Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0004246

Physical Location & Seq

Genomic Coordinates Reverse (-)

44671867 .. 44691570

Gene Structure 19704 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG335300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1167 bp

ATGAATGGGATTATCCATCCCTGCTTTCACCCGGAAGAAGAAGATGATGATGGTTATGGACTTGCACCACCAAGAACTTATGAAGATGTCTTCAACAATATTTTCGAACACATTGATCGGCTTTTCAATATTGTTAGACCAAGGAAACTACTCTACATAGCCATTGATGGAGTTGCTCCAAGGGCTAAAATGAATCAACAGCGCGCCAGGCGTTTTAAGTCAGCAATGGACAAGAATCTTGCTGAGGCTGAAGAAGAGAAACTAAGACAGCAATTTGAAAAGGAATGGAAAAAAATCCTACTAGAACAGGAGTCCGAAGTTTCTGATTCTAATATAATCACCCCTGGAACGGATTTCATGTACAAGTTATCCAAGGCTCTTCAAAGCTACATCAATCTACGTTTAAGCCAAGATTCAGGCTGGAGGGACATCAAGGGTGCAATTGATTTACTGATGACAGTCTACAAGAAAGAATTCAAGAATATTGGTGGCTATTTGATTGATATGATTCAGACAATCAATGAACACGAGCTTATAGAAACAGTTCTATGGCATGAATGTCAGGGAAATGTGACCACCCGAAGCATCCAGCAAGTACAGGCAAGGTTTAGAAAACCAAATGATTTGGGATATGCAAGTTTTCACAATGGTAAATTCACTTCAAGCTCTCCTGCCAATTCAATTCACAAATTTGCTGGTTCTGGATGGGGGTGTGGTAGAGGAACAAATGGTAGTTGTAAGTCAGGAGACCGAGTTTATGCTCCAAAAGGAATATCCAGGGATCAAAGAGTAGTGTCATCTCCTAGCTCATACTATGCCAAGGGTACCTCAGATTATAGAAAAGGCGCATTACAACACGGCTTCAGGGAATTAAATATAACAGAGTCAGGCCAATGCTGGAGGCCTAATGGAAGGGGAGTTCAGTCATTGAATAATGATTTATGGCCATCTAGAAATAGTGTCTCTCAAGACACAAACTTTGCTGGTCATGGTTCACAGTCATATCATACTTGGGGCCGTGGCAGAGGGCAACACAATTCGTGGCAGCACACCTATCCATTTGCTGGTACAGGTAGAGGCCAGCAAAACCCTTGGACACACACCCGACCTTATTTTGCTGCTAACCGTTCATCATCACATGCCGGTGGAAGAGGGAACTTTGTTTAA

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

388

Amino Acids

44.03

Weight (kDa)

9.27

Isoelectric Point (pI)

47.53

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
XRN_N	PF03159	1 - 145	3.8e-48	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: OG0004246)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_7g18720 FvH4_7g18720 FvH4_7g18720 FvH4_7g18720
malus_domestica	MD00G1128400.v1.1 MD11G1172900.v1.1
prunus_persica	Prupe.6G141200_v2.0.a1 Prupe.6G141200_v2.0.a1 Prupe.6G141200_v2.0.a1 Prupe.6G141200_v2.0.a1
pyrus_communis	pycom11g14580 pycom520g00080
rosa_chinensis	RchiOBHm_Chr1g0334231 RchiOBHm_Chr5g0047421 RchiOBHm_Chr5g0047601 RchiOBHm_Chr5g0047631 RchiOBHm_Chr5g0047791 RchiOBHm_Chr5g0047991
rosa_multiflora	Rmu_sc0000148.1_g000001 Rmu_sc0000148.1_g000016 Rmu_sc0003441.1_g000004
rosa_roxburghii	Rroxscaffold_1G00029700 Rroxscaffold_1G00033910
rosa_rugosa	Rorug05G0236400
rosa_samantha	Rh1CG129900 Rh5AG315300 Rh5AG315400 Rh5DG335300 Rh5DG335400
rosa_wichuraiana	Rw0G017980 Rw5G029460 Rw5G029520 Rw5G029550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	824
AccB1I	GGYRCC	1 cut(s)	824
AccB7I	CCANNNNNTGG	1 cut(s)	1064
AccI	GTMKAC	1 cut(s)	462
AccII	CGCG	1 cut(s)	204
AclWI	GGATC	1 cut(s)	789
AcoI	YGGCCR	1 cut(s)	944
AcsI	RAATTY	3 cut(s)	473, 653, 689
AcuI	CTGAAG	2 cut(s)	270, 847
AfaI	GTAC	4 cut(s)	362, 597, 826, 1069
AfiI	CCNNNNNNNGG	2 cut(s)	349, 1064
AgsI	TTSAA	8 cut(s)	94, 127, 278, 383, 478, 663, 681, 931
AjnI	CCWGG	3 cut(s)	206, 343, 776
AloI	GAACNNNNNNTCC	2 cut(s)	903, 935
AluBI	AGCT	4 cut(s)	387, 532, 666, 807
AluI	AGCT	4 cut(s)	387, 532, 666, 807
Alw26I	GTCTC	2 cut(s)	741, 967
AlwI	GGATC	1 cut(s)	789
AoxI	GGCC	5 cut(s)	889, 902, 944, 1015, 1078
ApeKI	GCWGC	2 cut(s)	1045, 1118
ApoI	RAATTY	3 cut(s)	473, 653, 689
ArsI	GACNNNNNNTTYG	2 cut(s)	962, 994
Asp700I	GAANNNNTTC	2 cut(s)	473, 543
Asp718I	GGTACC	1 cut(s)	824
AspLEI	GCGC	3 cut(s)	204, 206, 848
AspS9I	GGNCC	1 cut(s)	1015
AsuC2I	CCSGG	1 cut(s)	32
AsuHPI	GGTGA	2 cut(s)	20, 331
AsuII	TTCGAA	1 cut(s)	105
BalI	TGGCCA	1 cut(s)	946
BanI	GGYRCC	1 cut(s)	824
BarI	GAAGNNNNNNTAC	2 cut(s)	643, 675
BauI	CACGAG	1 cut(s)	527
BbsI	GAAGAC	1 cut(s)	82
BbvCI	CCTCAGC	1 cut(s)	243
BbvI	GCAGC	2 cut(s)	1057, 1105
BccI	CCATC	5 cut(s)	24, 44, 161, 699, 955
BceAI	ACGGC	2 cut(s)	874, 1002
BciT130I	CCWGG	3 cut(s)	208, 345, 778
BcnI	CCSGG	1 cut(s)	32
BcoDI	GTCTC	2 cut(s)	741, 967
BfaI	CTAG	3 cut(s)	302, 804, 951
BisI	GCNGC	2 cut(s)	1046, 1119
BlsI	GCNGC	2 cut(s)	1047, 1120
Bme1390I	CCNGG	4 cut(s)	32, 208, 345, 778
BmgT120I	GGNCC	1 cut(s)	1015
BmiI	GGNNCC	2 cut(s)	826, 1016
BmrFI	CCNGG	4 cut(s)	32, 208, 345, 778
BmsI	GCATC	1 cut(s)	594
BpiI	GAAGAC	1 cut(s)	82
BpmI	CTGGAG	2 cut(s)	442, 919
Bpu10I	CCTNAGC	1 cut(s)	243
Bpu14I	TTCGAA	1 cut(s)	105
BpuEI	CTTGAG	1 cut(s)	951
BpuMI	CCSGG	1 cut(s)	32
BsaI	GGTCTC	1 cut(s)	741
BsaJI	CCNNGG	8 cut(s)	140, 179, 343, 372, 777, 819, 1018, 1091
BsaXI	ACNNNNNCTCC	2 cut(s)	738, 768
Bsc4I	CCNNNNNNNGG	2 cut(s)	349, 1064
Bse118I	RCCGGY	1 cut(s)	1142
Bse3DI	GCAATG	1 cut(s)	231
BseBI	CCWGG	3 cut(s)	208, 345, 778
BseDI	CCNNGG	8 cut(s)	140, 179, 343, 372, 777, 819, 1018, 1091
BseGI	GGATG	3 cut(s)	16, 585, 710
BseLI	CCNNNNNNNGG	2 cut(s)	349, 1064
BseMI	GCAATG	1 cut(s)	231
BseMII	CTCAG	2 cut(s)	234, 843
BsePI	GCGCGC	1 cut(s)	202
BseXI	GCAGC	2 cut(s)	1057, 1105
Bsh1236I	CGCG	1 cut(s)	204
BshFI	GGCC	5 cut(s)	891, 904, 946, 1017, 1080
BshNI	GGYRCC	1 cut(s)	824
BsiSI	CCGG	2 cut(s)	32, 1143
BslFI	GGGAC	1 cut(s)	440
BslI	CCNNNNNNNGG	2 cut(s)	349, 1064
BsmAI	GTCTC	2 cut(s)	741, 967
BsmFI	GGGAC	1 cut(s)	440
BsnI	GGCC	5 cut(s)	891, 904, 946, 1017, 1080
Bso31I	GGTCTC	1 cut(s)	741
Bsp119I	TTCGAA	1 cut(s)	105
Bsp1407I	TGTACA	1 cut(s)	360
Bsp143I	GATC	2 cut(s)	115, 781
BspANI	GGCC	5 cut(s)	891, 904, 946, 1017, 1080
BspCNI	CTCAG	2 cut(s)	235, 842
BspFNI	CGCG	1 cut(s)	204
BspLI	GGNNCC	2 cut(s)	826, 1016
BspPI	GGATC	1 cut(s)	789
BspQI	GCTCTTC	1 cut(s)	384
BspT104I	TTCGAA	1 cut(s)	105
BspT107I	GGYRCC	1 cut(s)	824
BspTNI	GGTCTC	1 cut(s)	741
BsrDI	GCAATG	1 cut(s)	231
BsrFI	RCCGGY	1 cut(s)	1142
BsrGI	TGTACA	1 cut(s)	360
BssAI	RCCGGY	1 cut(s)	1142
BssECI	CCNNGG	8 cut(s)	140, 179, 343, 372, 777, 819, 1018, 1091
BssHII	GCGCGC	1 cut(s)	202
BssMI	GATC	2 cut(s)	115, 781
BssSI	CACGAG	1 cut(s)	527
BssT1I	CCWWGG	5 cut(s)	140, 179, 372, 819, 1091
Bst2BI	CACGAG	1 cut(s)	527
Bst2UI	CCWGG	3 cut(s)	208, 345, 778
Bst4CI	ACNGT	4 cut(s)	460, 544, 999, 1127
Bst6I	CTCTTC	3 cut(s)	249, 384, 1144
BstAUI	TGTACA	1 cut(s)	360
BstBI	TTCGAA	1 cut(s)	105
BstC8I	GCNNGC	2 cut(s)	204, 1082
BstDEI	CTNAG	3 cut(s)	243, 263, 829
BstDSI	CCRYGG	1 cut(s)	1018
BstF5I	GGATG	3 cut(s)	16, 585, 710
BstFNI	CGCG	1 cut(s)	204
BstHHI	GCGC	3 cut(s)	204, 206, 848
BstKTI	GATC	2 cut(s)	118, 784
BstMAI	GTCTC	2 cut(s)	741, 967
BstMBI	GATC	2 cut(s)	115, 781
BstMWI	GCNNNNNNNGC	2 cut(s)	182, 208
BstNI	CCWGG	3 cut(s)	208, 345, 778
BstNSI	RCATGY	1 cut(s)	1142
BstSCI	CCNGG	4 cut(s)	30, 206, 343, 776
BstUI	CGCG	1 cut(s)	204
BstV1I	GCAGC	2 cut(s)	1057, 1105
BstV2I	GAAGAC	1 cut(s)	82
BsuRI	GGCC	5 cut(s)	891, 904, 946, 1017, 1080
BtgI	CCRYGG	1 cut(s)	1018
BtsCI	GGATG	3 cut(s)	16, 585, 710
Cac8I	GCNNGC	2 cut(s)	204, 1082
CfoI	GCGC	3 cut(s)	204, 206, 848
Cfr10I	RCCGGY	1 cut(s)	1142
Cfr13I	GGNCC	1 cut(s)	1015
Csp6I	GTAC	4 cut(s)	361, 596, 825, 1068
CviAII	CATG	4 cut(s)	358, 554, 989, 1139
CviQI	GTAC	4 cut(s)	361, 596, 825, 1068
DdeI	CTNAG	3 cut(s)	243, 263, 829
DpnI	GATC	2 cut(s)	117, 783
DpnII	GATC	2 cut(s)	115, 781
EaeI	YGGCCR	1 cut(s)	944
Eam1104I	CTCTTC	3 cut(s)	249, 384, 1144
EarI	CTCTTC	3 cut(s)	249, 384, 1144
Eco130I	CCWWGG	5 cut(s)	140, 179, 372, 819, 1091
Eco147I	AGGCCT	1 cut(s)	904
Eco31I	GGTCTC	1 cut(s)	741
Eco57I	CTGAAG	2 cut(s)	270, 847
EcoRI	GAATTC	1 cut(s)	473
EcoRII	CCWGG	3 cut(s)	206, 343, 776
EcoT14I	CCWWGG	5 cut(s)	140, 179, 372, 819, 1091
ErhI	CCWWGG	5 cut(s)	140, 179, 372, 819, 1091
FaeI	CATG	4 cut(s)	361, 557, 992, 1142
FaqI	GGGAC	1 cut(s)	440
FatI	CATG	4 cut(s)	357, 553, 988, 1138
FblI	GTMKAC	1 cut(s)	462
Fnu4HI	GCNGC	2 cut(s)	1046, 1119
FokI	GGATG	3 cut(s)	3, 572, 717
Fsp4HI	GCNGC	2 cut(s)	1046, 1119
FspBI	CTAG	3 cut(s)	302, 804, 951
GlaI	GCGC	3 cut(s)	203, 205, 847
GluI	GCNGC	2 cut(s)	1046, 1119
GsuI	CTGGAG	2 cut(s)	442, 919
HaeIII	GGCC	5 cut(s)	891, 904, 946, 1017, 1080
HapII	CCGG	2 cut(s)	32, 1143
HhaI	GCGC	3 cut(s)	204, 206, 848
Hin1II	CATG	4 cut(s)	361, 557, 992, 1142
Hin6I	GCGC	3 cut(s)	202, 204, 846
HinP1I	GCGC	3 cut(s)	202, 204, 846
HinfI	GANTC	7 cut(s)	193, 235, 311, 326, 413, 508, 884
HpaII	CCGG	2 cut(s)	32, 1143
HphI	GGTGA	2 cut(s)	20, 331
Hpy166II	GTNNAC	2 cut(s)	463, 995
Hpy188I	TCNGA	4 cut(s)	316, 325, 513, 832
Hpy188III	TCNNGA	5 cut(s)	478, 702, 744, 951, 968
Hpy8I	GTNNAC	2 cut(s)	463, 995
HpyAV	CCTTC	1 cut(s)	906
HpyCH4III	ACNGT	4 cut(s)	460, 544, 999, 1127
HpyCH4IV	ACGT	1 cut(s)	400
HpyCH4V	TGCA	3 cut(s)	65, 440, 635
HpyF10VI	GCNNNNNNNGC	2 cut(s)	182, 208
HpyF3I	CTNAG	3 cut(s)	243, 263, 829
HpySE526I	ACGT	1 cut(s)	400
Hsp92II	CATG	4 cut(s)	361, 557, 992, 1142
HspAI	GCGC	3 cut(s)	202, 204, 846
KpnI	GGTACC	1 cut(s)	828
Kzo9I	GATC	2 cut(s)	115, 781
LguI	GCTCTTC	1 cut(s)	384
LmnI	GCTCC	2 cut(s)	181, 766
Lsp1109I	GCAGC	2 cut(s)	1057, 1105
LweI	GCATC	1 cut(s)	594
MaeI	CTAG	3 cut(s)	302, 804, 951
MaeII	ACGT	1 cut(s)	400
MaeIII	GTNAC	1 cut(s)	571
MalI	GATC	2 cut(s)	117, 783
MboI	GATC	2 cut(s)	115, 781
MboII	GAAGA	9 cut(s)	47, 50, 53, 82, 95, 263, 266, 371, 1161
MfeI	CAATTG	1 cut(s)	441
MlsI	TGGCCA	1 cut(s)	946
MluCI	AATT	9 cut(s)	272, 441, 473, 653, 676, 681, 689, 869, 1036
MluNI	TGGCCA	1 cut(s)	946
MlyI	GAGTC	2 cut(s)	320, 893
MnlI	CCTC	8 cut(s)	238, 417, 713, 838, 894, 1019, 1070, 1145
Mox20I	TGGCCA	1 cut(s)	946
MroXI	GAANNNNTTC	2 cut(s)	473, 543
MscI	TGGCCA	1 cut(s)	946
MseI	TTAA	4 cut(s)	216, 404, 872, 1165
MslI	CAYNNNNRTG	1 cut(s)	1143
Msp20I	TGGCCA	1 cut(s)	946
MspI	CCGG	2 cut(s)	32, 1143
MspR9I	CCNGG	4 cut(s)	32, 208, 345, 778
MunI	CAATTG	1 cut(s)	441
MvaI	CCWGG	3 cut(s)	208, 345, 778
MvnI	CGCG	1 cut(s)	204
MwoI	GCNNNNNNNGC	2 cut(s)	182, 208
NciI	CCSGG	1 cut(s)	32
NdeII	GATC	2 cut(s)	115, 781
NlaIII	CATG	4 cut(s)	361, 557, 992, 1142
NlaIV	GGNNCC	2 cut(s)	826, 1016
NmuCI	GTSAC	1 cut(s)	571
NspI	RCATGY	1 cut(s)	1142
NspV	TTCGAA	1 cut(s)	105
PauI	GCGCGC	1 cut(s)	202
PceI	AGGCCT	1 cut(s)	904
PciSI	GCTCTTC	1 cut(s)	384
PdmI	GAANNNNTTC	2 cut(s)	473, 543
PfeI	GAWTC	5 cut(s)	193, 235, 326, 413, 508
PflMI	CCANNNNNTGG	1 cut(s)	1064
PkrI	GCNGC	2 cut(s)	1047, 1120
PleI	GAGTC	2 cut(s)	319, 892
PpsI	GAGTC	2 cut(s)	319, 892
Psp6I	CCWGG	3 cut(s)	206, 343, 776
PspGI	CCWGG	3 cut(s)	206, 343, 776
PspN4I	GGNNCC	2 cut(s)	826, 1016
PspPI	GGNCC	1 cut(s)	1015
PteI	GCGCGC	1 cut(s)	202
RsaI	GTAC	4 cut(s)	362, 597, 826, 1069
RsaNI	GTAC	4 cut(s)	361, 596, 825, 1068
RseI	CAYNNNNRTG	1 cut(s)	1143
SapI	GCTCTTC	1 cut(s)	384
SaqAI	TTAA	4 cut(s)	216, 404, 872, 1165
SatI	GCNGC	2 cut(s)	1046, 1119
Sau3AI	GATC	2 cut(s)	115, 781
Sau96I	GGNCC	1 cut(s)	1015
SchI	GAGTC	2 cut(s)	320, 893
ScrFI	CCNGG	4 cut(s)	32, 208, 345, 778
SfaNI	GCATC	1 cut(s)	594
SfuI	TTCGAA	1 cut(s)	105
SmiMI	CAYNNNNRTG	1 cut(s)	1143
SmlI	CTYRAG	1 cut(s)	966
SmoI	CTYRAG	1 cut(s)	966
Sse9I	AATT	9 cut(s)	272, 441, 473, 653, 676, 681, 689, 869, 1036
SseBI	AGGCCT	1 cut(s)	904
SspI	AATATT	3 cut(s)	100, 130, 484
SspMI	CTAG	3 cut(s)	302, 804, 951
StuI	AGGCCT	1 cut(s)	904
StyD4I	CCNGG	4 cut(s)	30, 206, 343, 776
StyI	CCWWGG	5 cut(s)	140, 179, 372, 819, 1091
TaaI	ACNGT	4 cut(s)	460, 544, 999, 1127
TaiI	ACGT	1 cut(s)	403
TaqI	TCGA	1 cut(s)	105
TaqII	GACCGA	1 cut(s)	765
TasI	AATT	9 cut(s)	272, 441, 473, 653, 676, 681, 689, 869, 1036
TatI	WGTACW	2 cut(s)	360, 595
TfiI	GAWTC	5 cut(s)	193, 235, 326, 413, 508
Tru1I	TTAA	4 cut(s)	216, 404, 872, 1165
Tru9I	TTAA	4 cut(s)	216, 404, 872, 1165
TseFI	GTSAC	1 cut(s)	571
TseI	GCWGC	2 cut(s)	1045, 1118
Tsp45I	GTSAC	1 cut(s)	571
TspDTI	ATGAA	7 cut(s)	17, 96, 206, 346, 537, 570, 1119
TspGWI	ACGGA	1 cut(s)	365
Van91I	CCANNNNNTGG	1 cut(s)	1064
XapI	RAATTY	3 cut(s)	473, 653, 689
XbaI	TCTAGA	1 cut(s)	950
XceI	RCATGY	1 cut(s)	1142
XmiI	GTMKAC	1 cut(s)	462
XmnI	GAANNNNTTC	2 cut(s)	473, 543
XspI	CTAG	3 cut(s)	302, 804, 951

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