Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0001415

Physical Location & Seq

Genomic Coordinates Forward (+)

3453377 .. 3458990

Gene Structure 5614 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG027900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1062 bp

ATGAACTGCTTGTCGCAGGTCTCATCGTACACGGCGGCGATTTTCCGAACGGCAGGTCGTTCATTCGGGACCGGTGCTCTGTACGGACCCTGCAAGCGAAAATTGGACGTCTACGCTGGGGTGAAGCTAATCAGCTTCGAGTCGGCGGTTTCGAGGTTCCGGACTCAGCTCTACTCGTCTCAGAGCAAAGCGACGTCGTCTCGGCCGCGGAAGAAGAAGTCAGGACCCAAACGAGTTATGGACCCGGAAAAGGACGCATTCTATGTAGTCCGCAAAGGAAACGTCGTCGGTGTCTATAAGAGCTTCGCTGATTGCCAAGCTGAGCAAGCTTCTTCAATATGTGATCGTCCAATTAGTGTGTACAAAGGGTACTCTATGCCTAAGAAGGATGAGCAATATCTTGCTTCCTGTGGAATTCAGAATGCGCTTTACACTATTTCAGCTGCAGATATGAAAGATGAGCTTTTTGGCAAGCTTGTGGACTGTCCTTTTGGAGATCCAGCATCTTCAAAAGGCGAAACGTCTGAGAAGACTGCAGCCAAGAAGAGATCCCACCAAGAGGCTGAAACAGAAAATGTGGAAGTAATTGTTTCAACTTCTGTATCAGATACTCCTTCCAGAAAGCAGGCCAAGAAAAAGGCTGAAGTTGAAGTCCCCCCTTCTGGCTGTGGCTGTACCCTTCAATTTGATGGTGCATCAAAAGGAAATCCTGGAGCAGCTGGTGCTGGAGCTGTACTGCGAGCAGATGATGGAACCTTGATCTGTAAACTACGTGAAGGTCTGGGTGTTGCAACCAATAACGCTGCTGAGTACCGAGCTGTTATTTTAGGGTTAAAATATGCGCTTAAAAAAGGTTTTTCCAGGATTTTTGTTCAAGGTGACTCCAAGCTCGTCTGTATGCAGGTTCAGGGATTATGGCAGGTGAAAAATCAGAACTTGTCTACTTTGTATGAAGAGGTGAAGAAACTGAAGGATGGATTTGTCTCCTTCAAGATCAGTCATGTTCTTAGGGTGAGAGAAGTTGATTCTGTTTGTCTCCTCTATGGTACTTTTTGTGGATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Cauli_VI DUF393 RVT_3

Protein Analysis

353

Amino Acids

38.29

Weight (kDa)

9.34

Isoelectric Point (pI)

30.45

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNase_H	PF00075	228 - 322	2.9e-08	RNase H
RVT_3	PF13456	229 - 337	6e-23	Reverse transcriptase-like

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: OG0001415)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_2g39271 FvH4_2g39271 FvH4_2g39271 FvH4_2g39271 FvH4_2g39271 FvH4_2g39271 FvH4_2g39271 FvH4_2g39271 FvH4_4g34981 FvH4_4g34981 FvH4_4g34981 FvH4_4g34981 FvH4_4g34981 FvH4_4g34981 FvH4_4g34981 FvH4_4g34981 FvH4_4g34981
malus_domestica	MD15G1022000.v1.1 MD16G1087400.v1.1
prunus_persica	Prupe.1G259600_v2.0.a1 Prupe.1G373800_v2.0.a1 Prupe.1G373800_v2.0.a1 Prupe.1G373800_v2.0.a1 Prupe.1G373800_v2.0.a1 Prupe.1G373800_v2.0.a1
pyrus_communis	pycom09g11760 pycom15g01830 pycom16g07500
rosa_chinensis	RchiOBHm_Chr4g0444511 RchiOBHm_Chr6g0245201 RchiOBHm_Chr6g0301731
rosa_laevigata	RLG00000005828 RLG00000011227 RLG00000015316
rosa_roxburghii	Rroxscaffold_3G00242180 Rroxscaffold_5G00384990 Rroxscaffold_7G00166470 Rroxscaffold_7G00215360
rosa_rugosa	Rorug03G0154200
rosa_samantha	Rh4AG413500 Rh4BG425000 Rh4CG439600 Rh4DG420500 Rh6AG027900 Rh6AG421000 Rh6BG024100 Rh6BG427700 Rh6CG434300 Rh6DG421200
rosa_wichuraiana	Rw4G035520 Rw6G002360 Rw6G036440

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	910
AatII	GACGTC	2 cut(s)	111, 197
Acc36I	ACCTGC	4 cut(s)	7, 44, 892, 910
AccI	GTMKAC	2 cut(s)	111, 941
AccII	CGCG	1 cut(s)	208
AccIII	TCCGGA	1 cut(s)	159
AciI	CCGC	5 cut(s)	35, 146, 206, 208, 271
AclWI	GGATC	2 cut(s)	491, 543
AcoI	YGGCCR	1 cut(s)	203
AcsI	RAATTY	1 cut(s)	414
AcuI	CTGAAG	2 cut(s)	663, 989
AcyI	GRCGYC	2 cut(s)	108, 194
AfaI	GTAC	8 cut(s)	29, 83, 362, 371, 676, 735, 812, 1048
AfiI	CCNNNNNNNGG	3 cut(s)	250, 559, 662
AgeI	ACCGGT	1 cut(s)	71
AgsI	TTSAA	7 cut(s)	336, 510, 594, 650, 683, 875, 991
AjnI	CCWGG	2 cut(s)	709, 860
Alw21I	GWGCWC	1 cut(s)	79
Alw26I	GTCTC	5 cut(s)	25, 183, 204, 988, 1040
AlwI	GGATC	2 cut(s)	491, 543
Aor13HI	TCCGGA	1 cut(s)	159
AoxI	GGCC	2 cut(s)	203, 627
ApeKI	GCWGC	4 cut(s)	443, 536, 716, 803
ApoI	RAATTY	1 cut(s)	414
ArsI	GACNNNNNNTTYG	6 cut(s)	40, 72, 267, 299, 473, 505
AsiGI	ACCGGT	1 cut(s)	71
AspLEI	GCGC	2 cut(s)	427, 844
AspS9I	GGNCC	4 cut(s)	69, 86, 224, 241
AsuC2I	CCSGG	1 cut(s)	245
AsuHPI	GGTGA	5 cut(s)	133, 890, 934, 970, 1024
AvaII	GGWCC	4 cut(s)	69, 86, 224, 241
BaeI	ACNNNNGTAYC	2 cut(s)	585, 618
BbsI	GAAGAC	1 cut(s)	536
Bbv12I	GWGCWC	1 cut(s)	79
BbvI	GCAGC	4 cut(s)	430, 548, 728, 790
BccI	CCATC	3 cut(s)	683, 743, 968
BceAI	ACGGC	2 cut(s)	48, 66
BciT130I	CCWGG	2 cut(s)	711, 862
BcnI	CCSGG	1 cut(s)	245
BcoDI	GTCTC	5 cut(s)	25, 183, 204, 988, 1040
BfmI	CTRYAG	2 cut(s)	444, 534
BfuAI	ACCTGC	4 cut(s)	7, 44, 892, 910
BisI	GCNGC	6 cut(s)	36, 206, 444, 537, 717, 804
BlpI	GCTNAGC	1 cut(s)	321
BlsI	GCNGC	6 cut(s)	37, 207, 445, 538, 718, 805
Bme1390I	CCNGG	3 cut(s)	245, 711, 862
Bme18I	GGWCC	4 cut(s)	69, 86, 224, 241
BmgT120I	GGNCC	4 cut(s)	69, 86, 224, 241
BmiI	GGNNCC	6 cut(s)	70, 88, 158, 226, 243, 754
BmrFI	CCNGG	3 cut(s)	245, 711, 862
BmsI	GCATC	2 cut(s)	512, 704
BpiI	GAAGAC	1 cut(s)	536
BpmI	CTGGAG	2 cut(s)	732, 747
Bpu1102I	GCTNAGC	1 cut(s)	321
BpuMI	CCSGG	1 cut(s)	245
BsaAI	YACGTR	1 cut(s)	773
BsaHI	GRCGYC	2 cut(s)	108, 194
BsaI	GGTCTC	1 cut(s)	25
BsaJI	CCNNGG	1 cut(s)	206
BsaWI	WCCGGW	2 cut(s)	71, 159
Bsc4I	CCNNNNNNNGG	3 cut(s)	250, 559, 662
Bse118I	RCCGGY	1 cut(s)	71
BseAI	TCCGGA	1 cut(s)	159
BseBI	CCWGG	2 cut(s)	711, 862
BseDI	CCNNGG	1 cut(s)	206
BseGI	GGATG	2 cut(s)	394, 979
BseLI	CCNNNNNNNGG	3 cut(s)	250, 559, 662
BseMII	CTCAG	5 cut(s)	179, 194, 312, 516, 798
BseRI	GAGGAG	1 cut(s)	1028
BseX3I	CGGCCG	1 cut(s)	203
BseXI	GCAGC	4 cut(s)	430, 548, 728, 790
BseYI	CCCAGC	1 cut(s)	116
Bsh1236I	CGCG	1 cut(s)	208
Bsh1285I	CGRYCG	1 cut(s)	206
BshFI	GGCC	2 cut(s)	205, 629
BshTI	ACCGGT	1 cut(s)	71
BsiEI	CGRYCG	1 cut(s)	206
BsiHKAI	GWGCWC	1 cut(s)	79
BsiSI	CCGG	3 cut(s)	72, 160, 245
BslFI	GGGAC	2 cut(s)	82, 638
BslI	CCNNNNNNNGG	3 cut(s)	250, 559, 662
BsmAI	GTCTC	5 cut(s)	25, 183, 204, 988, 1040
BsmBI	CGTCTC	2 cut(s)	183, 204
BsmFI	GGGAC	2 cut(s)	82, 638
BsmI	GAATGC	2 cut(s)	257, 427
BsnI	GGCC	2 cut(s)	205, 629
Bso31I	GGTCTC	1 cut(s)	25
Bsp1286I	GDGCHC	1 cut(s)	79
Bsp13I	TCCGGA	1 cut(s)	159
Bsp1407I	TGTACA	1 cut(s)	360
Bsp143I	GATC	5 cut(s)	343, 496, 548, 759, 993
Bsp1720I	GCTNAGC	1 cut(s)	321
BspACI	CCGC	5 cut(s)	35, 146, 206, 208, 271
BspANI	GGCC	2 cut(s)	205, 629
BspCNI	CTCAG	5 cut(s)	178, 193, 313, 517, 799
BspEI	TCCGGA	1 cut(s)	159
BspFNI	CGCG	1 cut(s)	208
BspLI	GGNNCC	6 cut(s)	70, 88, 158, 226, 243, 754
BspMAI	CTGCAG	2 cut(s)	448, 538
BspMI	ACCTGC	4 cut(s)	7, 44, 892, 910
BspPI	GGATC	2 cut(s)	491, 543
BspTNI	GGTCTC	1 cut(s)	25
BsrFI	RCCGGY	1 cut(s)	71
BsrGI	TGTACA	1 cut(s)	360
BssAI	RCCGGY	1 cut(s)	71
BssECI	CCNNGG	1 cut(s)	206
BssMI	GATC	5 cut(s)	343, 496, 548, 759, 993
BssNI	GRCGYC	2 cut(s)	108, 194
Bst2UI	CCWGG	2 cut(s)	711, 862
Bst4CI	ACNGT	1 cut(s)	485
Bst6I	CTCTTC	2 cut(s)	539, 948
BstACI	GRCGYC	2 cut(s)	108, 194
BstAPI	GCANNNNNTGC	1 cut(s)	722
BstAUI	TGTACA	1 cut(s)	360
BstBAI	YACGTR	1 cut(s)	773
BstC8I	GCNNGC	5 cut(s)	95, 327, 473, 627, 741
BstDEI	CTNAG	7 cut(s)	165, 180, 321, 381, 525, 807, 1007
BstDSI	CCRYGG	1 cut(s)	206
BstF5I	GGATG	2 cut(s)	394, 979
BstFNI	CGCG	1 cut(s)	208
BstHHI	GCGC	2 cut(s)	427, 844
BstKTI	GATC	5 cut(s)	346, 499, 551, 762, 996
BstMAI	GTCTC	5 cut(s)	25, 183, 204, 988, 1040
BstMBI	GATC	5 cut(s)	343, 496, 548, 759, 993
BstMCI	CGRYCG	1 cut(s)	206
BstMWI	GCNNNNNNNGC	2 cut(s)	326, 722
BstNI	CCWGG	2 cut(s)	711, 862
BstSCI	CCNGG	3 cut(s)	243, 709, 860
BstSFI	CTRYAG	2 cut(s)	444, 534
BstUI	CGCG	1 cut(s)	208
BstV1I	GCAGC	4 cut(s)	430, 548, 728, 790
BstV2I	GAAGAC	1 cut(s)	536
BstX2I	RGATCY	2 cut(s)	496, 548
BstYI	RGATCY	2 cut(s)	496, 548
BstZI	CGGCCG	1 cut(s)	203
BsuRI	GGCC	2 cut(s)	205, 629
BtgI	CCRYGG	1 cut(s)	206
BtsCI	GGATG	2 cut(s)	394, 979
BveI	ACCTGC	4 cut(s)	7, 44, 892, 910
Cac8I	GCNNGC	5 cut(s)	95, 327, 473, 627, 741
CfoI	GCGC	2 cut(s)	427, 844
Cfr10I	RCCGGY	1 cut(s)	71
Cfr13I	GGNCC	4 cut(s)	69, 86, 224, 241
Cfr42I	CCGCGG	1 cut(s)	209
CseI	GACGC	1 cut(s)	263
Csp6I	GTAC	8 cut(s)	28, 82, 361, 370, 675, 734, 811, 1047
CspAI	ACCGGT	1 cut(s)	71
CviAII	CATG	1 cut(s)	1001
CviQI	GTAC	8 cut(s)	28, 82, 361, 370, 675, 734, 811, 1047
DdeI	CTNAG	7 cut(s)	165, 180, 321, 381, 525, 807, 1007
DpnI	GATC	5 cut(s)	345, 498, 550, 761, 995
DpnII	GATC	5 cut(s)	343, 496, 548, 759, 993
EaeI	YGGCCR	1 cut(s)	203
EagI	CGGCCG	1 cut(s)	203
Eam1104I	CTCTTC	2 cut(s)	539, 948
EarI	CTCTTC	2 cut(s)	539, 948
EclXI	CGGCCG	1 cut(s)	203
Eco31I	GGTCTC	1 cut(s)	25
Eco47I	GGWCC	4 cut(s)	69, 86, 224, 241
Eco52I	CGGCCG	1 cut(s)	203
Eco57I	CTGAAG	2 cut(s)	663, 989
EcoO109I	RGGNCCY	1 cut(s)	224
EcoRI	GAATTC	1 cut(s)	414
EcoRII	CCWGG	2 cut(s)	709, 860
Esp3I	CGTCTC	2 cut(s)	183, 204
FaeI	CATG	1 cut(s)	1004
FalI	AAGNNNNNCTT	2 cut(s)	447, 479
FaqI	GGGAC	2 cut(s)	82, 638
FatI	CATG	1 cut(s)	1000
FblI	GTMKAC	2 cut(s)	111, 941
Fnu4HI	GCNGC	6 cut(s)	36, 206, 444, 537, 717, 804
FokI	GGATG	2 cut(s)	401, 986
Fsp4HI	GCNGC	6 cut(s)	36, 206, 444, 537, 717, 804
GlaI	GCGC	2 cut(s)	426, 843
GluI	GCNGC	6 cut(s)	36, 206, 444, 537, 717, 804
GsaI	CCCAGC	1 cut(s)	120
GsuI	CTGGAG	2 cut(s)	732, 747
HaeIII	GGCC	2 cut(s)	205, 629
HapII	CCGG	3 cut(s)	72, 160, 245
HgaI	GACGC	1 cut(s)	263
HhaI	GCGC	2 cut(s)	427, 844
Hin1I	GRCGYC	2 cut(s)	108, 194
Hin1II	CATG	1 cut(s)	1004
Hin6I	GCGC	2 cut(s)	425, 842
HinP1I	GCGC	2 cut(s)	425, 842
HindIII	AAGCTT	2 cut(s)	327, 473
HinfI	GANTC	4 cut(s)	140, 163, 881, 1025
HpaII	CCGG	3 cut(s)	72, 160, 245
HphI	GGTGA	5 cut(s)	133, 890, 934, 970, 1024
Hpy166II	GTNNAC	6 cut(s)	30, 112, 361, 481, 767, 942
Hpy188I	TCNGA	6 cut(s)	47, 183, 420, 526, 607, 933
Hpy188III	TCNNGA	5 cut(s)	67, 160, 222, 618, 991
Hpy8I	GTNNAC	6 cut(s)	30, 112, 361, 481, 767, 942
Hpy99I	CGWCG	4 cut(s)	196, 199, 287, 290
HpyAV	CCTTC	7 cut(s)	379, 624, 669, 689, 770, 964, 997
HpyCH4III	ACNGT	1 cut(s)	485
HpyCH4IV	ACGT	5 cut(s)	108, 194, 282, 521, 772
HpyCH4V	TGCA	6 cut(s)	93, 446, 536, 695, 791, 901
HpyF10VI	GCNNNNNNNGC	2 cut(s)	326, 722
HpyF3I	CTNAG	7 cut(s)	165, 180, 321, 381, 525, 807, 1007
HpySE526I	ACGT	5 cut(s)	108, 194, 282, 521, 772
Hsp92I	GRCGYC	2 cut(s)	108, 194
Hsp92II	CATG	1 cut(s)	1004
HspAI	GCGC	2 cut(s)	425, 842
Kpn2I	TCCGGA	1 cut(s)	159
KspI	CCGCGG	1 cut(s)	209
Kzo9I	GATC	5 cut(s)	343, 496, 548, 759, 993
LmnI	GCTCC	2 cut(s)	713, 728
Lsp1109I	GCAGC	4 cut(s)	430, 548, 728, 790
LweI	GCATC	2 cut(s)	512, 704
MaeII	ACGT	5 cut(s)	108, 194, 282, 521, 772
MaeIII	GTNAC	1 cut(s)	878
MalI	GATC	5 cut(s)	345, 498, 550, 761, 995
MboI	GATC	5 cut(s)	343, 496, 548, 759, 993
MboII	GAAGA	8 cut(s)	223, 226, 324, 498, 541, 556, 965, 973
MflI	RGATCY	2 cut(s)	496, 548
MhlI	GDGCHC	1 cut(s)	79
MluCI	AATT	5 cut(s)	101, 351, 414, 585, 683
MlyI	GAGTC	3 cut(s)	149, 157, 875
MnlI	CCTC	4 cut(s)	147, 553, 949, 1049
MroI	TCCGGA	1 cut(s)	159
MseI	TTAA	2 cut(s)	833, 846
MspA1I	CMGCKG	3 cut(s)	208, 443, 719
MspI	CCGG	3 cut(s)	72, 160, 245
MspR9I	CCNGG	3 cut(s)	245, 711, 862
Mva1269I	GAATGC	2 cut(s)	257, 427
MvaI	CCWGG	2 cut(s)	711, 862
MvnI	CGCG	1 cut(s)	208
MwoI	GCNNNNNNNGC	2 cut(s)	326, 722
NciI	CCSGG	1 cut(s)	245
NdeII	GATC	5 cut(s)	343, 496, 548, 759, 993
NlaIII	CATG	1 cut(s)	1004
NlaIV	GGNNCC	6 cut(s)	70, 88, 158, 226, 243, 754
NmeAIII	GCCGAG	1 cut(s)	181
NmuCI	GTSAC	1 cut(s)	878
PaqCI	CACCTGC	1 cut(s)	910
PcsI	WCGNNNNNNNCGW	1 cut(s)	149
PctI	GAATGC	2 cut(s)	257, 427
PfeI	GAWTC	1 cut(s)	1025
PflFI	GACNNNGTC	1 cut(s)	196
PfoI	TCCNGGA	2 cut(s)	709, 860
PinAI	ACCGGT	1 cut(s)	71
PkrI	GCNGC	6 cut(s)	37, 207, 445, 538, 718, 805
PleI	GAGTC	3 cut(s)	148, 157, 875
PpsI	GAGTC	3 cut(s)	148, 157, 875
Ppu21I	YACGTR	1 cut(s)	773
PpuMI	RGGWCCY	1 cut(s)	224
Psp5II	RGGWCCY	1 cut(s)	224
Psp6I	CCWGG	2 cut(s)	709, 860
PspFI	CCCAGC	1 cut(s)	116
PspGI	CCWGG	2 cut(s)	709, 860
PspN4I	GGNNCC	6 cut(s)	70, 88, 158, 226, 243, 754
PspPI	GGNCC	4 cut(s)	69, 86, 224, 241
PspPPI	RGGWCCY	1 cut(s)	224
PstI	CTGCAG	2 cut(s)	448, 538
PsuI	RGATCY	2 cut(s)	496, 548
PsyI	GACNNNGTC	1 cut(s)	196
PvuII	CAGCTG	2 cut(s)	443, 719
RsaI	GTAC	8 cut(s)	29, 83, 362, 371, 676, 735, 812, 1048
RsaNI	GTAC	8 cut(s)	28, 82, 361, 370, 675, 734, 811, 1047
SacII	CCGCGG	1 cut(s)	209
SaqAI	TTAA	2 cut(s)	833, 846
SatI	GCNGC	6 cut(s)	36, 206, 444, 537, 717, 804
Sau3AI	GATC	5 cut(s)	343, 496, 548, 759, 993
Sau96I	GGNCC	4 cut(s)	69, 86, 224, 241
SchI	GAGTC	3 cut(s)	149, 157, 875
ScrFI	CCNGG	3 cut(s)	245, 711, 862
SduI	GDGCHC	1 cut(s)	79
SfaNI	GCATC	2 cut(s)	512, 704
SfcI	CTRYAG	2 cut(s)	444, 534
Sfr303I	CCGCGG	1 cut(s)	209
SgrBI	CCGCGG	1 cut(s)	209
SinI	GGWCC	4 cut(s)	69, 86, 224, 241
Sse9I	AATT	5 cut(s)	101, 351, 414, 585, 683
SsiI	CCGC	5 cut(s)	35, 146, 206, 208, 271
StyD4I	CCNGG	3 cut(s)	243, 709, 860
TaaI	ACNGT	1 cut(s)	485
TaiI	ACGT	5 cut(s)	111, 197, 285, 524, 775
TaqI	TCGA	2 cut(s)	138, 152
TasI	AATT	5 cut(s)	101, 351, 414, 585, 683
TatI	WGTACW	2 cut(s)	360, 733
TauI	GCSGC	2 cut(s)	38, 208
TfiI	GAWTC	1 cut(s)	1025
Tru1I	TTAA	2 cut(s)	833, 846
Tru9I	TTAA	2 cut(s)	833, 846
TseFI	GTSAC	1 cut(s)	878
TseI	GCWGC	4 cut(s)	443, 536, 716, 803
Tsp45I	GTSAC	1 cut(s)	878
TspDTI	ATGAA	4 cut(s)	17, 51, 467, 966
TspGWI	ACGGA	1 cut(s)	99
Tth111I	GACNNNGTC	1 cut(s)	196
VpaK11BI	GGWCC	4 cut(s)	69, 86, 224, 241
XapI	RAATTY	1 cut(s)	414
XcmI	CCANNNNNNNNNTGG	1 cut(s)	235
XmiI	GTMKAC	2 cut(s)	111, 941
ZraI	GACGTC	2 cut(s)	109, 195

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