Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0001415

Physical Location & Seq

Genomic Coordinates Forward (+)

67684426 .. 67686567

Gene Structure 2142 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG439600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1032 bp

ATGAACCCAATCTCTTCTCTGGTTCAGAGGAGTTACCGATACCTGGAGACTGGAGTGATGAACTTCTCGTCACACGTTTCGTACACGACGGGTCGTACTTTCGCCACCACCTCTTCTCCTTCTTCTTCGTGGAGAACAAAACCGAACCTTTCCGCTGGAATTAAGTCAAATAAAGTTGACTTTGCGCTGACCAGAGTCCATGTTCAGCTTCGAAGTAATGGCAGCAGCAGCAGCAGCCGCCGCAAAACGACGTCGTGTTGTGCTCGGACGAACGCAATGGAAGTGGAAAAAGAAGCGTTCTATTTAGTCCGGAAAGGAGATATTGTTGGCGTGTATAGGAATTTCGGTGACTGTGAGGCCCAGATTGGTTCTTCGATATGTGATCCTCCTGTTAGTGTGTACAAAGGTTACTCCTTGCCTAAGGACACTGAAGAACATCTTGTGTCTTTTGGACTTACCAATGCAATTTACACTATCAGAGCTGAAGATTTGAAGCAGGACCATTTCGGCAAGCTTATGCTCTGCCCTTTTCATGAGCCAGCAGCTTCAGAATGTGAAGAGTCTGTCACGGATACATCTGTAAACGGTTCCGATGAAGTGCCTGGATCAGAATATGTGGGCTTCTGTACCCTCGAGTTTGATGGTGCATCAAAGGGAAATCCTGGACTAGCTGGTGCTGGAGCTGTGCTGCGAGCTGATGATGGAAGTTTGATCTGTAAAGTTCATGAAGGACTGGGTATCAAGACCAATAATGTTGCTGAGTACCGAGCTCTGATTTTAGGGTTAAGATGTGCTCTCAAGAAAGGTTTTACCAAGATTCGAGTCCAGGGTGATTCCAAACTTGTTTGTATGCAGGTTCAAGGTTTATGGAAGGTCAAAAACCAGAATCTGTCTGATTTGTGTGAAGAGGTGAAGGAACTAAAAGAAAAATTTGTCTCCTTTGAGATCAGTCATGTTCTGAGGGACAAAAATTCAGAGGCAGATGCTCAAGCAAACTTGGCAGTTCGTCTTAGTGGTGAGCCTTTCAAATGA

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

343

Amino Acids

37.53

Weight (kDa)

7.94

Isoelectric Point (pI)

29.79

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RVT_3	PF13456	213 - 333	5.1e-28	Reverse transcriptase-like
RNase_H	PF00075	214 - 315	8.1e-09	RNase H

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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AatII	GACGTC	1 cut(s)	254
Acc36I	ACCTGC	1 cut(s)	844
AccIII	TCCGGA	1 cut(s)	309
AciI	CCGC	3 cut(s)	153, 238, 241
AclWI	GGATC	2 cut(s)	377, 613
AcsI	RAATTY	3 cut(s)	340, 929, 970
AcuI	CTGAAG	3 cut(s)	450, 504, 531
AcyI	GRCGYC	1 cut(s)	251
AfaI	GTAC	5 cut(s)	83, 97, 401, 628, 764
AfiI	CCNNNNNNNGG	1 cut(s)	43
AflIII	ACRYGT	1 cut(s)	73
AgsI	TTSAA	3 cut(s)	493, 860, 1027
AjnI	CCWGG	4 cut(s)	42, 601, 661, 825
AluBI	AGCT	8 cut(s)	208, 482, 514, 545, 671, 683, 695, 770
AluI	AGCT	8 cut(s)	208, 482, 514, 545, 671, 683, 695, 770
Alw21I	GWGCWC	3 cut(s)	265, 772, 796
Alw26I	GTCTC	2 cut(s)	41, 940
AlwI	GGATC	2 cut(s)	377, 613
AlwNI	CAGNNNCTG	1 cut(s)	889
Ama87I	CYCGRG	1 cut(s)	632
Aor13HI	TCCGGA	1 cut(s)	309
AoxI	GGCC	1 cut(s)	357
ApeKI	GCWGC	7 cut(s)	222, 225, 228, 231, 234, 542, 688
ApoI	RAATTY	3 cut(s)	340, 929, 970
AspLEI	GCGC	1 cut(s)	187
AspS9I	GGNCC	2 cut(s)	358, 499
AsuHPI	GGTGA	4 cut(s)	359, 842, 922, 1028
AsuII	TTCGAA	1 cut(s)	211
AvaI	CYCGRG	1 cut(s)	632
AvaII	GGWCC	1 cut(s)	499
AxyI	CCTNAGG	1 cut(s)	420
BaeI	ACNNNNGTAYC	2 cut(s)	564, 597
BanII	GRGCYC	1 cut(s)	772
Bbv12I	GWGCWC	3 cut(s)	265, 772, 796
BbvI	GCAGC	7 cut(s)	234, 237, 240, 243, 246, 554, 675
BccI	CCATC	2 cut(s)	635, 695
BciT130I	CCWGG	4 cut(s)	44, 603, 663, 827
BciVI	GTATCC	1 cut(s)	565
BcoDI	GTCTC	2 cut(s)	41, 940
BfaI	CTAG	1 cut(s)	668
BfuAI	ACCTGC	1 cut(s)	844
BfuI	GTATCC	1 cut(s)	565
BisI	GCNGC	9 cut(s)	223, 226, 229, 232, 235, 238, 241, 543, 689
BlsI	GCNGC	9 cut(s)	224, 227, 230, 233, 236, 239, 242, 544, 690
Bme1390I	CCNGG	4 cut(s)	44, 603, 663, 827
Bme18I	GGWCC	1 cut(s)	499
BmeT110I	CYCGRG	1 cut(s)	632
BmgT120I	GGNCC	2 cut(s)	358, 499
BmiI	GGNNCC	1 cut(s)	589
BmrFI	CCNGG	4 cut(s)	44, 603, 663, 827
BmrI	ACTGGG	1 cut(s)	743
BmsI	GCATC	2 cut(s)	656, 973
BmuI	ACTGGG	1 cut(s)	743
BoxI	GACNNNNGTC	1 cut(s)	194
BpmI	CTGGAG	3 cut(s)	65, 72, 699
Bpu14I	TTCGAA	1 cut(s)	211
BpuEI	CTTGAG	2 cut(s)	782, 972
BsaHI	GRCGYC	1 cut(s)	251
BsaJI	CCNNGG	1 cut(s)	826
BsaWI	WCCGGW	1 cut(s)	309
BsaXI	ACNNNNNCTCC	4 cut(s)	100, 130, 309, 339
Bsc4I	CCNNNNNNNGG	1 cut(s)	43
Bse1I	ACTGG	2 cut(s)	55, 738
Bse21I	CCTNAGG	1 cut(s)	420
Bse3DI	GCAATG	1 cut(s)	282
BseAI	TCCGGA	1 cut(s)	309
BseBI	CCWGG	4 cut(s)	44, 603, 663, 827
BseDI	CCNNGG	1 cut(s)	826
BseLI	CCNNNNNNNGG	1 cut(s)	43
BseMI	GCAATG	1 cut(s)	282
BseMII	CTCAG	2 cut(s)	750, 950
BseNI	ACTGG	2 cut(s)	55, 738
BseRI	GAGGAG	1 cut(s)	43
BseXI	GCAGC	7 cut(s)	234, 237, 240, 243, 246, 554, 675
BshFI	GGCC	1 cut(s)	359
BsiHKAI	GWGCWC	3 cut(s)	265, 772, 796
BsiHKCI	CYCGRG	1 cut(s)	632
BsiSI	CCGG	1 cut(s)	310
BslFI	GGGAC	1 cut(s)	977
BslI	CCNNNNNNNGG	1 cut(s)	43
BsmAI	GTCTC	2 cut(s)	41, 940
BsmFI	GGGAC	1 cut(s)	977
BsnI	GGCC	1 cut(s)	359
BsoBI	CYCGRG	1 cut(s)	632
Bsp119I	TTCGAA	1 cut(s)	211
Bsp1286I	GDGCHC	3 cut(s)	265, 772, 796
Bsp13I	TCCGGA	1 cut(s)	309
Bsp1407I	TGTACA	1 cut(s)	399
Bsp143I	GATC	4 cut(s)	382, 605, 711, 945
BspACI	CCGC	3 cut(s)	153, 238, 241
BspANI	GGCC	1 cut(s)	359
BspCNI	CTCAG	2 cut(s)	751, 951
BspEI	TCCGGA	1 cut(s)	309
BspHI	TCATGA	2 cut(s)	532, 724
BspLI	GGNNCC	1 cut(s)	589
BspMI	ACCTGC	1 cut(s)	844
BspPI	GGATC	2 cut(s)	377, 613
BspT104I	TTCGAA	1 cut(s)	211
BsrDI	GCAATG	1 cut(s)	282
BsrGI	TGTACA	1 cut(s)	399
BsrI	ACTGG	2 cut(s)	55, 738
BssECI	CCNNGG	1 cut(s)	826
BssMI	GATC	4 cut(s)	382, 605, 711, 945
BssNI	GRCGYC	1 cut(s)	251
Bst2UI	CCWGG	4 cut(s)	44, 603, 663, 827
Bst4CI	ACNGT	2 cut(s)	353, 587
Bst6I	CTCTTC	4 cut(s)	19, 118, 552, 900
BstACI	GRCGYC	1 cut(s)	251
BstAUI	TGTACA	1 cut(s)	399
BstBI	TTCGAA	1 cut(s)	211
BstC8I	GCNNGC	3 cut(s)	512, 540, 693
BstDEI	CTNAG	4 cut(s)	420, 759, 959, 1010
BstHHI	GCGC	1 cut(s)	187
BstKTI	GATC	4 cut(s)	385, 608, 714, 948
BstMAI	GTCTC	2 cut(s)	41, 940
BstMBI	GATC	4 cut(s)	382, 605, 711, 945
BstMWI	GCNNNNNNNGC	6 cut(s)	228, 231, 234, 237, 240, 998
BstNI	CCWGG	4 cut(s)	44, 603, 663, 827
BstPAI	GACNNNNGTC	1 cut(s)	194
BstSCI	CCNGG	4 cut(s)	42, 601, 661, 825
BstV1I	GCAGC	7 cut(s)	234, 237, 240, 243, 246, 554, 675
Bsu36I	CCTNAGG	1 cut(s)	420
BsuI	GTATCC	1 cut(s)	565
BsuRI	GGCC	1 cut(s)	359
BtsIMutI	CAGTG	1 cut(s)	426
BveI	ACCTGC	1 cut(s)	844
Cac8I	GCNNGC	3 cut(s)	512, 540, 693
CaiI	CAGNNNCTG	1 cut(s)	889
CciI	TCATGA	2 cut(s)	532, 724
CfoI	GCGC	1 cut(s)	187
Cfr13I	GGNCC	2 cut(s)	358, 499
Csp6I	GTAC	5 cut(s)	82, 96, 400, 627, 763
CspCI	CAANNNNNGTGG	2 cut(s)	264, 299
CviAII	CATG	4 cut(s)	200, 533, 725, 953
CviQI	GTAC	5 cut(s)	82, 96, 400, 627, 763
DdeI	CTNAG	4 cut(s)	420, 759, 959, 1010
DpnI	GATC	4 cut(s)	384, 607, 713, 947
DpnII	GATC	4 cut(s)	382, 605, 711, 945
Eam1104I	CTCTTC	4 cut(s)	19, 118, 552, 900
EarI	CTCTTC	4 cut(s)	19, 118, 552, 900
Ecl136II	GAGCTC	1 cut(s)	770
Eco24I	GRGCYC	1 cut(s)	772
Eco47I	GGWCC	1 cut(s)	499
Eco53kI	GAGCTC	1 cut(s)	770
Eco57I	CTGAAG	3 cut(s)	450, 504, 531
Eco81I	CCTNAGG	1 cut(s)	420
Eco88I	CYCGRG	1 cut(s)	632
EcoICRI	GAGCTC	1 cut(s)	770
EcoRII	CCWGG	4 cut(s)	42, 601, 661, 825
EcoT38I	GRGCYC	1 cut(s)	772
FaeI	CATG	4 cut(s)	203, 536, 728, 956
FalI	AAGNNNNNCTT	2 cut(s)	423, 455
FaqI	GGGAC	1 cut(s)	977
FatI	CATG	4 cut(s)	199, 532, 724, 952
Fnu4HI	GCNGC	9 cut(s)	223, 226, 229, 232, 235, 238, 241, 543, 689
FriOI	GRGCYC	1 cut(s)	772
Fsp4HI	GCNGC	9 cut(s)	223, 226, 229, 232, 235, 238, 241, 543, 689
FspBI	CTAG	1 cut(s)	668
GlaI	GCGC	1 cut(s)	186
GluI	GCNGC	9 cut(s)	223, 226, 229, 232, 235, 238, 241, 543, 689
GsuI	CTGGAG	3 cut(s)	65, 72, 699
HaeIII	GGCC	1 cut(s)	359
HapII	CCGG	1 cut(s)	310
HhaI	GCGC	1 cut(s)	187
Hin1I	GRCGYC	1 cut(s)	251
Hin1II	CATG	4 cut(s)	203, 536, 728, 956
Hin6I	GCGC	1 cut(s)	185
HinP1I	GCGC	1 cut(s)	185
HincII	GTYRAC	1 cut(s)	178
HindII	GTYRAC	1 cut(s)	178
HindIII	AAGCTT	1 cut(s)	512
HinfI	GANTC	6 cut(s)	195, 560, 817, 822, 833, 886
HpaII	CCGG	1 cut(s)	310
HphI	GGTGA	4 cut(s)	359, 842, 922, 1028
Hpy166II	GTNNAC	4 cut(s)	84, 178, 400, 583
Hpy188III	TCNNGA	5 cut(s)	310, 533, 725, 742, 799
Hpy8I	GTNNAC	4 cut(s)	84, 178, 400, 583
Hpy99I	CGWCG	3 cut(s)	91, 253, 256
HpyAV	CCTTC	4 cut(s)	129, 722, 865, 907
HpyCH4III	ACNGT	2 cut(s)	353, 587
HpyCH4IV	ACGT	2 cut(s)	75, 251
HpyCH4V	TGCA	3 cut(s)	464, 647, 853
HpyF10VI	GCNNNNNNNGC	6 cut(s)	228, 231, 234, 237, 240, 998
HpyF3I	CTNAG	4 cut(s)	420, 759, 959, 1010
HpySE526I	ACGT	2 cut(s)	75, 251
Hsp92I	GRCGYC	1 cut(s)	251
Hsp92II	CATG	4 cut(s)	203, 536, 728, 956
HspAI	GCGC	1 cut(s)	185
Kpn2I	TCCGGA	1 cut(s)	309
Kzo9I	GATC	4 cut(s)	382, 605, 711, 945
LmnI	GCTCC	1 cut(s)	680
Lsp1109I	GCAGC	7 cut(s)	234, 237, 240, 243, 246, 554, 675
LweI	GCATC	2 cut(s)	656, 973
MaeI	CTAG	1 cut(s)	668
MaeII	ACGT	2 cut(s)	75, 251
MaeIII	GTNAC	5 cut(s)	32, 69, 347, 407, 565
MalI	GATC	4 cut(s)	384, 607, 713, 947
MboI	GATC	4 cut(s)	382, 605, 711, 945
MboII	GAAGA	9 cut(s)	6, 105, 114, 117, 363, 443, 497, 569, 917
MhlI	GDGCHC	3 cut(s)	265, 772, 796
MluCI	AATT	5 cut(s)	159, 340, 465, 929, 970
MlyI	GAGTC	3 cut(s)	204, 569, 831
MnlI	CCTC	8 cut(s)	21, 121, 349, 396, 641, 901, 954, 970
MroI	TCCGGA	1 cut(s)	309
MseI	TTAA	2 cut(s)	162, 785
MspA1I	CMGCKG	1 cut(s)	155
MspI	CCGG	1 cut(s)	310
MspR9I	CCNGG	4 cut(s)	44, 603, 663, 827
MvaI	CCWGG	4 cut(s)	44, 603, 663, 827
MwoI	GCNNNNNNNGC	6 cut(s)	228, 231, 234, 237, 240, 998
NdeII	GATC	4 cut(s)	382, 605, 711, 945
NlaIII	CATG	4 cut(s)	203, 536, 728, 956
NlaIV	GGNNCC	1 cut(s)	589
NmuCI	GTSAC	3 cut(s)	69, 347, 565
NspV	TTCGAA	1 cut(s)	211
PaeR7I	CTCGAG	1 cut(s)	632
PagI	TCATGA	2 cut(s)	532, 724
PfeI	GAWTC	3 cut(s)	817, 833, 886
PfoI	TCCNGGA	1 cut(s)	661
PkrI	GCNGC	9 cut(s)	224, 227, 230, 233, 236, 239, 242, 544, 690
PleI	GAGTC	3 cut(s)	203, 568, 830
PpsI	GAGTC	3 cut(s)	203, 568, 830
PshAI	GACNNNNGTC	1 cut(s)	194
Psp124BI	GAGCTC	1 cut(s)	772
Psp6I	CCWGG	4 cut(s)	42, 601, 661, 825
PspGI	CCWGG	4 cut(s)	42, 601, 661, 825
PspN4I	GGNNCC	1 cut(s)	589
PspPI	GGNCC	2 cut(s)	358, 499
PspXI	VCTCGAGB	1 cut(s)	632
PstNI	CAGNNNCTG	1 cut(s)	889
RsaI	GTAC	5 cut(s)	83, 97, 401, 628, 764
RsaNI	GTAC	5 cut(s)	82, 96, 400, 627, 763
SacI	GAGCTC	1 cut(s)	772
SaqAI	TTAA	2 cut(s)	162, 785
SatI	GCNGC	9 cut(s)	223, 226, 229, 232, 235, 238, 241, 543, 689
Sau3AI	GATC	4 cut(s)	382, 605, 711, 945
Sau96I	GGNCC	2 cut(s)	358, 499
SchI	GAGTC	3 cut(s)	204, 569, 831
ScrFI	CCNGG	4 cut(s)	44, 603, 663, 827
SduI	GDGCHC	3 cut(s)	265, 772, 796
SfaNI	GCATC	2 cut(s)	656, 973
Sfr274I	CTCGAG	1 cut(s)	632
SfuI	TTCGAA	1 cut(s)	211
SinI	GGWCC	1 cut(s)	499
SlaI	CTCGAG	1 cut(s)	632
SmlI	CTYRAG	3 cut(s)	632, 797, 987
SmoI	CTYRAG	3 cut(s)	632, 797, 987
Sse9I	AATT	5 cut(s)	159, 340, 465, 929, 970
SsiI	CCGC	3 cut(s)	153, 238, 241
SspMI	CTAG	1 cut(s)	668
SstI	GAGCTC	1 cut(s)	772
StyD4I	CCNGG	4 cut(s)	42, 601, 661, 825
TaaI	ACNGT	2 cut(s)	353, 587
TaiI	ACGT	2 cut(s)	78, 254
TaqI	TCGA	4 cut(s)	211, 374, 633, 820
TasI	AATT	5 cut(s)	159, 340, 465, 929, 970
TatI	WGTACW	1 cut(s)	399
TauI	GCSGC	2 cut(s)	240, 243
TfiI	GAWTC	3 cut(s)	817, 833, 886
Tru1I	TTAA	2 cut(s)	162, 785
Tru9I	TTAA	2 cut(s)	162, 785
TscAI	CASTG	1 cut(s)	433
TseFI	GTSAC	3 cut(s)	69, 347, 565
TseI	GCWGC	7 cut(s)	222, 225, 228, 231, 234, 542, 688
Tsp45I	GTSAC	3 cut(s)	69, 347, 565
TspDTI	ATGAA	6 cut(s)	17, 74, 521, 609, 713, 741
TspGWI	ACGGA	1 cut(s)	584
TspRI	CASTG	1 cut(s)	433
VpaK11BI	GGWCC	1 cut(s)	499
XapI	RAATTY	3 cut(s)	340, 929, 970
XhoI	CTCGAG	1 cut(s)	632
XspI	CTAG	1 cut(s)	668
ZraI	GACGTC	1 cut(s)	252

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