Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0000495

Physical Location & Seq

Genomic Coordinates Reverse (-)

53908464 .. 53924431

Gene Structure 15968 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG403900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 417 bp

ATGCTCTGCTATGACGCCGTAGTCACCTCAATTCCTTGTCCCCAGGTTGCAGGGGCTCAAATGAAAGCATTTGCATTTTCTGTTGTTGAGCAGTTTCAGGCATTAGCAGAGTTGTATGTCATTGATGGGCAATATGAGAAAGCCTTTTCAATATATGCGGATGTCGTCCCACTGATGATACTGGATTGCAAGCACGCTGTTCCTTTATTGATTCAAAATAAGGACTTGATTACTTCATCTCAAGTTGTCAAACAACTTTTGAATGCGAGTGATAAGTGCGATTCCAGAAATTACTTGCATCTATATTTGCATTCACTATCTGAAGTAAACCCTCATGCTGGAAAAGATTTCCATGATATGCAGGTATTGTGGAAGGCTTGGCTTGGCATTTTTTTTTTGTCCGAAGGCTTCACTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005768 GO:0005770 GO:0006605 GO:0006623 GO:0006810 GO:0006886 GO:0006996 GO:0007033 GO:0007034 GO:0008104 GO:0008150 GO:0009987 GO:0012505 GO:0015031 GO:0015833 GO:0016020 GO:0016043 GO:0019899 GO:0030897 GO:0031338 GO:0031410 GO:0031982 GO:0032879 GO:0032991 GO:0033036 GO:0033043 GO:0033263 GO:0033365 GO:0034613 GO:0035542 GO:0042144 GO:0042886 GO:0043226 GO:0043227 GO:0043229 GO:0043254 GO:0044087 GO:0044422 GO:0044424 GO:0044425 GO:0044433 GO:0044440 GO:0044444 GO:0044446 GO:0044464 GO:0045184 GO:0046907 GO:0048284 GO:0050789 GO:0050794 GO:0051020 GO:0051049 GO:0051128 GO:0051179 GO:0051234 GO:0051641 GO:0051649 GO:0060627 GO:0061024 GO:0061025 GO:0065007 GO:0070727 GO:0071702 GO:0071705 GO:0071840 GO:0072594 GO:0072665 GO:0072666 GO:0097576 GO:0097708 GO:0098796 GO:0099023

KEGG Pathways

Metabolic & Signaling

ko04138 map04138

Pfam Domains

Protein Families

Clathrin

Protein Analysis

138

Amino Acids

15.52

Weight (kDa)

5.36

Isoelectric Point (pI)

29.2

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TPR_Vps41	PF23556	54 - 122	1.7e-16	Vps41 TPR-like region

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)

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Publication-ready

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Orthologous Genes (Group: OG0000495)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G12500
fragaria_vesca	FvH4_1g10640 FvH4_1g10640 FvH4_1g10640 FvH4_1g10640 FvH4_1g10640 FvH4_1g10641 FvH4_1g10641 FvH4_1g10642 FvH4_1g10643 FvH4_1g10650 FvH4_1g10660 FvH4_1g10660 FvH4_1g10661 FvH4_2g16190
malus_domestica	MD02G1120200.v1.1 MD02G1120300.v1.1 MD15G1234400.v1.1
prunus_persica	Prupe.7G178500_v2.0.a1 Prupe.8G174900_v2.0.a1
pyrus_communis	pycom02g09370 pycom02g09380 pycom02g09390
rosa_chinensis	RchiOBHm_Chr2g0097671 RchiOBHm_Chr2g0097691 RchiOBHm_Chr2g0097731 RchiOBHm_Chr2g0097781 RchiOBHm_Chr2g0097801 RchiOBHm_Chr2g0097821 RchiOBHm_Chr6g0279811 RchiOBHm_Chr6g0279831 RchiOBHm_Chr6g0279841
rosa_laevigata	RLG00000013112 RLG00000013114 RLG00000016734 RLG00000016736 RLG00000016737 RLG00000016738
rosa_multiflora	Rmu_sc0000974.1_g000004 Rmu_sc0000974.1_g000013 Rmu_sc0000974.1_g000019 Rmu_sc0000974.1_g000025 Rmu_sc0002340.1_g000010 Rmu_sc0008442.1_g000003 Rmu_sc0008442.1_g000009 Rmu_sc0020401.1_g000002
rosa_roxburghii	Rroxscaffold_2G00140520 Rroxscaffold_2G00144540 Rroxscaffold_2G00144580 Rroxscaffold_2G00144590 Rroxscaffold_7G00188570 Rroxscaffold_7G00188590 Rroxscaffold_7G00188610
rosa_rugosa	Rorug02G0068300 Rorug02G0068400 Rorug06G0128600
rosa_samantha	Rh2AG114800 Rh2AG114900 Rh2AG115000 Rh2AG115100 Rh2BG117600 Rh2BG117800 Rh2BG117900 Rh2BG118000 Rh2CG119600 Rh2DG118500 Rh2DG118800 Rh2DG119100 Rh2DG119200 Rh2DG119300 Rh5AG369400 Rh5CG403900 Rh6AG236600 Rh6AG236700 Rh6AG236800 Rh6AG237300 Rh6BG241000 Rh6BG241200 Rh6BG241400 Rh6CG243300 Rh6CG243400 Rh6CG243600 Rh6DG234400 Rh6DG234500 Rh7AG282100
rosa_wichuraiana	Rw2G008980 Rw2G008990 Rw6G020640

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	20
Acc36I	ACCTGC	1 cut(s)	352
AciI	CCGC	1 cut(s)	158
AcuI	CTGAAG	1 cut(s)	342
AcyI	GRCGYC	1 cut(s)	15
AfiI	CCNNNNNNNGG	1 cut(s)	338
AgsI	TTSAA	3 cut(s)	150, 215, 262
AjnI	CCWGG	1 cut(s)	42
AsuHPI	GGTGA	1 cut(s)	16
BanII	GRGCYC	1 cut(s)	58
BccI	CCATC	1 cut(s)	119
BceAI	ACGGC	1 cut(s)	2
BciT130I	CCWGG	1 cut(s)	44
BfuAI	ACCTGC	1 cut(s)	352
Bme1390I	CCNGG	1 cut(s)	44
BmrFI	CCNGG	1 cut(s)	44
BmsI	GCATC	1 cut(s)	307
BpuEI	CTTGAG	1 cut(s)	225
BsaHI	GRCGYC	1 cut(s)	15
BsaJI	CCNNGG	1 cut(s)	42
Bsc4I	CCNNNNNNNGG	1 cut(s)	338
Bse1I	ACTGG	1 cut(s)	186
BseBI	CCWGG	1 cut(s)	44
BseDI	CCNNGG	1 cut(s)	42
BseGI	GGATG	1 cut(s)	166
BseLI	CCNNNNNNNGG	1 cut(s)	338
BseNI	ACTGG	1 cut(s)	186
BslFI	GGGAC	2 cut(s)	24, 152
BslI	CCNNNNNNNGG	1 cut(s)	338
BsmFI	GGGAC	2 cut(s)	24, 152
BsmI	GAATGC	2 cut(s)	268, 310
Bsp1286I	GDGCHC	1 cut(s)	58
BspACI	CCGC	1 cut(s)	158
BspMI	ACCTGC	1 cut(s)	352
BsrI	ACTGG	1 cut(s)	186
BssECI	CCNNGG	1 cut(s)	42
BssNI	GRCGYC	1 cut(s)	15
Bst2UI	CCWGG	1 cut(s)	44
BstACI	GRCGYC	1 cut(s)	15
BstC8I	GCNNGC	2 cut(s)	191, 195
BstDEI	CTNAG	1 cut(s)	414
BstF5I	GGATG	1 cut(s)	166
BstNI	CCWGG	1 cut(s)	44
BstSCI	CCNGG	1 cut(s)	42
BtsCI	GGATG	1 cut(s)	166
BtsIMutI	CAGTG	1 cut(s)	170
BveI	ACCTGC	1 cut(s)	352
Cac8I	GCNNGC	2 cut(s)	191, 195
CseI	GACGC	1 cut(s)	23
CviAII	CATG	2 cut(s)	335, 353
CviJI	RGCY	5 cut(s)	56, 143, 377, 382, 408
CviKI_1	RGCY	5 cut(s)	56, 143, 377, 382, 408
DdeI	CTNAG	1 cut(s)	414
DrdI	GACNNNNNNGTC	1 cut(s)	20
DseDI	GACNNNNNNGTC	1 cut(s)	20
Eco24I	GRGCYC	1 cut(s)	58
Eco57I	CTGAAG	1 cut(s)	342
EcoRII	CCWGG	1 cut(s)	42
EcoT38I	GRGCYC	1 cut(s)	58
FaeI	CATG	2 cut(s)	338, 356
FaiI	YATR	9 cut(s)	12, 117, 135, 154, 156, 304, 336, 354, 359
FaqI	GGGAC	2 cut(s)	24, 152
FatI	CATG	2 cut(s)	334, 352
FokI	GGATG	1 cut(s)	173
FriOI	GRGCYC	1 cut(s)	58
HgaI	GACGC	1 cut(s)	23
Hin1I	GRCGYC	1 cut(s)	15
Hin1II	CATG	2 cut(s)	338, 356
HinfI	GANTC	2 cut(s)	211, 281
HphI	GGTGA	1 cut(s)	16
Hpy166II	GTNNAC	1 cut(s)	328
Hpy188I	TCNGA	2 cut(s)	322, 403
Hpy188III	TCNNGA	1 cut(s)	285
Hpy8I	GTNNAC	1 cut(s)	328
HpyAV	CCTTC	2 cut(s)	367, 398
HpyCH4V	TGCA	6 cut(s)	50, 74, 189, 298, 310, 361
HpyF3I	CTNAG	1 cut(s)	414
Hsp92I	GRCGYC	1 cut(s)	15
Hsp92II	CATG	2 cut(s)	338, 356
LpnPI	CCDG	8 cut(s)	29, 36, 56, 83, 167, 298, 324, 347
LweI	GCATC	1 cut(s)	307
MaeIII	GTNAC	1 cut(s)	22
MhlI	GDGCHC	1 cut(s)	58
MluCI	AATT	2 cut(s)	30, 289
MnlI	CCTC	2 cut(s)	37, 342
MspR9I	CCNGG	1 cut(s)	44
Mva1269I	GAATGC	2 cut(s)	268, 310
MvaI	CCWGG	1 cut(s)	44
NlaIII	CATG	2 cut(s)	338, 356
NmuCI	GTSAC	1 cut(s)	22
PctI	GAATGC	2 cut(s)	268, 310
PfeI	GAWTC	2 cut(s)	211, 281
Psp6I	CCWGG	1 cut(s)	42
PspGI	CCWGG	1 cut(s)	42
ScrFI	CCNGG	1 cut(s)	44
SduI	GDGCHC	1 cut(s)	58
SetI	ASST	3 cut(s)	29, 48, 366
SfaNI	GCATC	1 cut(s)	307
SmlI	CTYRAG	1 cut(s)	240
SmoI	CTYRAG	1 cut(s)	240
Sse9I	AATT	2 cut(s)	30, 289
SsiI	CCGC	1 cut(s)	158
StyD4I	CCNGG	1 cut(s)	42
TasI	AATT	2 cut(s)	30, 289
TfiI	GAWTC	2 cut(s)	211, 281
TscAI	CASTG	1 cut(s)	177
TseFI	GTSAC	1 cut(s)	22
Tsp45I	GTSAC	1 cut(s)	22
TspDTI	ATGAA	2 cut(s)	77, 225
TspRI	CASTG	1 cut(s)	177

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