Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0006954

Physical Location & Seq

Genomic Coordinates Forward (+)

23960300 .. 23965300

Gene Structure 5001 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG110900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 765 bp

ATGTACCTGTTTCTCCCTCTGCAATGGATTGGCATGAATGCTATGCTTGTCTACGTTATGGCAGCTGAAGGTTGTGCTCTGCGTTTTAGGGGTCTTTACCTTGCAACTGCTGACACAGTGATCATATATGATAGTGATTGGAATCCTCATGCAGATCTACAAGCTATGGCAAGAGCTCATCGACTTGGGCAAACTAACAAGGTGATGATTTATAGGCTAATAACACGAGGAACAATTGAAGAAAGAATGATGCAACTGACTAAGAAGAAAATGGAAGAGCTAGATGATATCATTCGATACGGATCAAAGGAGTTATTTGCTGATGAAAATGATGAAGCGGGAAAATCCCGTCAAATTCATTATGATGATGCTGCGATAGAGAGATTACTTGATCGTGAACAAGCTGGGGATGATGACACTCCGTTGGAGGAAGGAGATGAAGATGGATTTTTAAAGGCCTTTAAGCATGAATTGAAATCTACTGAAGTGACCATACGGAAAGATAAGAACGAAGAAGAAGAAGCAAAGGTCATCTCCAACCCAATAAGAAGTCCAGTTCAGTCCAGGCCTTTCACTGTCACTATCAGCAGTTCCCAACTCCAACGAGTTCGGTTCCTCTATCGCTGGCATTTGGTGTTCAAAGTCACACCAATCGAGGAGGATAGACTCCTTGGAGGCCGGTTGGACCAGTTGGGTTTCAGACCTCGGAGCAACGACGTCGTGGCATTGAACGAGAAGCACCGGCAGAGGCGATGGCGCCGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001101 GO:0003674 GO:0003676 GO:0003677 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006325 GO:0006338 GO:0006355 GO:0006996 GO:0007154 GO:0007165 GO:0007275 GO:0008150 GO:0008283 GO:0009719 GO:0009725 GO:0009733 GO:0009735 GO:0009736 GO:0009739 GO:0009755 GO:0009787 GO:0009788 GO:0009889 GO:0009890 GO:0009892 GO:0009966 GO:0009968 GO:0009987 GO:0010033 GO:0010468 GO:0010556 GO:0010558 GO:0010605 GO:0010629 GO:0010646 GO:0010648 GO:0016043 GO:0019219 GO:0019222 GO:0022622 GO:0023051 GO:0023052 GO:0023057 GO:0031323 GO:0031324 GO:0031326 GO:0031327 GO:0032501 GO:0032502 GO:0032870 GO:0033993 GO:0042221 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0045892 GO:0045934 GO:0048364 GO:0048519 GO:0048523 GO:0048580 GO:0048583 GO:0048585 GO:0048731 GO:0048856 GO:0050789 GO:0050793 GO:0050794 GO:0050896 GO:0051171 GO:0051172 GO:0051239 GO:0051252 GO:0051253 GO:0051276 GO:0051716 GO:0060255 GO:0065007 GO:0070887 GO:0071310 GO:0071368 GO:0071495 GO:0071840 GO:0080090 GO:0097159 GO:0099402 GO:1901363 GO:1901419 GO:1901420 GO:1901700 GO:1902679 GO:1903506 GO:1903507 GO:1905957 GO:1905958 GO:2000023 GO:2000026 GO:2000069 GO:2000112 GO:2000113 GO:2000280 GO:2001141

KEGG Pathways

Metabolic & Signaling

ko05165 ko05203 map05165 map05203

Pfam Domains

Protein Families

CHDCT2 Chromo DUF1086 DUF1087 Helicase_C PHD SNF2_N

Protein Analysis

254

Amino Acids

29.72

Weight (kDa)

6.34

Isoelectric Point (pI)

55.25

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Helicase_C	PF00271	30 - 63	1.4e-06	Helicase conserved C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0006954)

Species	Orthologous Gene IDs
malus_domestica	MD09G1111500.v1.1 MD13G1012800.v1.1 MD14G1086800.v1.1
pyrus_communis	pycom16g23680
rosa_chinensis	RchiOBHm_Chr1g0327391 RchiOBHm_Chr2g0095571 RchiOBHm_Chr2g0161621 RchiOBHm_Chr2g0171851 RchiOBHm_Chr3g0494951 RchiOBHm_Chr4g0407971
rosa_multiflora	Rmu_co8049090.1_g000001 Rmu_sc0003610.1_g000015
rosa_roxburghii	Rroxscaffold_1G00001900 Rroxscaffold_1G00039140 Rroxscaffold_6G00388120
rosa_rugosa	Rorug02G0632300
rosa_samantha	Rh3AG069600 Rh3AG317900 Rh3BG072000 Rh3DG252300 Rh4AG109100 Rh4AG110900 Rh4CG284900 Rh6AG114600 Rh7AG464100
rosa_wichuraiana	Rw5G002470

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	720
AccB1I	GGYRCC	1 cut(s)	756
AccI	GTMKAC	1 cut(s)	51
AciI	CCGC	1 cut(s)	338
AclWI	GGATC	1 cut(s)	310
AcsI	RAATTY	1 cut(s)	354
AcuI	CTGAAG	2 cut(s)	87, 504
AcyI	GRCGYC	2 cut(s)	717, 757
AfaI	GTAC	1 cut(s)	5
AgsI	TTSAA	4 cut(s)	239, 475, 640, 730
AjnI	CCWGG	1 cut(s)	563
AluBI	AGCT	5 cut(s)	65, 164, 176, 280, 404
AluI	AGCT	5 cut(s)	65, 164, 176, 280, 404
Alw21I	GWGCWC	2 cut(s)	79, 178
AlwI	GGATC	1 cut(s)	310
AoxI	GGCC	3 cut(s)	456, 566, 676
ApeKI	GCWGC	2 cut(s)	62, 371
ApoI	RAATTY	1 cut(s)	354
AspLEI	GCGC	1 cut(s)	759
AspS9I	GGNCC	1 cut(s)	685
AsuHPI	GGTGA	1 cut(s)	214
AvaII	GGWCC	1 cut(s)	685
BanI	GGYRCC	1 cut(s)	756
BanII	GRGCYC	1 cut(s)	178
BarI	GAAGNNNNNNTAC	2 cut(s)	477, 509
BauI	CACGAG	1 cut(s)	225
Bbv12I	GWGCWC	2 cut(s)	79, 178
BbvI	GCAGC	2 cut(s)	74, 358
BccI	CCATC	2 cut(s)	437, 747
BcgI	CGANNNNNNTGC	2 cut(s)	700, 734
BciT130I	CCWGG	1 cut(s)	565
BclI	TGATCA	1 cut(s)	120
BfaI	CTAG	1 cut(s)	281
BfoI	RGCGCY	1 cut(s)	760
BglII	AGATCT	1 cut(s)	154
BisI	GCNGC	2 cut(s)	63, 372
BlsI	GCNGC	2 cut(s)	64, 373
Bme1390I	CCNGG	1 cut(s)	565
Bme18I	GGWCC	1 cut(s)	685
BmgT120I	GGNCC	1 cut(s)	685
BmiI	GGNNCC	2 cut(s)	614, 758
BmrFI	CCNGG	1 cut(s)	565
BmsI	GCATC	2 cut(s)	240, 358
BsaBI	GATNNNNATC	2 cut(s)	141, 301
BsaHI	GRCGYC	2 cut(s)	717, 757
BsaJI	CCNNGG	2 cut(s)	670, 704
Bse118I	RCCGGY	3 cut(s)	678, 741, 759
Bse1I	ACTGG	2 cut(s)	554, 688
Bse3DI	GCAATG	1 cut(s)	29
Bse8I	GATNNNNATC	2 cut(s)	141, 301
BseBI	CCWGG	1 cut(s)	565
BseDI	CCNNGG	2 cut(s)	670, 704
BseGI	GGATG	1 cut(s)	415
BseJI	GATNNNNATC	2 cut(s)	141, 301
BseMI	GCAATG	1 cut(s)	29
BseNI	ACTGG	2 cut(s)	554, 688
BseRI	GAGGAG	1 cut(s)	671
BseXI	GCAGC	2 cut(s)	74, 358
BseYI	CCCAGC	1 cut(s)	404
BshFI	GGCC	3 cut(s)	458, 568, 678
BshNI	GGYRCC	1 cut(s)	756
BsiHKAI	GWGCWC	2 cut(s)	79, 178
BsiSI	CCGG	3 cut(s)	679, 742, 760
BsmI	GAATGC	1 cut(s)	43
BsnI	GGCC	3 cut(s)	458, 568, 678
Bsp1286I	GDGCHC	2 cut(s)	79, 178
Bsp143I	GATC	4 cut(s)	120, 154, 302, 391
BspACI	CCGC	1 cut(s)	338
BspANI	GGCC	3 cut(s)	458, 568, 678
BspLI	GGNNCC	2 cut(s)	614, 758
BspPI	GGATC	1 cut(s)	310
BspQI	GCTCTTC	1 cut(s)	270
BspT107I	GGYRCC	1 cut(s)	756
BsrDI	GCAATG	1 cut(s)	29
BsrFI	RCCGGY	3 cut(s)	678, 741, 759
BsrI	ACTGG	2 cut(s)	554, 688
BssAI	RCCGGY	3 cut(s)	678, 741, 759
BssECI	CCNNGG	2 cut(s)	670, 704
BssMI	GATC	4 cut(s)	120, 154, 302, 391
BssNI	GRCGYC	2 cut(s)	717, 757
BssSI	CACGAG	1 cut(s)	225
BssT1I	CCWWGG	1 cut(s)	670
Bst2BI	CACGAG	1 cut(s)	225
Bst2UI	CCWGG	1 cut(s)	565
Bst4CI	ACNGT	2 cut(s)	118, 577
Bst6I	CTCTTC	1 cut(s)	270
BstACI	GRCGYC	2 cut(s)	717, 757
BstC8I	GCNNGC	1 cut(s)	626
BstDEI	CTNAG	1 cut(s)	261
BstF5I	GGATG	1 cut(s)	415
BstH2I	RGCGCY	1 cut(s)	760
BstHHI	GCGC	1 cut(s)	759
BstKTI	GATC	4 cut(s)	123, 157, 305, 394
BstMBI	GATC	4 cut(s)	120, 154, 302, 391
BstNI	CCWGG	1 cut(s)	565
BstSCI	CCNGG	1 cut(s)	563
BstV1I	GCAGC	2 cut(s)	74, 358
BstX2I	RGATCY	1 cut(s)	154
BstYI	RGATCY	1 cut(s)	154
BsuRI	GGCC	3 cut(s)	458, 568, 678
BtsCI	GGATG	1 cut(s)	415
BtsIMutI	CAGTG	2 cut(s)	123, 573
Cac8I	GCNNGC	1 cut(s)	626
CfoI	GCGC	1 cut(s)	759
Cfr10I	RCCGGY	3 cut(s)	678, 741, 759
Cfr13I	GGNCC	1 cut(s)	685
Csp6I	GTAC	1 cut(s)	4
CviAII	CATG	3 cut(s)	34, 149, 467
CviJI	RGCY	9 cut(s)	65, 164, 176, 217, 280, 404, 458, 568, 678
CviKI_1	RGCY	9 cut(s)	65, 164, 176, 217, 280, 404, 458, 568, 678
CviQI	GTAC	1 cut(s)	4
DdeI	CTNAG	1 cut(s)	261
DinI	GGCGCC	1 cut(s)	758
DpnI	GATC	4 cut(s)	122, 156, 304, 393
DpnII	GATC	4 cut(s)	120, 154, 302, 391
DraI	TTTAAA	1 cut(s)	453
Eam1104I	CTCTTC	1 cut(s)	270
EarI	CTCTTC	1 cut(s)	270
Ecl136II	GAGCTC	1 cut(s)	176
Eco130I	CCWWGG	1 cut(s)	670
Eco147I	AGGCCT	2 cut(s)	458, 568
Eco24I	GRGCYC	1 cut(s)	178
Eco32I	GATATC	1 cut(s)	289
Eco47I	GGWCC	1 cut(s)	685
Eco53kI	GAGCTC	1 cut(s)	176
Eco57I	CTGAAG	2 cut(s)	87, 504
EcoICRI	GAGCTC	1 cut(s)	176
EcoRII	CCWGG	1 cut(s)	563
EcoRV	GATATC	1 cut(s)	289
EcoT14I	CCWWGG	1 cut(s)	670
EcoT38I	GRGCYC	1 cut(s)	178
EgeI	GGCGCC	1 cut(s)	758
EheI	GGCGCC	1 cut(s)	758
ErhI	CCWWGG	1 cut(s)	670
FaeI	CATG	3 cut(s)	37, 152, 470
FatI	CATG	3 cut(s)	33, 148, 466
FauI	CCCGC	1 cut(s)	331
FbaI	TGATCA	1 cut(s)	120
FblI	GTMKAC	1 cut(s)	51
Fnu4HI	GCNGC	2 cut(s)	63, 372
FokI	GGATG	1 cut(s)	422
FriOI	GRGCYC	1 cut(s)	178
Fsp4HI	GCNGC	2 cut(s)	63, 372
FspBI	CTAG	1 cut(s)	281
GlaI	GCGC	1 cut(s)	758
GluI	GCNGC	2 cut(s)	63, 372
GsaI	CCCAGC	1 cut(s)	408
HaeII	RGCGCY	1 cut(s)	760
HaeIII	GGCC	3 cut(s)	458, 568, 678
HapII	CCGG	3 cut(s)	679, 742, 760
HhaI	GCGC	1 cut(s)	759
Hin1I	GRCGYC	2 cut(s)	717, 757
Hin1II	CATG	3 cut(s)	37, 152, 470
Hin6I	GCGC	1 cut(s)	757
HinP1I	GCGC	1 cut(s)	757
HinfI	GANTC	2 cut(s)	142, 666
HpaII	CCGG	3 cut(s)	679, 742, 760
HphI	GGTGA	1 cut(s)	214
Hpy166II	GTNNAC	2 cut(s)	52, 398
Hpy188I	TCNGA	2 cut(s)	701, 708
Hpy188III	TCNNGA	1 cut(s)	395
Hpy8I	GTNNAC	2 cut(s)	52, 398
Hpy99I	CGWCG	2 cut(s)	719, 722
HpyAV	CCTTC	2 cut(s)	62, 425
HpyCH4III	ACNGT	2 cut(s)	118, 577
HpyCH4IV	ACGT	2 cut(s)	54, 717
HpyCH4V	TGCA	4 cut(s)	22, 104, 152, 253
HpyF3I	CTNAG	1 cut(s)	261
HpySE526I	ACGT	2 cut(s)	54, 717
Hsp92I	GRCGYC	2 cut(s)	717, 757
Hsp92II	CATG	3 cut(s)	37, 152, 470
HspAI	GCGC	1 cut(s)	757
KasI	GGCGCC	1 cut(s)	756
Ksp22I	TGATCA	1 cut(s)	120
Kzo9I	GATC	4 cut(s)	120, 154, 302, 391
LguI	GCTCTTC	1 cut(s)	270
LmnI	GCTCC	1 cut(s)	708
LpnPI	CCDG	9 cut(s)	20, 390, 550, 567, 577, 610, 692, 701, 755
Lsp1109I	GCAGC	2 cut(s)	74, 358
LweI	GCATC	2 cut(s)	240, 358
MaeI	CTAG	1 cut(s)	281
MaeII	ACGT	2 cut(s)	54, 717
MaeIII	GTNAC	3 cut(s)	487, 577, 643
MalI	GATC	4 cut(s)	122, 156, 304, 393
MboI	GATC	4 cut(s)	120, 154, 302, 391
MboII	GAAGA	7 cut(s)	251, 277, 287, 452, 524, 527, 530
MfeI	CAATTG	1 cut(s)	234
MflI	RGATCY	1 cut(s)	154
MhlI	GDGCHC	2 cut(s)	79, 178
MluCI	AATT	3 cut(s)	234, 354, 470
Mly113I	GGCGCC	1 cut(s)	757
MlyI	GAGTC	1 cut(s)	660
MmeI	TCCRAC	4 cut(s)	405, 561, 625, 663
MseI	TTAA	2 cut(s)	452, 462
MslI	CAYNNNNRTG	1 cut(s)	363
MspA1I	CMGCKG	1 cut(s)	65
MspI	CCGG	3 cut(s)	679, 742, 760
MspR9I	CCNGG	1 cut(s)	565
MunI	CAATTG	1 cut(s)	234
Mva1269I	GAATGC	1 cut(s)	43
MvaI	CCWGG	1 cut(s)	565
NarI	GGCGCC	1 cut(s)	757
NdeII	GATC	4 cut(s)	120, 154, 302, 391
NlaIII	CATG	3 cut(s)	37, 152, 470
NlaIV	GGNNCC	2 cut(s)	614, 758
NmuCI	GTSAC	3 cut(s)	487, 577, 643
PceI	AGGCCT	2 cut(s)	458, 568
PciSI	GCTCTTC	1 cut(s)	270
PctI	GAATGC	1 cut(s)	43
PfeI	GAWTC	1 cut(s)	142
PkrI	GCNGC	2 cut(s)	64, 373
PleI	GAGTC	1 cut(s)	660
PluTI	GGCGCC	1 cut(s)	760
PpsI	GAGTC	1 cut(s)	660
Psp124BI	GAGCTC	1 cut(s)	178
Psp6I	CCWGG	1 cut(s)	563
PspFI	CCCAGC	1 cut(s)	404
PspGI	CCWGG	1 cut(s)	563
PspN4I	GGNNCC	2 cut(s)	614, 758
PspPI	GGNCC	1 cut(s)	685
PsuI	RGATCY	1 cut(s)	154
PvuII	CAGCTG	1 cut(s)	65
RsaI	GTAC	1 cut(s)	5
RsaNI	GTAC	1 cut(s)	4
RseI	CAYNNNNRTG	1 cut(s)	363
SacI	GAGCTC	1 cut(s)	178
SapI	GCTCTTC	1 cut(s)	270
SaqAI	TTAA	2 cut(s)	452, 462
SatI	GCNGC	2 cut(s)	63, 372
Sau3AI	GATC	4 cut(s)	120, 154, 302, 391
Sau96I	GGNCC	1 cut(s)	685
SchI	GAGTC	1 cut(s)	660
ScrFI	CCNGG	1 cut(s)	565
SduI	GDGCHC	2 cut(s)	79, 178
SfaNI	GCATC	2 cut(s)	240, 358
SfoI	GGCGCC	1 cut(s)	758
SgrAI	CRCCGGYG	1 cut(s)	759
SinI	GGWCC	1 cut(s)	685
SmiMI	CAYNNNNRTG	1 cut(s)	363
Sse9I	AATT	3 cut(s)	234, 354, 470
SseBI	AGGCCT	2 cut(s)	458, 568
SsiI	CCGC	1 cut(s)	338
SspDI	GGCGCC	1 cut(s)	756
SspMI	CTAG	1 cut(s)	281
SstI	GAGCTC	1 cut(s)	178
StuI	AGGCCT	2 cut(s)	458, 568
StyD4I	CCNGG	1 cut(s)	563
StyI	CCWWGG	1 cut(s)	670
TaaI	ACNGT	2 cut(s)	118, 577
TaiI	ACGT	2 cut(s)	57, 720
TaqI	TCGA	3 cut(s)	181, 295, 654
TasI	AATT	3 cut(s)	234, 354, 470
TfiI	GAWTC	1 cut(s)	142
Tru1I	TTAA	2 cut(s)	452, 462
Tru9I	TTAA	2 cut(s)	452, 462
TscAI	CASTG	2 cut(s)	123, 580
TseFI	GTSAC	3 cut(s)	487, 577, 643
TseI	GCWGC	2 cut(s)	62, 371
Tsp45I	GTSAC	3 cut(s)	487, 577, 643
TspDTI	ATGAA	6 cut(s)	50, 339, 347, 348, 453, 483
TspGWI	ACGGA	3 cut(s)	315, 411, 511
TspRI	CASTG	2 cut(s)	123, 580
VpaK11BI	GGWCC	1 cut(s)	685
XapI	RAATTY	1 cut(s)	354
XmiI	GTMKAC	1 cut(s)	51
XspI	CTAG	1 cut(s)	281
ZraI	GACGTC	1 cut(s)	718

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