	1 cut(s)	393
BpuMI	CCSGG	1 cut(s)	435
BsaHI	GRCGYC	2 cut(s)	74, 893
BsaI	GGTCTC	1 cut(s)	873
BsaJI	CCNNGG	2 cut(s)	315, 887
BsaWI	WCCGGW	1 cut(s)	1028
BsaXI	ACNNNNNCTCC	4 cut(s)	853, 883, 1072, 1102
Bsc4I	CCNNNNNNNGG	7 cut(s)	230, 317, 521, 650, 902, 1002, 1109
Bse1I	ACTGG	2 cut(s)	584, 829
Bse21I	CCTNAGG	2 cut(s)	669, 1092
BseBI	CCWGG	3 cut(s)	865, 888, 1118
BseDI	CCNNGG	2 cut(s)	315, 887
BseGI	GGATG	4 cut(s)	64, 300, 515, 834
BseLI	CCNNNNNNNGG	7 cut(s)	230, 317, 521, 650, 902, 1002, 1109
BseMII	CTCAG	3 cut(s)	180, 683, 1106
BseNI	ACTGG	2 cut(s)	584, 829
BseRI	GAGGAG	1 cut(s)	1080
BseXI	GCAGC	2 cut(s)	479, 553
BseYI	CCCAGC	1 cut(s)	605
BsgI	GTGCAG	2 cut(s)	734, 956
BshFI	GGCC	3 cut(s)	424, 610, 688
BshNI	GGYRCC	1 cut(s)	992
BsiHKAI	GWGCWC	1 cut(s)	697
BsiHKCI	CYCGRG	1 cut(s)	314
BsiSI	CCGG	2 cut(s)	435, 1029
BslFI	GGGAC	3 cut(s)	99, 381, 904
BslI	CCNNNNNNNGG	7 cut(s)	230, 317, 521, 650, 902, 1002, 1109
BsmAI	GTCTC	1 cut(s)	873
BsmFI	GGGAC	3 cut(s)	99, 381, 904
BsnI	GGCC	3 cut(s)	424, 610, 688
Bso31I	GGTCTC	1 cut(s)	873
BsoBI	CYCGRG	1 cut(s)	314
Bsp1286I	GDGCHC	1 cut(s)	697
Bsp143I	GATC	3 cut(s)	324, 532, 975
BspACI	CCGC	3 cut(s)	811, 959, 1038
BspANI	GGCC	3 cut(s)	424, 610, 688
BspCNI	CTCAG	3 cut(s)	181, 682, 1105
BspLI	GGNNCC	2 cut(s)	397, 994
BspMI	ACCTGC	1 cut(s)	1045
BspPI	GGATC	2 cut(s)	540, 983
BspQI	GCTCTTC	1 cut(s)	957
BspT107I	GGYRCC	1 cut(s)	992
BspTNI	GGTCTC	1 cut(s)	873
BsrI	ACTGG	2 cut(s)	584, 829
BssECI	CCNNGG	2 cut(s)	315, 887
BssMI	GATC	3 cut(s)	324, 532, 975
BssNI	GRCGYC	2 cut(s)	74, 893
Bst2UI	CCWGG	3 cut(s)	865, 888, 1118
Bst4CI	ACNGT	4 cut(s)	251, 454, 756, 807
Bst6I	CTCTTC	2 cut(s)	6, 957
BstACI	GRCGYC	2 cut(s)	74, 893
BstAPI	GCANNNNNTGC	1 cut(s)	934
BstDEI	CTNAG	3 cut(s)	189, 669, 1092
BstF5I	GGATG	4 cut(s)	64, 300, 515, 834
BstH2I	RGCGCY	1 cut(s)	951
BstHHI	GCGC	1 cut(s)	950
BstKTI	GATC	3 cut(s)	327, 535, 978
BstMAI	GTCTC	1 cut(s)	873
BstMBI	GATC	3 cut(s)	324, 532, 975
BstMWI	GCNNNNNNNGC	2 cut(s)	43, 934
BstNI	CCWGG	3 cut(s)	865, 888, 1118
BstPAI	GACNNNNGTC	1 cut(s)	393
BstSCI	CCNGG	4 cut(s)	433, 863, 886, 1116
BstSFI	CTRYAG	2 cut(s)	285, 873
BstV1I	GCAGC	2 cut(s)	479, 553
BstV2I	GAAGAC	1 cut(s)	393
Bsu36I	CCTNAGG	2 cut(s)	669, 1092
BsuI	GTATCC	1 cut(s)	899
BsuRI	GGCC	3 cut(s)	424, 610, 688
BtrI	CACGTC	1 cut(s)	1085
BtsCI	GGATG	4 cut(s)	64, 300, 515, 834
BveI	ACCTGC	1 cut(s)	1045
CfoI	GCGC	1 cut(s)	950
Cfr13I	GGNCC	4 cut(s)	395, 608, 687, 1040
CseI	GACGC	3 cut(s)	63, 411, 901
CsiI	ACCWGGT	1 cut(s)	863
Csp6I	GTAC	2 cut(s)	91, 808
CviAII	CATG	7 cut(s)	122, 230, 328, 383, 679, 817, 943
CviQI	GTAC	2 cut(s)	91, 808
DdeI	CTNAG	3 cut(s)	189, 669, 1092
DpnI	GATC	3 cut(s)	326, 534, 977
DpnII	GATC	3 cut(s)	324, 532, 975
Eam1104I	CTCTTC	2 cut(s)	6, 957
EarI	CTCTTC	2 cut(s)	6, 957
EciI	GGCGGA	1 cut(s)	1053
Ecl136II	GAGCTC	1 cut(s)	695
Eco24I	GRGCYC	1 cut(s)	697
Eco31I	GGTCTC	1 cut(s)	873
Eco32I	GATATC	1 cut(s)	358
Eco47I	GGWCC	2 cut(s)	395, 1040
Eco53kI	GAGCTC	1 cut(s)	695
Eco81I	CCTNAGG	2 cut(s)	669, 1092
Eco88I	CYCGRG	1 cut(s)	314
EcoICRI	GAGCTC	1 cut(s)	695
EcoRI	GAATTC	1 cut(s)	986
EcoRII	CCWGG	3 cut(s)	863, 886, 1116
EcoRV	GATATC	1 cut(s)	358
EcoT38I	GRGCYC	1 cut(s)	697
FaeI	CATG	7 cut(s)	125, 233, 331, 386, 682, 820, 946
FaqI	GGGAC	3 cut(s)	99, 381, 904
FatI	CATG	7 cut(s)	121, 229, 327, 382, 678, 816, 942
FauNDI	CATATG	2 cut(s)	274, 1045
FbaI	TGATCA	1 cut(s)	324
Fnu4HI	GCNGC	2 cut(s)	468, 542
FokI	GGATG	4 cut(s)	51, 287, 502, 841
FriOI	GRGCYC	1 cut(s)	697
Fsp4HI	GCNGC	2 cut(s)	468, 542
FspBI	CTAG	2 cut(s)	507, 684
GlaI	GCGC	1 cut(s)	949
GluI	GCNGC	2 cut(s)	468, 542
GsaI	CCCAGC	1 cut(s)	609
HaeII	RGCGCY	1 cut(s)	951
HaeIII	GGCC	3 cut(s)	424, 610, 688
HapII	CCGG	2 cut(s)	435, 1029
HgaI	GACGC	3 cut(s)	63, 411, 901
HhaI	GCGC	1 cut(s)	950
Hin1I	GRCGYC	2 cut(s)	74, 893
Hin1II	CATG	7 cut(s)	125, 233, 331, 386, 682, 820, 946
Hin6I	GCGC	1 cut(s)	948
HinP1I	GCGC	1 cut(s)	948
HincII	GTYRAC	1 cut(s)	589
HindII	GTYRAC	1 cut(s)	589
HinfI	GANTC	2 cut(s)	112, 174
HpaII	CCGG	2 cut(s)	435, 1029
HphI	GGTGA	2 cut(s)	731, 1069
Hpy166II	GTNNAC	1 cut(s)	589
Hpy188I	TCNGA	3 cut(s)	79, 111, 190
Hpy8I	GTNNAC	1 cut(s)	589
Hpy99I	CGWCG	2 cut(s)	79, 405
HpyAV	CCTTC	3 cut(s)	69, 228, 842
HpyCH4III	ACNGT	4 cut(s)	251, 454, 756, 807
HpyCH4IV	ACGT	2 cut(s)	210, 1084
HpyCH4V	TGCA	5 cut(s)	4, 229, 715, 883, 937
HpyF10VI	GCNNNNNNNGC	2 cut(s)	43, 934
HpyF3I	CTNAG	3 cut(s)	189, 669, 1092
HpySE526I	ACGT	2 cut(s)	210, 1084
Hsp92I	GRCGYC	2 cut(s)	74, 893
Hsp92II	CATG	7 cut(s)	125, 233, 331, 386, 682, 820, 946
HspAI	GCGC	1 cut(s)	948
Ksp22I	TGATCA	1 cut(s)	324
Kzo9I	GATC	3 cut(s)	324, 532, 975
LguI	GCTCTTC	1 cut(s)	957
LmnI	GCTCC	2 cut(s)	437, 700
Lsp1109I	GCAGC	2 cut(s)	479, 553
LweI	GCATC	3 cut(s)	24, 684, 1027
MabI	ACCWGGT	1 cut(s)	863
MaeI	CTAG	2 cut(s)	507, 684
MaeII	ACGT	2 cut(s)	210, 1084
MaeIII	GTNAC	3 cut(s)	251, 268, 719
MalI	GATC	3 cut(s)	326, 534, 977
MboI	GATC	3 cut(s)	324, 532, 975
MboII	GAAGA	5 cut(s)	23, 398, 549, 650, 944
MfeI	CAATTG	1 cut(s)	441
MhlI	GDGCHC	1 cut(s)	697
MluCI	AATT	6 cut(s)	441, 496, 646, 655, 898, 986
MlyI	GAGTC	1 cut(s)	121
MmeI	TCCRAC	1 cut(s)	57
MnlI	CCTC	9 cut(s)	186, 310, 321, 375, 529, 678, 770, 1098, 1101
MroXI	GAANNNNTTC	2 cut(s)	173, 556
MseI	TTAA	3 cut(s)	263, 663, 839
MspA1I	CMGCKG	1 cut(s)	605
MspI	CCGG	2 cut(s)	435, 1029
MspR9I	CCNGG	4 cut(s)	435, 865, 888, 1118
MunI	CAATTG	1 cut(s)	441
MvaI	CCWGG	3 cut(s)	865, 888, 1118
MwoI	GCNNNNNNNGC	2 cut(s)	43, 934
NciI	CCSGG	1 cut(s)	435
NdeI	CATATG	2 cut(s)	274, 1045
NdeII	GATC	3 cut(s)	324, 532, 975
NlaIII	CATG	7 cut(s)	125, 233, 331, 386, 682, 820, 946
NlaIV	GGNNCC	2 cut(s)	397, 994
NmuCI	GTSAC	1 cut(s)	719
PaqCI	CACCTGC	1 cut(s)	1045
PciSI	GCTCTTC	1 cut(s)	957
PdmI	GAANNNNTTC	2 cut(s)	173, 556
PfeI	GAWTC	1 cut(s)	174
PflMI	CCANNNNNTGG	3 cut(s)	521, 650, 1109
PkrI	GCNGC	2 cut(s)	469, 543
PleI	GAGTC	1 cut(s)	120
PpsI	GAGTC	1 cut(s)	120
PshAI	GACNNNNGTC	1 cut(s)	393
Psp124BI	GAGCTC	1 cut(s)	697
Psp6I	CCWGG	3 cut(s)	863, 886, 1116
PspFI	CCCAGC	1 cut(s)	605
PspGI	CCWGG	3 cut(s)	863, 886, 1116
PspN4I	GGNNCC	2 cut(s)	397, 994
PspPI	GGNCC	4 cut(s)	395, 608, 687, 1040
PvuII	CAGCTG	1 cut(s)	605
RsaI	GTAC	2 cut(s)	92, 809
RsaNI	GTAC	2 cut(s)	91, 808
SacI	GAGCTC	1 cut(s)	697
SapI	GCTCTTC	1 cut(s)	957
SaqAI	TTAA	3 cut(s)	263, 663, 839
SatI	GCNGC	2 cut(s)	468, 542
Sau3AI	GATC	3 cut(s)	324, 532, 975
Sau96I	GGNCC	4 cut(s)	395, 608, 687, 1040
SchI	GAGTC	1 cut(s)	121
ScrFI	CCNGG	4 cut(s)	435, 865, 888, 1118
SduI	GDGCHC	1 cut(s)	697
SexAI	ACCWGGT	1 cut(s)	863
SfaNI	GCATC	3 cut(s)	24, 684, 1027
SfcI	CTRYAG	2 cut(s)	285, 873
SinI	GGWCC	2 cut(s)	395, 1040
Sse9I	AATT	6 cut(s)	441, 496, 646, 655, 898, 986
SsiI	CCGC	3 cut(s)	811, 959, 1038
SspMI	CTAG	2 cut(s)	507, 684
SstI	GAGCTC	1 cut(s)	697
StyD4I	CCNGG	4 cut(s)	433, 863, 886, 1116
TaaI	ACNGT	4 cut(s)	251, 454, 756, 807
TaiI	ACGT	2 cut(s)	213, 1087
TaqI	TCGA	2 cut(s)	22, 475
TasI	AATT	6 cut(s)	441, 496, 646, 655, 898, 986
TatI	WGTACW	1 cut(s)	90
TfiI	GAWTC	1 cut(s)	174
Tru1I	TTAA	3 cut(s)	263, 663, 839
Tru9I	TTAA	3 cut(s)	263, 663, 839
TseFI	GTSAC	1 cut(s)	719
TseI	GCWGC	2 cut(s)	467, 541
Tsp45I	GTSAC	1 cut(s)	719
TspDTI	ATGAA	5 cut(s)	138, 182, 399, 636, 1062
TspGWI	ACGGA	2 cut(s)	368, 623
Van91I	CCANNNNNTGG	3 cut(s)	521, 650, 1109
VpaK11BI	GGWCC	2 cut(s)	395, 1040
XapI	RAATTY	4 cut(s)	496, 655, 898, 986
XcmI	CCANNNNNNNNNTGG	1 cut(s)	969
XmnI	GAANNNNTTC	2 cut(s)	173, 556
XspI	CTAG	2 cut(s)	507, 684

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