Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0011353

Physical Location & Seq

Genomic Coordinates Reverse (-)

5345611 .. 5347655

Gene Structure 2045 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG063500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 279 bp

ATGGTGTGTGGATCTTGCCGCCACCTGCTTACATACCCACCAGGAGCCAAGCATGTTCAATGCTCATGCTGTCAGACTGTCAACTTTGTGCTAGAAGCCCATCAGGTTGGCCAAGTCAAATGCGGCAGTTGTACAACGCTGCTGATGTACCCATATGGAGCTCTATCCGTTAGGTGTTCCTCGTGCAGTTTTGTGACAGAAGTTAGGGATCACAACATGCGCCCTCCATGGTCTGTTCAACAAGGACAACTAACTCCTCCGTCCAATTCTGTTCACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0008150 GO:0009605 GO:0009607 GO:0009617 GO:0031347 GO:0031349 GO:0040008 GO:0043207 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0045927 GO:0048518 GO:0048583 GO:0048584 GO:0050789 GO:0050896 GO:0051704 GO:0051707 GO:0065007 GO:0080134

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

zf-LSD1

Protein Analysis

92

Amino Acids

10.08

Weight (kDa)

8.43

Isoelectric Point (pI)

42.39

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
zf-LSD1	PF06943	3 - 27	2.7e-11	LSD1 zinc finger
zf-LSD1	PF06943	41 - 65	9e-12	LSD1 zinc finger

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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Orthologous Genes (Group: OG0011353)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G21610 AT4G21610
fragaria_vesca	FvH4_3g09310 FvH4_3g09310
malus_domestica	MD05G1313200.v1.1 MD10G1295400.v1.1
prunus_persica	Prupe.4G046600_v2.0.a1
pyrus_communis	pycom05g29120 pycom10g24730
rosa_chinensis	RchiOBHm_Chr5g0008291
rosa_laevigata	RLG00000031559
rosa_multiflora	Rmu_co8513525.1_g000001
rosa_roxburghii	Rroxscaffold_1G00068170
rosa_rugosa	Rorug04G0434800 Rorug04G0434800
rosa_samantha	Rh5AG063500 Rh5BG060000 Rh5CG070300 Rh5DG059500
rosa_wichuraiana	Rw5G005740

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	33
Acc36I	ACCTGC	1 cut(s)	33
AciI	CCGC	2 cut(s)	19, 123
AclWI	GGATC	2 cut(s)	19, 216
AcoI	YGGCCR	1 cut(s)	109
AfaI	GTAC	2 cut(s)	133, 149
AgsI	TTSAA	2 cut(s)	59, 239
AjnI	CCWGG	1 cut(s)	40
AluBI	AGCT	1 cut(s)	161
AluI	AGCT	1 cut(s)	161
Alw21I	GWGCWC	1 cut(s)	163
AlwI	GGATC	2 cut(s)	19, 216
AoxI	GGCC	1 cut(s)	109
ApeKI	GCWGC	1 cut(s)	139
AspLEI	GCGC	1 cut(s)	222
BalI	TGGCCA	1 cut(s)	111
BanII	GRGCYC	1 cut(s)	163
BauI	CACGAG	1 cut(s)	181
Bbv12I	GWGCWC	1 cut(s)	163
BbvI	GCAGC	1 cut(s)	126
BccI	CCATC	1 cut(s)	108
BciT130I	CCWGG	1 cut(s)	42
BfaI	CTAG	1 cut(s)	92
BfuAI	ACCTGC	1 cut(s)	33
BisI	GCNGC	3 cut(s)	19, 124, 140
BlsI	GCNGC	3 cut(s)	20, 125, 141
Bme1390I	CCNGG	1 cut(s)	42
BmiI	GGNNCC	1 cut(s)	46
BmrFI	CCNGG	1 cut(s)	42
BsaJI	CCNNGG	1 cut(s)	227
BseBI	CCWGG	1 cut(s)	42
BseDI	CCNNGG	1 cut(s)	227
BseRI	GAGGAG	1 cut(s)	246
BseXI	GCAGC	1 cut(s)	126
BsgI	GTGCAG	1 cut(s)	205
BshFI	GGCC	1 cut(s)	111
BsiHKAI	GWGCWC	1 cut(s)	163
BsnI	GGCC	1 cut(s)	111
Bsp1286I	GDGCHC	1 cut(s)	163
Bsp1407I	TGTACA	1 cut(s)	131
Bsp143I	GATC	2 cut(s)	11, 208
Bsp19I	CCATGG	1 cut(s)	227
BspACI	CCGC	2 cut(s)	19, 123
BspANI	GGCC	1 cut(s)	111
BspLI	GGNNCC	1 cut(s)	46
BspMI	ACCTGC	1 cut(s)	33
BspPI	GGATC	2 cut(s)	19, 216
BsrGI	TGTACA	1 cut(s)	131
BssECI	CCNNGG	1 cut(s)	227
BssMI	GATC	2 cut(s)	11, 208
BssSI	CACGAG	1 cut(s)	181
BssT1I	CCWWGG	1 cut(s)	227
Bst2BI	CACGAG	1 cut(s)	181
Bst2UI	CCWGG	1 cut(s)	42
Bst4CI	ACNGT	1 cut(s)	79
BstAUI	TGTACA	1 cut(s)	131
BstDSI	CCRYGG	1 cut(s)	227
BstHHI	GCGC	1 cut(s)	222
BstKTI	GATC	2 cut(s)	14, 211
BstMBI	GATC	2 cut(s)	11, 208
BstNI	CCWGG	1 cut(s)	42
BstNSI	RCATGY	2 cut(s)	56, 220
BstSCI	CCNGG	1 cut(s)	40
BstV1I	GCAGC	1 cut(s)	126
BstX2I	RGATCY	1 cut(s)	11
BstXI	CCANNNNNNTGG	1 cut(s)	107
BstYI	RGATCY	1 cut(s)	11
BsuRI	GGCC	1 cut(s)	111
BtgI	CCRYGG	1 cut(s)	227
BveI	ACCTGC	1 cut(s)	33
CfoI	GCGC	1 cut(s)	222
Csp6I	GTAC	2 cut(s)	132, 148
CviAII	CATG	4 cut(s)	53, 66, 217, 228
CviJI	RGCY	4 cut(s)	47, 98, 111, 161
CviKI_1	RGCY	4 cut(s)	47, 98, 111, 161
CviQI	GTAC	2 cut(s)	132, 148
DpnI	GATC	2 cut(s)	13, 210
DpnII	GATC	2 cut(s)	11, 208
EaeI	YGGCCR	1 cut(s)	109
Ecl136II	GAGCTC	1 cut(s)	161
Eco130I	CCWWGG	1 cut(s)	227
Eco24I	GRGCYC	1 cut(s)	163
Eco53kI	GAGCTC	1 cut(s)	161
EcoICRI	GAGCTC	1 cut(s)	161
EcoRII	CCWGG	1 cut(s)	40
EcoT14I	CCWWGG	1 cut(s)	227
EcoT38I	GRGCYC	1 cut(s)	163
ErhI	CCWWGG	1 cut(s)	227
FaeI	CATG	4 cut(s)	56, 69, 220, 231
FaiI	YATR	7 cut(s)	34, 54, 67, 154, 156, 218, 229
FatI	CATG	4 cut(s)	52, 65, 216, 227
FauNDI	CATATG	1 cut(s)	154
Fnu4HI	GCNGC	3 cut(s)	19, 124, 140
FriOI	GRGCYC	1 cut(s)	163
Fsp4HI	GCNGC	3 cut(s)	19, 124, 140
FspBI	CTAG	1 cut(s)	92
GlaI	GCGC	1 cut(s)	221
GluI	GCNGC	3 cut(s)	19, 124, 140
HaeIII	GGCC	1 cut(s)	111
HhaI	GCGC	1 cut(s)	222
Hin1II	CATG	4 cut(s)	56, 69, 220, 231
Hin6I	GCGC	1 cut(s)	220
HinP1I	GCGC	1 cut(s)	220
HincII	GTYRAC	1 cut(s)	82
HindII	GTYRAC	1 cut(s)	82
Hpy166II	GTNNAC	2 cut(s)	82, 274
Hpy188I	TCNGA	1 cut(s)	75
Hpy8I	GTNNAC	2 cut(s)	82, 274
HpyCH4III	ACNGT	1 cut(s)	79
HpyCH4V	TGCA	1 cut(s)	186
Hsp92II	CATG	4 cut(s)	56, 69, 220, 231
HspAI	GCGC	1 cut(s)	220
Kzo9I	GATC	2 cut(s)	11, 208
LmnI	GCTCC	2 cut(s)	44, 158
LpnPI	CCDG	4 cut(s)	27, 38, 54, 89
Lsp1109I	GCAGC	1 cut(s)	126
MaeI	CTAG	1 cut(s)	92
MaeIII	GTNAC	1 cut(s)	193
MalI	GATC	2 cut(s)	13, 210
MboI	GATC	2 cut(s)	11, 208
MflI	RGATCY	1 cut(s)	11
MhlI	GDGCHC	1 cut(s)	163
MlsI	TGGCCA	1 cut(s)	111
MluCI	AATT	1 cut(s)	265
MluNI	TGGCCA	1 cut(s)	111
MnlI	CCTC	3 cut(s)	190, 234, 267
Mox20I	TGGCCA	1 cut(s)	111
MscI	TGGCCA	1 cut(s)	111
Msp20I	TGGCCA	1 cut(s)	111
MspR9I	CCNGG	1 cut(s)	42
MvaI	CCWGG	1 cut(s)	42
NcoI	CCATGG	1 cut(s)	227
NdeI	CATATG	1 cut(s)	154
NdeII	GATC	2 cut(s)	11, 208
NlaIII	CATG	4 cut(s)	56, 69, 220, 231
NlaIV	GGNNCC	1 cut(s)	46
NmuCI	GTSAC	1 cut(s)	193
NspI	RCATGY	2 cut(s)	56, 220
PaqCI	CACCTGC	1 cut(s)	33
PkrI	GCNGC	3 cut(s)	20, 125, 141
Psp124BI	GAGCTC	1 cut(s)	163
Psp6I	CCWGG	1 cut(s)	40
PspGI	CCWGG	1 cut(s)	40
PspN4I	GGNNCC	1 cut(s)	46
PsuI	RGATCY	1 cut(s)	11
RsaI	GTAC	2 cut(s)	133, 149
RsaNI	GTAC	2 cut(s)	132, 148
SacI	GAGCTC	1 cut(s)	163
SatI	GCNGC	3 cut(s)	19, 124, 140
Sau3AI	GATC	2 cut(s)	11, 208
ScrFI	CCNGG	1 cut(s)	42
SduI	GDGCHC	1 cut(s)	163
SetI	ASST	4 cut(s)	27, 108, 163, 176
Sse9I	AATT	1 cut(s)	265
SsiI	CCGC	2 cut(s)	19, 123
SspMI	CTAG	1 cut(s)	92
SstI	GAGCTC	1 cut(s)	163
StyD4I	CCNGG	1 cut(s)	40
StyI	CCWWGG	1 cut(s)	227
TaaI	ACNGT	1 cut(s)	79
TasI	AATT	1 cut(s)	265
TatI	WGTACW	1 cut(s)	131
TauI	GCSGC	2 cut(s)	21, 126
TseFI	GTSAC	1 cut(s)	193
TseI	GCWGC	1 cut(s)	139
Tsp45I	GTSAC	1 cut(s)	193
TspGWI	ACGGA	2 cut(s)	157, 249
XceI	RCATGY	2 cut(s)	56, 220
XspI	CTAG	1 cut(s)	92

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