Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr08

Orthogroup ID

OG0001006

Physical Location & Seq

Genomic Coordinates Reverse (-)

20541992 .. 20544850

Gene Structure 2859 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD08G1171400.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 741 bp

ATGCACATCACAAATTCATTACATGGTTTTGAGAAACAAAAGGAAACTAATTGTTTCAACGTTTATGTTGGAGAAGGGACAAGGGTAGATGTAGAAGCTGTTGGGATGGTTAGACTAAAGTTAAACACAGGCTTCATAATGCAATTGGATAGTGTCTTATATGTCCCCACCATGAGAAGAAGCCTAATATCTGCATCAAAATTGGTTAAACAGAAGTATGTGTTCATTGGTGATGACAAATGTATTAAGTTTTTCTTCAAAGGGTCTTTAATTGGTAAAGCATTCATGTTTGATCACCTATGGAGATTACAATGCACATTAGAACTGAGTCACCCACAAGTTTTACATGTCACAACTAAGAGGATGCACGGTTTTGGTCACTCTTTCATGCTTTGGCGTAAAAGATTGGGGTACGTTTCAAAAGACCAGTGTCCCAAGAGTGAGCATGAGGCAAATTTAATGAAGTCAAAACCTTACGCTTCATTAGTTGGTAGTCTCATGTATGCTAACATTTGCACCAGACCAGATTTGGGGTTTATTGTTGGTGTGTTAGAAAGGTTTCAATCAAATCCGGGAGAGGCTCACTGGGTTGCTGCAAAGAAAGTTCTAAGATATTTGTTGAGAACAAAAGGACATATGCCAGTGTATGGCAGAGAAAATTCATTGGAGTTAGTGGGATTCACAGACTCGGGGGTGATAGAGATGAAAGAAAGTCCACCAGTGGCTATGTATTTATGTTGA

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

Retrotran_gag_2 zf-CCHC

Protein Analysis

247

Amino Acids

28.08

Weight (kDa)

9.46

Isoelectric Point (pI)

38.66

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pol_BBD	PF22936	2 - 73	4.6e-13	Pol polyprotein, beta-barrel 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

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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: OG0001006)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_3g28582 FvH4_4g04791 FvH4_5g37183 FvH4_6g21376 FvH4_7g12362
malus_domestica	MD04G1043200.v1.1 MD08G1171400.v1.1 MD16G1163300.v1.1
pyrus_communis	pycom01g08240 pycom02g13280 pycom02g13290 pycom03g16600 pycom04g18500 pycom06g06360 pycom12g01620 pycom15g38160
rosa_chinensis	RchiOBHm_Chr1g0317711 RchiOBHm_Chr1g0337471 RchiOBHm_Chr1g0365501 RchiOBHm_Chr1g0375591 RchiOBHm_Chr1g0383411 RchiOBHm_Chr2g0115341 RchiOBHm_Chr2g0144381 RchiOBHm_Chr2g0150761 RchiOBHm_Chr2g0159601 RchiOBHm_Chr3g0453781 RchiOBHm_Chr3g0467131 RchiOBHm_Chr3g0491311 RchiOBHm_Chr3g0495711 RchiOBHm_Chr4g0385651 RchiOBHm_Chr4g0390931 RchiOBHm_Chr4g0441701 RchiOBHm_Chr5g0040291 RchiOBHm_Chr5g0040891 RchiOBHm_Chr5g0066231 RchiOBHm_Chr5g0076641 RchiOBHm_Chr6g0259091 RchiOBHm_Chr6g0300011 RchiOBHm_Chr6g0304531 RchiOBHm_Chr7g0192701 RchiOBHm_Chr7g0194431
rosa_roxburghii	Rroxscaffold_2G00112920 Rroxscaffold_3G00225970 Rroxscaffold_3G00227430 Rroxscaffold_4G00301360 Rroxscaffold_4G00305440 Rroxscaffold_5G00386330
rosa_wichuraiana	Rw0G010510 Rw1G007900 Rw1G018220 Rw1G022080 Rw2G040570 Rw2G046740 Rw4G002540 Rw5G013410 Rw5G017210 Rw5G017940 Rw7G005960 Rw7G007520 Rw7G012200 Rw7G030860 Rw7G032010

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	647
AclI	AACGTT	1 cut(s)	60
AcsI	RAATTY	3 cut(s)	13, 454, 658
AfaI	GTAC	1 cut(s)	413
AfiI	CCNNNNNNNGG	2 cut(s)	530, 647
AflIII	ACRYGT	1 cut(s)	346
AgsI	TTSAA	4 cut(s)	58, 259, 420, 563
AluBI	AGCT	1 cut(s)	98
AluI	AGCT	1 cut(s)	98
Alw26I	GTCTC	1 cut(s)	500
Ama87I	CYCGRG	1 cut(s)	688
ApeKI	GCWGC	1 cut(s)	593
ApoI	RAATTY	3 cut(s)	13, 454, 658
Asp700I	GAANNNNTTC	1 cut(s)	558
AsuC2I	CCSGG	1 cut(s)	573
AsuHPI	GGTGA	4 cut(s)	242, 287, 323, 706
AvaI	CYCGRG	1 cut(s)	688
BbvI	GCAGC	1 cut(s)	580
BccI	CCATC	1 cut(s)	100
BclI	TGATCA	1 cut(s)	292
BcnI	CCSGG	1 cut(s)	573
BcoDI	GTCTC	1 cut(s)	500
BisI	GCNGC	1 cut(s)	594
BlsI	GCNGC	1 cut(s)	595
Bme1390I	CCNGG	1 cut(s)	573
BmeT110I	CYCGRG	1 cut(s)	688
BmrFI	CCNGG	1 cut(s)	573
BmrI	ACTGGG	1 cut(s)	595
BmsI	GCATC	2 cut(s)	203, 354
BmuI	ACTGGG	1 cut(s)	595
BoxI	GACNNNNGTC	1 cut(s)	429
BpuMI	CCSGG	1 cut(s)	573
Bsc4I	CCNNNNNNNGG	2 cut(s)	530, 647
Bse1I	ACTGG	4 cut(s)	427, 590, 641, 719
BseGI	GGATG	2 cut(s)	111, 369
BseLI	CCNNNNNNNGG	2 cut(s)	530, 647
BseMII	CTCAG	1 cut(s)	317
BseNI	ACTGG	4 cut(s)	427, 590, 641, 719
BseXI	GCAGC	1 cut(s)	580
BsiHKCI	CYCGRG	1 cut(s)	688
BsiSI	CCGG	1 cut(s)	572
BslFI	GGGAC	3 cut(s)	91, 149, 417
BslI	CCNNNNNNNGG	2 cut(s)	530, 647
BsmAI	GTCTC	1 cut(s)	500
BsmFI	GGGAC	3 cut(s)	91, 149, 417
BsmI	GAATGC	1 cut(s)	281
BsoBI	CYCGRG	1 cut(s)	688
Bsp143I	GATC	1 cut(s)	292
BspCNI	CTCAG	1 cut(s)	318
BsrI	ACTGG	4 cut(s)	427, 590, 641, 719
BssMI	GATC	1 cut(s)	292
Bst4CI	ACNGT	1 cut(s)	371
BstDEI	CTNAG	3 cut(s)	326, 357, 608
BstF5I	GGATG	2 cut(s)	111, 369
BstKTI	GATC	1 cut(s)	295
BstMAI	GTCTC	1 cut(s)	500
BstMBI	GATC	1 cut(s)	292
BstNSI	RCATGY	1 cut(s)	350
BstPAI	GACNNNNGTC	1 cut(s)	429
BstSCI	CCNGG	1 cut(s)	571
BstV1I	GCAGC	1 cut(s)	580
BtsCI	GGATG	2 cut(s)	111, 369
BtsIMutI	CAGTG	4 cut(s)	434, 583, 648, 726
Csp6I	GTAC	1 cut(s)	412
CviAII	CATG	7 cut(s)	23, 172, 286, 347, 388, 446, 499
CviJI	RGCY	5 cut(s)	98, 132, 183, 581, 725
CviKI_1	RGCY	5 cut(s)	98, 132, 183, 581, 725
CviQI	GTAC	1 cut(s)	412
DdeI	CTNAG	3 cut(s)	326, 357, 608
DpnI	GATC	1 cut(s)	294
DpnII	GATC	1 cut(s)	292
Eco88I	CYCGRG	1 cut(s)	688
FaeI	CATG	7 cut(s)	26, 175, 289, 350, 391, 449, 502
FalI	AAGNNNNNCTT	2 cut(s)	239, 271
FaqI	GGGAC	3 cut(s)	91, 149, 417
FatI	CATG	7 cut(s)	22, 171, 285, 346, 387, 445, 498
FauNDI	CATATG	1 cut(s)	636
FbaI	TGATCA	1 cut(s)	292
Fnu4HI	GCNGC	1 cut(s)	594
FokI	GGATG	2 cut(s)	118, 376
Fsp4HI	GCNGC	1 cut(s)	594
GluI	GCNGC	1 cut(s)	594
HapII	CCGG	1 cut(s)	572
Hin1II	CATG	7 cut(s)	26, 175, 289, 350, 391, 449, 502
HinfI	GANTC	3 cut(s)	328, 678, 686
HpaII	CCGG	1 cut(s)	572
HphI	GGTGA	4 cut(s)	242, 287, 323, 706
Hpy166II	GTNNAC	1 cut(s)	716
Hpy8I	GTNNAC	1 cut(s)	716
HpyAV	CCTTC	1 cut(s)	68
HpyCH4III	ACNGT	1 cut(s)	371
HpyCH4IV	ACGT	2 cut(s)	60, 414
HpyCH4V	TGCA	7 cut(s)	4, 142, 194, 315, 367, 516, 596
HpyF3I	CTNAG	3 cut(s)	326, 357, 608
HpySE526I	ACGT	2 cut(s)	60, 414
Hsp92II	CATG	7 cut(s)	26, 175, 289, 350, 391, 449, 502
Ksp22I	TGATCA	1 cut(s)	292
Kzo9I	GATC	1 cut(s)	292
LpnPI	CCDG	8 cut(s)	114, 440, 532, 537, 571, 585, 654, 732
Lsp1109I	GCAGC	1 cut(s)	580
LweI	GCATC	2 cut(s)	203, 354
MaeII	ACGT	2 cut(s)	60, 414
MaeIII	GTNAC	3 cut(s)	329, 349, 377
MalI	GATC	1 cut(s)	294
MboI	GATC	1 cut(s)	292
MboII	GAAGA	2 cut(s)	189, 247
MfeI	CAATTG	1 cut(s)	143
MluCI	AATT	7 cut(s)	13, 49, 143, 200, 270, 454, 658
MlyI	GAGTC	2 cut(s)	337, 680
MmeI	TCCRAC	1 cut(s)	49
MnlI	CCTC	3 cut(s)	354, 442, 571
MroXI	GAANNNNTTC	1 cut(s)	558
MseI	TTAA	5 cut(s)	122, 207, 246, 269, 458
MspI	CCGG	1 cut(s)	572
MspR9I	CCNGG	1 cut(s)	573
MunI	CAATTG	1 cut(s)	143
Mva1269I	GAATGC	1 cut(s)	281
NciI	CCSGG	1 cut(s)	573
NdeI	CATATG	1 cut(s)	636
NdeII	GATC	1 cut(s)	292
NlaIII	CATG	7 cut(s)	26, 175, 289, 350, 391, 449, 502
NmuCI	GTSAC	3 cut(s)	329, 349, 377
NspI	RCATGY	1 cut(s)	350
PciI	ACATGT	1 cut(s)	346
PctI	GAATGC	1 cut(s)	281
PdmI	GAANNNNTTC	1 cut(s)	558
PfeI	GAWTC	1 cut(s)	678
PflMI	CCANNNNNTGG	1 cut(s)	647
PfoI	TCCNGGA	1 cut(s)	571
PkrI	GCNGC	1 cut(s)	595
PleI	GAGTC	2 cut(s)	336, 680
PpsI	GAGTC	2 cut(s)	336, 680
PscI	ACATGT	1 cut(s)	346
PshAI	GACNNNNGTC	1 cut(s)	429
Psp1406I	AACGTT	1 cut(s)	60
RsaI	GTAC	1 cut(s)	413
RsaNI	GTAC	1 cut(s)	412
SaqAI	TTAA	5 cut(s)	122, 207, 246, 269, 458
SatI	GCNGC	1 cut(s)	594
Sau3AI	GATC	1 cut(s)	292
SchI	GAGTC	2 cut(s)	337, 680
ScrFI	CCNGG	1 cut(s)	573
SetI	ASST	6 cut(s)	63, 100, 300, 417, 475, 560
SfaNI	GCATC	2 cut(s)	203, 354
Sse9I	AATT	7 cut(s)	13, 49, 143, 200, 270, 454, 658
StyD4I	CCNGG	1 cut(s)	571
TaaI	ACNGT	1 cut(s)	371
TaiI	ACGT	2 cut(s)	63, 417
TasI	AATT	7 cut(s)	13, 49, 143, 200, 270, 454, 658
TfiI	GAWTC	1 cut(s)	678
Tru1I	TTAA	5 cut(s)	122, 207, 246, 269, 458
Tru9I	TTAA	5 cut(s)	122, 207, 246, 269, 458
TscAI	CASTG	4 cut(s)	434, 590, 648, 726
TseFI	GTSAC	3 cut(s)	329, 349, 377
TseI	GCWGC	1 cut(s)	593
Tsp45I	GTSAC	3 cut(s)	329, 349, 377
TspDTI	ATGAA	9 cut(s)	6, 124, 214, 274, 376, 471, 476, 651, 719
TspRI	CASTG	4 cut(s)	434, 590, 648, 726
Van91I	CCANNNNNTGG	1 cut(s)	647
XapI	RAATTY	3 cut(s)	13, 454, 658
XceI	RCATGY	1 cut(s)	350
XcmI	CCANNNNNNNNNTGG	1 cut(s)	526
XmnI	GAANNNNTTC	1 cut(s)	558

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