Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr14

Orthogroup ID

OG0006436

Physical Location & Seq

Genomic Coordinates Reverse (-)

554538 .. 555570

Gene Structure 1033 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD14G1005300.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 666 bp

ATGAAGAACTTTCAGGACCTTCGCTCGGGGAAGATGATTGGGACAGGAACTGAAAGGGATGGACTTTACTACCTCGACCCATCAAAGAAAGGAACATGCAACAATATTCAAACCGTCTCACCAAAGCTTTGGCACCAACGCCTAGGACACCCATCTCATAAAGTCACTTCGTTATTACCTTTATTTAACAATAAGGCTTGTGATTTAGAAAAATGTTTAATTTGCCCATTGGCCAAACAAACAAGATCACCCTTTCCTTTGAGCTCTATTTCTACCAAATCATGTTTTGAATTATTGCATATTGATATTTGGGGTGGTTATCAAGTTGCTTCTATTTCAGGTGCCAAGTATTTCCTTACCATCGTAGATGACTACACTAGAAGCACTTGGGTTTATTTGATGAAACATAAATCTGACACAAAAGACATTTTAGTCGGATTCACTCAAATGATTGAGACTCAATTCAATACCAGAGTTCAAATCATACGAAGTGACAATGGCCCTGAGTTTAAGCCTGAGCAATTTTATGCTCTCAAAGGCATCATACATCAATCTAGTTGTGTCAACACACCACAACAAAATGGTGTTGCCGAACGTAAACACCGGCATTTGCTCAATGTTGCTCGGGCTTTGCTCTTTCAAGCTTGTTTGCCAAAACGTTTTTGA

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

RVT_2 Retrotran_gag_3 Retrotrans_gag gag_pre-integrs rve

Protein Analysis

222

Amino Acids

25.19

Weight (kDa)

9.47

Isoelectric Point (pI)

53.59

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
gag_pre-integrs	PF13976	21 - 80	7.3e-10	GAG-pre-integrase domain
rve	PF00665	97 - 177	1.3e-11	Integrase core domain

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)

Image

Tree File

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Publication-ready

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

Orthologous Genes (Group: OG0006436)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G21280
fragaria_vesca	FvH4_3g37931 FvH4_3g37931 FvH4_3g37931
malus_domestica	MD01G1094300.v1.1 MD02G1156200.v1.1 MD10G1309400.v1.1 MD14G1005300.v1.1
pyrus_communis	pycom02g16670 pycom03g10030 pycom04g21390 pycom05g29420 pycom07g08570 pycom08g06430 pycom15g03080 pycom15g21690
rosa_chinensis	RchiOBHm_Chr4g0394011 RchiOBHm_Chr4g0436631
rosa_multiflora	Rmu_sc0002646.1_g000018 Rmu_sc0004135.1_g000007
rosa_roxburghii	Rroxscaffold_2G00099130
rosa_samantha	Rh1AG086000 Rh2BG003200 Rh5DG450100 Rh7AG095400
rosa_wichuraiana	Rw1G012660

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	431
AccB1I	GGYRCC	2 cut(s)	132, 341
AclI	AACGTT	1 cut(s)	658
AcoI	YGGCCR	1 cut(s)	231
AfiI	CCNNNNNNNGG	1 cut(s)	25
AgsI	TTSAA	5 cut(s)	110, 290, 466, 479, 641
AluBI	AGCT	3 cut(s)	127, 264, 644
AluI	AGCT	3 cut(s)	127, 264, 644
Alw21I	GWGCWC	1 cut(s)	266
Alw26I	GTCTC	2 cut(s)	121, 449
AlwNI	CAGNNNCTG	1 cut(s)	50
Ama87I	CYCGRG	2 cut(s)	25, 624
AoxI	GGCC	2 cut(s)	231, 499
AspA2I	CCTAGG	1 cut(s)	142
AspS9I	GGNCC	2 cut(s)	16, 500
AsuHPI	GGTGA	2 cut(s)	111, 240
AvaI	CYCGRG	2 cut(s)	25, 624
AvaII	GGWCC	1 cut(s)	16
AvrII	CCTAGG	1 cut(s)	142
BalI	TGGCCA	1 cut(s)	233
BanI	GGYRCC	2 cut(s)	132, 341
BanII	GRGCYC	1 cut(s)	266
Bbv12I	GWGCWC	1 cut(s)	266
BccI	CCATC	4 cut(s)	53, 88, 160, 368
BcoDI	GTCTC	2 cut(s)	121, 449
BfaI	CTAG	3 cut(s)	143, 378, 555
BlnI	CCTAGG	1 cut(s)	142
Bme18I	GGWCC	1 cut(s)	16
BmeT110I	CYCGRG	2 cut(s)	25, 624
BmgT120I	GGNCC	2 cut(s)	16, 500
BmiI	GGNNCC	2 cut(s)	134, 343
BmsI	GCATC	1 cut(s)	549
Bpu10I	CCTNAGC	1 cut(s)	516
BsaJI	CCNNGG	1 cut(s)	142
Bsc4I	CCNNNNNNNGG	1 cut(s)	25
Bse118I	RCCGGY	1 cut(s)	603
BseDI	CCNNGG	1 cut(s)	142
BseGI	GGATG	1 cut(s)	64
BseLI	CCNNNNNNNGG	1 cut(s)	25
BseMII	CTCAG	2 cut(s)	495, 507
BshFI	GGCC	2 cut(s)	233, 501
BshNI	GGYRCC	2 cut(s)	132, 341
BsiHKAI	GWGCWC	1 cut(s)	266
BsiHKCI	CYCGRG	2 cut(s)	25, 624
BsiSI	CCGG	1 cut(s)	604
BslFI	GGGAC	1 cut(s)	55
BslI	CCNNNNNNNGG	1 cut(s)	25
BsmAI	GTCTC	2 cut(s)	121, 449
BsmBI	CGTCTC	1 cut(s)	121
BsmFI	GGGAC	1 cut(s)	55
BsnI	GGCC	2 cut(s)	233, 501
BsoBI	CYCGRG	2 cut(s)	25, 624
Bsp1286I	GDGCHC	1 cut(s)	266
Bsp143I	GATC	1 cut(s)	245
BspANI	GGCC	2 cut(s)	233, 501
BspCNI	CTCAG	2 cut(s)	496, 508
BspLI	GGNNCC	2 cut(s)	134, 343
BspT107I	GGYRCC	2 cut(s)	132, 341
BsrFI	RCCGGY	1 cut(s)	603
BssAI	RCCGGY	1 cut(s)	603
BssECI	CCNNGG	1 cut(s)	142
BssMI	GATC	1 cut(s)	245
BssT1I	CCWWGG	1 cut(s)	142
Bst4CI	ACNGT	1 cut(s)	115
BstDEI	CTNAG	2 cut(s)	504, 516
BstF5I	GGATG	1 cut(s)	64
BstKTI	GATC	1 cut(s)	248
BstMAI	GTCTC	2 cut(s)	121, 449
BstMBI	GATC	1 cut(s)	245
BstNSI	RCATGY	1 cut(s)	99
BstXI	CCANNNNNNTGG	1 cut(s)	129
BsuRI	GGCC	2 cut(s)	233, 501
BtsCI	GGATG	1 cut(s)	64
CaiI	CAGNNNCTG	1 cut(s)	50
Cfr10I	RCCGGY	1 cut(s)	603
Cfr13I	GGNCC	2 cut(s)	16, 500
CviAII	CATG	2 cut(s)	96, 282
CviJI	RGCY	8 cut(s)	127, 197, 233, 264, 501, 514, 629, 644
CviKI_1	RGCY	8 cut(s)	127, 197, 233, 264, 501, 514, 629, 644
DdeI	CTNAG	2 cut(s)	504, 516
DpnI	GATC	1 cut(s)	247
DpnII	GATC	1 cut(s)	245
DrdI	GACNNNNNNGTC	1 cut(s)	431
DseDI	GACNNNNNNGTC	1 cut(s)	431
EaeI	YGGCCR	1 cut(s)	231
Ecl136II	GAGCTC	1 cut(s)	264
Eco130I	CCWWGG	1 cut(s)	142
Eco24I	GRGCYC	1 cut(s)	266
Eco47I	GGWCC	1 cut(s)	16
Eco53kI	GAGCTC	1 cut(s)	264
Eco88I	CYCGRG	2 cut(s)	25, 624
EcoICRI	GAGCTC	1 cut(s)	264
EcoO109I	RGGNCCY	1 cut(s)	16
EcoT14I	CCWWGG	1 cut(s)	142
EcoT38I	GRGCYC	1 cut(s)	266
ErhI	CCWWGG	1 cut(s)	142
Esp3I	CGTCTC	1 cut(s)	121
FaeI	CATG	2 cut(s)	99, 285
FaiI	YATR	8 cut(s)	97, 159, 283, 300, 408, 485, 528, 545
FaqI	GGGAC	1 cut(s)	55
FatI	CATG	2 cut(s)	95, 281
FokI	GGATG	1 cut(s)	71
FriOI	GRGCYC	1 cut(s)	266
FspBI	CTAG	3 cut(s)	143, 378, 555
HaeIII	GGCC	2 cut(s)	233, 501
HapII	CCGG	1 cut(s)	604
Hin1II	CATG	2 cut(s)	99, 285
HincII	GTYRAC	1 cut(s)	565
HindII	GTYRAC	1 cut(s)	565
HindIII	AAGCTT	2 cut(s)	125, 642
HinfI	GANTC	2 cut(s)	438, 457
HpaII	CCGG	1 cut(s)	604
HphI	GGTGA	2 cut(s)	111, 240
Hpy166II	GTNNAC	2 cut(s)	565, 599
Hpy188I	TCNGA	2 cut(s)	415, 437
Hpy188III	TCNNGA	1 cut(s)	14
Hpy8I	GTNNAC	2 cut(s)	565, 599
HpyAV	CCTTC	1 cut(s)	29
HpyCH4III	ACNGT	1 cut(s)	115
HpyCH4IV	ACGT	2 cut(s)	595, 658
HpyCH4V	TGCA	2 cut(s)	99, 298
HpyF3I	CTNAG	2 cut(s)	504, 516
HpySE526I	ACGT	2 cut(s)	595, 658
Hsp92II	CATG	2 cut(s)	99, 285
Kzo9I	GATC	1 cut(s)	245
LpnPI	CCDG	6 cut(s)	30, 324, 484, 516, 528, 617
LweI	GCATC	1 cut(s)	549
MaeI	CTAG	3 cut(s)	143, 378, 555
MaeII	ACGT	2 cut(s)	595, 658
MaeIII	GTNAC	2 cut(s)	163, 491
MalI	GATC	1 cut(s)	247
MboI	GATC	1 cut(s)	245
MboII	GAAGA	2 cut(s)	16, 43
MhlI	GDGCHC	1 cut(s)	266
MlsI	TGGCCA	1 cut(s)	233
MluCI	AATT	4 cut(s)	219, 290, 461, 521
MluNI	TGGCCA	1 cut(s)	233
MlyI	GAGTC	1 cut(s)	451
MmeI	TCCRAC	1 cut(s)	415
MnlI	CCTC	1 cut(s)	83
Mox20I	TGGCCA	1 cut(s)	233
MscI	TGGCCA	1 cut(s)	233
MseI	TTAA	3 cut(s)	186, 218, 510
MslI	CAYNNNNRTG	1 cut(s)	446
Msp20I	TGGCCA	1 cut(s)	233
MspI	CCGG	1 cut(s)	604
NdeII	GATC	1 cut(s)	245
NlaIII	CATG	2 cut(s)	99, 285
NlaIV	GGNNCC	2 cut(s)	134, 343
NmuCI	GTSAC	2 cut(s)	163, 491
NspI	RCATGY	1 cut(s)	99
PfeI	GAWTC	1 cut(s)	438
PleI	GAGTC	1 cut(s)	451
PpsI	GAGTC	1 cut(s)	451
PpuMI	RGGWCCY	1 cut(s)	16
Psp124BI	GAGCTC	1 cut(s)	266
Psp1406I	AACGTT	1 cut(s)	658
Psp5II	RGGWCCY	1 cut(s)	16
PspN4I	GGNNCC	2 cut(s)	134, 343
PspPI	GGNCC	2 cut(s)	16, 500
PspPPI	RGGWCCY	1 cut(s)	16
PstNI	CAGNNNCTG	1 cut(s)	50
RseI	CAYNNNNRTG	1 cut(s)	446
SacI	GAGCTC	1 cut(s)	266
SaqAI	TTAA	3 cut(s)	186, 218, 510
Sau3AI	GATC	1 cut(s)	245
Sau96I	GGNCC	2 cut(s)	16, 500
SchI	GAGTC	1 cut(s)	451
SduI	GDGCHC	1 cut(s)	266
SetI	ASST	9 cut(s)	21, 75, 129, 181, 266, 343, 598, 646, 661
SfaNI	GCATC	1 cut(s)	549
SinI	GGWCC	1 cut(s)	16
SmiMI	CAYNNNNRTG	1 cut(s)	446
Sse9I	AATT	4 cut(s)	219, 290, 461, 521
SspI	AATATT	1 cut(s)	106
SspMI	CTAG	3 cut(s)	143, 378, 555
SstI	GAGCTC	1 cut(s)	266
StyI	CCWWGG	1 cut(s)	142
TaaI	ACNGT	1 cut(s)	115
TaiI	ACGT	2 cut(s)	598, 661
TaqI	TCGA	1 cut(s)	75
TasI	AATT	4 cut(s)	219, 290, 461, 521
TfiI	GAWTC	1 cut(s)	438
Tru1I	TTAA	3 cut(s)	186, 218, 510
Tru9I	TTAA	3 cut(s)	186, 218, 510
TseFI	GTSAC	2 cut(s)	163, 491
Tsp45I	GTSAC	2 cut(s)	163, 491
TspDTI	ATGAA	2 cut(s)	17, 416
VpaK11BI	GGWCC	1 cut(s)	16
XceI	RCATGY	1 cut(s)	99
XmaJI	CCTAGG	1 cut(s)	142
XspI	CTAG	3 cut(s)	143, 378, 555

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