Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr01

Orthogroup ID

OG0009688

Physical Location & Seq

Genomic Coordinates Reverse (-)

31464369 .. 31466000

Gene Structure 1632 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD01G1222200.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 450 bp

ATGGGAGATCTTCAAGTTGTTGGAGGAATCAAAAAGTTGAACAACAAAAATTACAACACATGGGCGACGTGTATGGAGTCTTACCTACAAGGCCAAGATCTTTGGGATATCGTTAGCGGTAATGAAGTTACGGATCCGGCTCCGGTTGCGGATCCGGCTCCGGTTGAGGATCCGGCTCCGGTTGAGGATCCGGCTCCAGTTGCGGATCCGACTCCGCCTACGCAGATTTCGAGGGAGAGGAAAATCAAAGAAGGTAAAGCCATGTTTGCCTTAAAAACCACAGTTGAAGATGACATGTTGGAGTACATATGGAAGGCCAAGACACCAAAAGAAGCGTGGGACACCTTCGCCAGACTCTTTTCAAATAGGAAAGTTACAAGATTGCAGCTTCTCGAGAACGAATCAAGAAGCTTTGGCAAAGCAAATGGCAGAGGTCTCATTAAGAGGTGA

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

DUF4219 Retrotran_gag_2 zf-CCHC

Protein Analysis

150

Amino Acids

16.68

Weight (kDa)

5.6

Isoelectric Point (pI)

39.93

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DUF4219	PF13961	13 - 39	1.9e-13	Domain of unknown function (DUF4219)
Retrotran_gag_2	PF14223	25 - 130	5.2e-07	gag-polypeptide of LTR copia-type

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

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

Orthologous Genes (Group: OG0009688)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_5g19322 FvH4_5g31431
malus_domestica	MD01G1222200.v1.1 MD14G1034300.v1.1
prunus_persica	Prupe.2G033500_v2.0.a1 Prupe.7G032100_v2.0.a1
pyrus_communis	pycom02g19670 pycom03g19000 pycom11g04720 pycom11g04870 pycom11g07640 pycom12g10550 pycom13g07730 pycom16g07450 pycom520g00380
rosa_chinensis	RchiOBHm_Chr3g0481931 RchiOBHm_Chr3g0481941 RchiOBHm_Chr5g0017901 RchiOBHm_Chr5g0017911
rosa_roxburghii	Rroxscaffold_1G00053310 Rroxscaffold_4G00308650
rosa_rugosa	Rorug07G0315400

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	4 cut(s)	117, 149, 203, 215
AfaI	GTAC	1 cut(s)	305
AflIII	ACRYGT	2 cut(s)	68, 294
AgsI	TTSAA	4 cut(s)	14, 40, 287, 363
AjiI	CACGTC	1 cut(s)	69
AluBI	AGCT	2 cut(s)	388, 411
AluI	AGCT	2 cut(s)	388, 411
Alw26I	GTCTC	1 cut(s)	440
Ama87I	CYCGRG	1 cut(s)	392
AoxI	GGCC	2 cut(s)	91, 315
ApeKI	GCWGC	1 cut(s)	385
AvaI	CYCGRG	1 cut(s)	392
BamHI	GGATCC	5 cut(s)	133, 151, 169, 187, 205
BbvI	GCAGC	1 cut(s)	397
BcoDI	GTCTC	1 cut(s)	440
BglII	AGATCT	2 cut(s)	7, 97
BisI	GCNGC	1 cut(s)	386
BlsI	GCNGC	1 cut(s)	387
BmeT110I	CYCGRG	1 cut(s)	392
BmgBI	CACGTC	1 cut(s)	69
BmiI	GGNNCC	9 cut(s)	135, 141, 153, 159, 171, 177, 189, 195, 207
BpmI	CTGGAG	1 cut(s)	180
BsaI	GGTCTC	1 cut(s)	440
BsaWI	WCCGGW	3 cut(s)	142, 160, 178
Bse1I	ACTGG	1 cut(s)	197
BseNI	ACTGG	1 cut(s)	197
BseXI	GCAGC	1 cut(s)	397
BshFI	GGCC	2 cut(s)	93, 317
BsiHKCI	CYCGRG	1 cut(s)	392
BsiSI	CCGG	7 cut(s)	137, 143, 155, 161, 173, 179, 191
BslFI	GGGAC	1 cut(s)	353
BsmAI	GTCTC	1 cut(s)	440
BsmFI	GGGAC	1 cut(s)	353
BsnI	GGCC	2 cut(s)	93, 317
Bso31I	GGTCTC	1 cut(s)	440
BsoBI	CYCGRG	1 cut(s)	392
Bsp143I	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
BspACI	CCGC	4 cut(s)	117, 149, 203, 215
BspANI	GGCC	2 cut(s)	93, 317
BspLI	GGNNCC	9 cut(s)	135, 141, 153, 159, 171, 177, 189, 195, 207
BspTNI	GGTCTC	1 cut(s)	440
BsrI	ACTGG	1 cut(s)	197
BssMI	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
Bst4CI	ACNGT	1 cut(s)	283
BstKTI	GATC	7 cut(s)	10, 100, 136, 154, 172, 190, 208
BstMAI	GTCTC	1 cut(s)	440
BstMBI	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
BstMWI	GCNNNNNNNGC	4 cut(s)	146, 155, 200, 266
BstNSI	RCATGY	1 cut(s)	298
BstV1I	GCAGC	1 cut(s)	397
BstX2I	RGATCY	7 cut(s)	7, 97, 133, 151, 169, 187, 205
BstYI	RGATCY	7 cut(s)	7, 97, 133, 151, 169, 187, 205
BsuRI	GGCC	2 cut(s)	93, 317
BtrI	CACGTC	1 cut(s)	69
Csp6I	GTAC	1 cut(s)	304
CviAII	CATG	3 cut(s)	60, 262, 295
CviJI	RGCY	9 cut(s)	93, 140, 158, 176, 194, 260, 317, 388, 411
CviKI_1	RGCY	9 cut(s)	93, 140, 158, 176, 194, 260, 317, 388, 411
CviQI	GTAC	1 cut(s)	304
DpnI	GATC	7 cut(s)	9, 99, 135, 153, 171, 189, 207
DpnII	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
EciI	GGCGGA	1 cut(s)	204
Eco31I	GGTCTC	1 cut(s)	440
Eco32I	GATATC	1 cut(s)	109
Eco88I	CYCGRG	1 cut(s)	392
EcoRV	GATATC	1 cut(s)	109
FaeI	CATG	3 cut(s)	63, 265, 298
FaiI	YATR	6 cut(s)	61, 74, 263, 296, 308, 310
FaqI	GGGAC	1 cut(s)	353
FatI	CATG	3 cut(s)	59, 261, 294
FauNDI	CATATG	1 cut(s)	308
Fnu4HI	GCNGC	1 cut(s)	386
Fsp4HI	GCNGC	1 cut(s)	386
GluI	GCNGC	1 cut(s)	386
GsuI	CTGGAG	1 cut(s)	180
HaeIII	GGCC	2 cut(s)	93, 317
HapII	CCGG	7 cut(s)	137, 143, 155, 161, 173, 179, 191
Hin1II	CATG	3 cut(s)	63, 265, 298
HindIII	AAGCTT	1 cut(s)	409
HinfI	GANTC	5 cut(s)	27, 77, 211, 354, 401
HpaII	CCGG	7 cut(s)	137, 143, 155, 161, 173, 179, 191
Hpy188I	TCNGA	1 cut(s)	210
Hpy188III	TCNNGA	3 cut(s)	392, 394, 405
Hpy99I	CGWCG	1 cut(s)	70
HpyAV	CCTTC	3 cut(s)	245, 307, 355
HpyCH4III	ACNGT	1 cut(s)	283
HpyCH4IV	ACGT	1 cut(s)	68
HpyCH4V	TGCA	1 cut(s)	385
HpyF10VI	GCNNNNNNNGC	4 cut(s)	146, 155, 200, 266
HpySE526I	ACGT	1 cut(s)	68
Hsp92II	CATG	3 cut(s)	63, 265, 298
Kzo9I	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
LmnI	GCTCC	4 cut(s)	145, 163, 181, 199
LpnPI	CCDG	9 cut(s)	150, 156, 168, 174, 186, 192, 204, 210, 364
Lsp1109I	GCAGC	1 cut(s)	397
MaeII	ACGT	1 cut(s)	68
MaeIII	GTNAC	2 cut(s)	127, 373
MalI	GATC	7 cut(s)	9, 99, 135, 153, 171, 189, 207
MboI	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
MboII	GAAGA	1 cut(s)	299
MflI	RGATCY	7 cut(s)	7, 97, 133, 151, 169, 187, 205
MluCI	AATT	1 cut(s)	49
MlyI	GAGTC	3 cut(s)	86, 205, 348
MmeI	TCCRAC	2 cut(s)	233, 279
MnlI	CCTC	7 cut(s)	17, 160, 178, 225, 231, 425, 438
MseI	TTAA	2 cut(s)	272, 441
MspI	CCGG	7 cut(s)	137, 143, 155, 161, 173, 179, 191
MwoI	GCNNNNNNNGC	4 cut(s)	146, 155, 200, 266
NdeI	CATATG	1 cut(s)	308
NdeII	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
NlaIII	CATG	3 cut(s)	63, 265, 298
NlaIV	GGNNCC	9 cut(s)	135, 141, 153, 159, 171, 177, 189, 195, 207
NspI	RCATGY	1 cut(s)	298
PaeR7I	CTCGAG	1 cut(s)	392
PciI	ACATGT	1 cut(s)	294
PcsI	WCGNNNNNNNCGW	1 cut(s)	227
PfeI	GAWTC	2 cut(s)	27, 401
PkrI	GCNGC	1 cut(s)	387
PleI	GAGTC	3 cut(s)	85, 205, 348
PpsI	GAGTC	3 cut(s)	85, 205, 348
PscI	ACATGT	1 cut(s)	294
PspN4I	GGNNCC	9 cut(s)	135, 141, 153, 159, 171, 177, 189, 195, 207
PsuI	RGATCY	7 cut(s)	7, 97, 133, 151, 169, 187, 205
RsaI	GTAC	1 cut(s)	305
RsaNI	GTAC	1 cut(s)	304
SaqAI	TTAA	2 cut(s)	272, 441
SatI	GCNGC	1 cut(s)	386
Sau3AI	GATC	7 cut(s)	7, 97, 133, 151, 169, 187, 205
SchI	GAGTC	3 cut(s)	86, 205, 348
SetI	ASST	8 cut(s)	71, 87, 256, 347, 390, 413, 436, 449
Sfr274I	CTCGAG	1 cut(s)	392
SlaI	CTCGAG	1 cut(s)	392
SmlI	CTYRAG	1 cut(s)	392
SmoI	CTYRAG	1 cut(s)	392
Sse9I	AATT	1 cut(s)	49
SsiI	CCGC	4 cut(s)	117, 149, 203, 215
TaaI	ACNGT	1 cut(s)	283
TaiI	ACGT	1 cut(s)	71
TaqI	TCGA	2 cut(s)	230, 393
TasI	AATT	1 cut(s)	49
TatI	WGTACW	1 cut(s)	303
TfiI	GAWTC	2 cut(s)	27, 401
Tru1I	TTAA	2 cut(s)	272, 441
Tru9I	TTAA	2 cut(s)	272, 441
TseI	GCWGC	1 cut(s)	385
TspDTI	ATGAA	1 cut(s)	138
TspGWI	ACGGA	1 cut(s)	146
XceI	RCATGY	1 cut(s)	298
XcmI	CCANNNNNNNNNTGG	1 cut(s)	333
XhoI	CTCGAG	1 cut(s)	392

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