Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0001009

Physical Location & Seq

Genomic Coordinates Forward (+)

44026825 .. 44042948

Gene Structure 16124 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG318500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 543 bp

ATGATGCAACTGACTAAGAAGAAAATGGTATTGGAACATTTAGTTGTTGGAAGGTTAAAGGCTCGAAACATCAACCAGGAAGAGCTAGATGATATCATTCGATACGGATCAAAGGAGTTATTTGCTGATGAAAATGATGAAGCGGGAAAATCCCGTCAAATTCATTATGATGATGCTGCGATAGAGAGATTACTTGATCGTGAACAAGCTGGGGATGATGACACTCCGTTGGAGGAAGGAGATGAAGATGGATTTTTAAAGGCCTTTAAGGTTGCAAATTTTGAATACATTGACGAAGCAGAGGGCGTAGAAGAGGAGGAACCAAAAAAGGCTGCAGTTGACAGTAGTCCTACTGACAATGATAAATCAAATTTCTGGGAAGATTTGTTAAAGGACAGATATGAAGTGCATAAAGTTGAAGAATTAAACGCTTTAGGCAAAGGGAAGAGAAGTCGTAAGCAGGTGATGGTGTCCAAGCGGATCTTGAAAGAGCTCAAGGACCTCCAGAAAGATCCTCCTATCTCTTACAGAGTTGGTATTTGA

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

180

Amino Acids

20.75

Weight (kDa)

4.86

Isoelectric Point (pI)

41.35

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DUF1087	PF06465	104 - 159	6.1e-22	CHD subfamily II, DUF1087

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0001009)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_6g21872
rosa_chinensis	RchiOBHm_Chr2g0123681 RchiOBHm_Chr3g0479491 RchiOBHm_Chr3g0495041 RchiOBHm_Chr4g0441021 RchiOBHm_Chr5g0077811
rosa_laevigata	RLG00000002955 RLG00000006128 RLG00000014337 RLG00000017254 RLG00000017794 RLG00000018824 RLG00000020500 RLG00000021064 RLG00000022633 RLG00000023474 RLG00000034052 RLG00000034977 RLG00000035113
rosa_multiflora	Rmu_co7982184.1_g000001 Rmu_sc0001018.1_g000026 Rmu_sc0002302.1_g000019 Rmu_sc0004092.1_g000029 Rmu_sc0006432.1_g000003 Rmu_sc0014274.1_g000001 Rmu_sc0018911.1_g000009 Rmu_sc0028049.1_g000001
rosa_roxburghii	Rroxscaffold_1G00025310 Rroxscaffold_1G00070230 Rroxscaffold_2G00096810 Rroxscaffold_2G00096990 Rroxscaffold_3G00225320 Rroxscaffold_3G00247800 Rroxscaffold_3G00274690 Rroxscaffold_4G00297310 Rroxscaffold_4G00307210 Rroxscaffold_5G00336010 Rroxscaffold_5G00381920 Rroxscaffold_6G00398320
rosa_rugosa	Rorug02G0632200 Rorug07G0125300
rosa_samantha	Rh1AG414900 Rh1BG210400 Rh1CG235800 Rh2AG532500 Rh2BG232700 Rh2BG314600 Rh3AG318500 Rh3DG143100 Rh3DG252200 Rh4DG388600 Rh5AG088200 Rh5CG447300 Rh5DG116100 Rh6AG138700 Rh6BG076200 Rh6CG272500 Rh7AG212400 Rh7BG356600 Rh7BG449300 Rh7DG357700
rosa_wichuraiana	Rw6G042780

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	451
Acc36I	ACCTGC	1 cut(s)	451
AciI	CCGC	2 cut(s)	143, 478
AclWI	GGATC	3 cut(s)	115, 488, 506
AcsI	RAATTY	3 cut(s)	159, 277, 370
AgsI	TTSAA	3 cut(s)	284, 419, 487
AjnI	CCWGG	1 cut(s)	75
AjuI	GAANNNNNNNTTGG	2 cut(s)	14, 46
AluBI	AGCT	3 cut(s)	85, 209, 493
AluI	AGCT	3 cut(s)	85, 209, 493
Alw21I	GWGCWC	1 cut(s)	495
AlwI	GGATC	3 cut(s)	115, 488, 506
AoxI	GGCC	1 cut(s)	261
ApeKI	GCWGC	2 cut(s)	176, 332
ApoI	RAATTY	3 cut(s)	159, 277, 370
AspS9I	GGNCC	1 cut(s)	499
AsuHPI	GGTGA	1 cut(s)	475
AvaII	GGWCC	1 cut(s)	499
BanII	GRGCYC	1 cut(s)	495
Bbv12I	GWGCWC	1 cut(s)	495
BbvI	GCAGC	2 cut(s)	163, 319
BccI	CCATC	2 cut(s)	242, 460
BciT130I	CCWGG	1 cut(s)	77
BfaI	CTAG	1 cut(s)	86
BfmI	CTRYAG	1 cut(s)	333
BfuAI	ACCTGC	1 cut(s)	451
BisI	GCNGC	2 cut(s)	177, 333
BlsI	GCNGC	2 cut(s)	178, 334
Bme1390I	CCNGG	1 cut(s)	77
Bme18I	GGWCC	1 cut(s)	499
BmgT120I	GGNCC	1 cut(s)	499
BmiI	GGNNCC	1 cut(s)	321
BmrFI	CCNGG	1 cut(s)	77
BmsI	GCATC	1 cut(s)	163
BoxI	GACNNNNGTC	1 cut(s)	345
BpmI	CTGGAG	1 cut(s)	488
BpuEI	CTTGAG	1 cut(s)	479
BsaBI	GATNNNNATC	1 cut(s)	106
Bse8I	GATNNNNATC	1 cut(s)	106
BseBI	CCWGG	1 cut(s)	77
BseGI	GGATG	1 cut(s)	220
BseJI	GATNNNNATC	1 cut(s)	106
BseRI	GAGGAG	1 cut(s)	329
BseXI	GCAGC	2 cut(s)	163, 319
BseYI	CCCAGC	1 cut(s)	209
BshFI	GGCC	1 cut(s)	263
BsiHKAI	GWGCWC	1 cut(s)	495
BsnI	GGCC	1 cut(s)	263
Bsp1286I	GDGCHC	1 cut(s)	495
Bsp143I	GATC	4 cut(s)	107, 196, 480, 511
BspACI	CCGC	2 cut(s)	143, 478
BspANI	GGCC	1 cut(s)	263
BspLI	GGNNCC	1 cut(s)	321
BspMAI	CTGCAG	1 cut(s)	337
BspMI	ACCTGC	1 cut(s)	451
BspPI	GGATC	3 cut(s)	115, 488, 506
BspQI	GCTCTTC	1 cut(s)	75
BssMI	GATC	4 cut(s)	107, 196, 480, 511
Bst2UI	CCWGG	1 cut(s)	77
Bst4CI	ACNGT	1 cut(s)	344
Bst6I	CTCTTC	3 cut(s)	75, 306, 440
BstDEI	CTNAG	1 cut(s)	15
BstF5I	GGATG	1 cut(s)	220
BstKTI	GATC	4 cut(s)	110, 199, 483, 514
BstMBI	GATC	4 cut(s)	107, 196, 480, 511
BstNI	CCWGG	1 cut(s)	77
BstPAI	GACNNNNGTC	1 cut(s)	345
BstSCI	CCNGG	1 cut(s)	75
BstSFI	CTRYAG	1 cut(s)	333
BstV1I	GCAGC	2 cut(s)	163, 319
BstX2I	RGATCY	2 cut(s)	480, 511
BstYI	RGATCY	2 cut(s)	480, 511
BsuRI	GGCC	1 cut(s)	263
BtsCI	GGATG	1 cut(s)	220
BveI	ACCTGC	1 cut(s)	451
Cfr13I	GGNCC	1 cut(s)	499
CviJI	RGCY	6 cut(s)	62, 85, 209, 263, 332, 493
CviKI_1	RGCY	6 cut(s)	62, 85, 209, 263, 332, 493
DdeI	CTNAG	1 cut(s)	15
DpnI	GATC	4 cut(s)	109, 198, 482, 513
DpnII	GATC	4 cut(s)	107, 196, 480, 511
DraI	TTTAAA	1 cut(s)	258
Eam1104I	CTCTTC	3 cut(s)	75, 306, 440
EarI	CTCTTC	3 cut(s)	75, 306, 440
Ecl136II	GAGCTC	1 cut(s)	493
Eco147I	AGGCCT	1 cut(s)	263
Eco24I	GRGCYC	1 cut(s)	495
Eco32I	GATATC	1 cut(s)	94
Eco47I	GGWCC	1 cut(s)	499
Eco53kI	GAGCTC	1 cut(s)	493
EcoICRI	GAGCTC	1 cut(s)	493
EcoO109I	RGGNCCY	1 cut(s)	499
EcoRII	CCWGG	1 cut(s)	75
EcoRV	GATATC	1 cut(s)	94
EcoT38I	GRGCYC	1 cut(s)	495
FaiI	YATR	3 cut(s)	168, 402, 411
FalI	AAGNNNNNCTT	2 cut(s)	467, 499
FauI	CCCGC	1 cut(s)	136
Fnu4HI	GCNGC	2 cut(s)	177, 333
FokI	GGATG	1 cut(s)	227
FriOI	GRGCYC	1 cut(s)	495
Fsp4HI	GCNGC	2 cut(s)	177, 333
FspBI	CTAG	1 cut(s)	86
GluI	GCNGC	2 cut(s)	177, 333
GsaI	CCCAGC	1 cut(s)	213
GsuI	CTGGAG	1 cut(s)	488
HaeIII	GGCC	1 cut(s)	263
HincII	GTYRAC	1 cut(s)	340
HindII	GTYRAC	1 cut(s)	340
HphI	GGTGA	1 cut(s)	475
Hpy166II	GTNNAC	2 cut(s)	203, 340
Hpy188III	TCNNGA	3 cut(s)	200, 484, 505
Hpy8I	GTNNAC	2 cut(s)	203, 340
HpyAV	CCTTC	2 cut(s)	45, 230
HpyCH4III	ACNGT	1 cut(s)	344
HpyCH4V	TGCA	4 cut(s)	7, 275, 335, 409
HpyF3I	CTNAG	1 cut(s)	15
Kzo9I	GATC	4 cut(s)	107, 196, 480, 511
LguI	GCTCTTC	1 cut(s)	75
LpnPI	CCDG	6 cut(s)	62, 89, 195, 361, 446, 518
Lsp1109I	GCAGC	2 cut(s)	163, 319
LweI	GCATC	1 cut(s)	163
MaeI	CTAG	1 cut(s)	86
MalI	GATC	4 cut(s)	109, 198, 482, 513
MboI	GATC	4 cut(s)	107, 196, 480, 511
MboII	GAAGA	7 cut(s)	31, 92, 257, 323, 392, 431, 457
MflI	RGATCY	2 cut(s)	480, 511
MhlI	GDGCHC	1 cut(s)	495
MluCI	AATT	4 cut(s)	159, 277, 370, 422
MmeI	TCCRAC	2 cut(s)	28, 210
MnlI	CCTC	6 cut(s)	226, 295, 307, 310, 512, 525
MseI	TTAA	5 cut(s)	56, 257, 267, 389, 425
MslI	CAYNNNNRTG	1 cut(s)	168
MspR9I	CCNGG	1 cut(s)	77
MvaI	CCWGG	1 cut(s)	77
NdeII	GATC	4 cut(s)	107, 196, 480, 511
NlaIV	GGNNCC	1 cut(s)	321
PaqCI	CACCTGC	1 cut(s)	451
PceI	AGGCCT	1 cut(s)	263
PciSI	GCTCTTC	1 cut(s)	75
PkrI	GCNGC	2 cut(s)	178, 334
PpuMI	RGGWCCY	1 cut(s)	499
PshAI	GACNNNNGTC	1 cut(s)	345
Psp124BI	GAGCTC	1 cut(s)	495
Psp5II	RGGWCCY	1 cut(s)	499
Psp6I	CCWGG	1 cut(s)	75
PspFI	CCCAGC	1 cut(s)	209
PspGI	CCWGG	1 cut(s)	75
PspN4I	GGNNCC	1 cut(s)	321
PspPI	GGNCC	1 cut(s)	499
PspPPI	RGGWCCY	1 cut(s)	499
PstI	CTGCAG	1 cut(s)	337
PsuI	RGATCY	2 cut(s)	480, 511
RseI	CAYNNNNRTG	1 cut(s)	168
SacI	GAGCTC	1 cut(s)	495
SapI	GCTCTTC	1 cut(s)	75
SaqAI	TTAA	5 cut(s)	56, 257, 267, 389, 425
SatI	GCNGC	2 cut(s)	177, 333
Sau3AI	GATC	4 cut(s)	107, 196, 480, 511
Sau96I	GGNCC	1 cut(s)	499
ScrFI	CCNGG	1 cut(s)	77
SduI	GDGCHC	1 cut(s)	495
SetI	ASST	7 cut(s)	56, 87, 211, 273, 465, 495, 504
SfaNI	GCATC	1 cut(s)	163
SfcI	CTRYAG	1 cut(s)	333
SinI	GGWCC	1 cut(s)	499
SmiMI	CAYNNNNRTG	1 cut(s)	168
SmlI	CTYRAG	1 cut(s)	494
SmoI	CTYRAG	1 cut(s)	494
Sse9I	AATT	4 cut(s)	159, 277, 370, 422
SseBI	AGGCCT	1 cut(s)	263
SsiI	CCGC	2 cut(s)	143, 478
SspMI	CTAG	1 cut(s)	86
SstI	GAGCTC	1 cut(s)	495
StuI	AGGCCT	1 cut(s)	263
StyD4I	CCNGG	1 cut(s)	75
TaaI	ACNGT	1 cut(s)	344
TaqI	TCGA	2 cut(s)	64, 100
TasI	AATT	4 cut(s)	159, 277, 370, 422
Tru1I	TTAA	5 cut(s)	56, 257, 267, 389, 425
Tru9I	TTAA	5 cut(s)	56, 257, 267, 389, 425
TseI	GCWGC	2 cut(s)	176, 332
TspDTI	ATGAA	5 cut(s)	144, 152, 153, 258, 417
TspGWI	ACGGA	2 cut(s)	120, 216
VpaK11BI	GGWCC	1 cut(s)	499
XapI	RAATTY	3 cut(s)	159, 277, 370
XspI	CTAG	1 cut(s)	86

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