Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr02

Orthogroup ID

OG0006436

Physical Location & Seq

Genomic Coordinates Reverse (-)

13011686 .. 13012828

Gene Structure 1143 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD02G1156200.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 903 bp

ATGGCATCTGCAAAGGACGATTCCTTACAAGCTATTGGTGTGAAATTGAATGGAAATAATTATGTGTATTGGGCATATGTGATGAAGAATTTTTTGATTGGAAAAGGTTTGTGGGGCTATGTTTCTGGAATGATTTCTATTCCAAATAACCCTAAAGATGAGAAACATTTTGAATTGGTTGCTGCATGGGAGATGAATAATTCAAAGATTATTACGTGGATTAATAATTCTGTTGATTTGGCTATTGGAATGCAACTAGCTAAGTTCTCAACGTCTAAGGAAGTTTGGGATCACTTGGCAAAGTTGTATACCAAGGCTAATTTTGCTAAGAGGTATCAATTGGAAATGGAGATTCGTACAATCCAGCAAGGTGATAAGAGTATTCAAGTGTTTTACAATGAACTGACCAATCTTTGGGATCAACTTGCATTAACTGAGCCTGAAGAACTCGGCATTGTCAAGCTCTATTATAAATATAGAGAAGAACAACGTCTTGTTCAGTTTCTAATGCCTCTTCGGGATGAGTTCGAGACACTCCGTAGCTCCATCCTTCATCGAACTTCTCTTCCATCTGTTGATTCTGTTCTTAATGAGTTACAAGCAGAAGAAGTTCGTGTGCAGTCGCATAGGCTCTCTTCATCGTCGTCAAATACTTCAGCATTTGCTGCGGCAAGGTCTCGTAGGTTGGCATCGGCACTGACATGGTTGTGTTTTGAAGTTGGCATCGACATTAGCATGGTTGTGTTTTTCGCATCGGCATTGGCACTGGAATTTGGAGTCTTGCATCCATATCTACTTTGGCAAACCCATGGCGTGTACCGCCATGAGTTTGACGGGGGGTGTTGGAAAATATTATTATTTAGATTTATTTTAATGTTTGGTTTTTTGGGCTTAGCCCGTTAG

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 Retrotran_gag_3

Protein Analysis

301

Amino Acids

34.52

Weight (kDa)

7.06

Isoelectric Point (pI)

31.08

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Retrotran_gag_3	PF14244	6 - 48	3.9e-10	gag-polypeptide of LTR copia-type
Retrotran_gag_2	PF14223	28 - 208	1.3e-14	gag-polypeptide of LTR copia-type
Retrotrans_gag	PF03732	93 - 147	6.2e-06	Retrotransposon gag protein

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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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)
AanI	TTATAA	1 cut(s)	471
AccB7I	CCANNNNNTGG	1 cut(s)	414
AccI	GTMKAC	1 cut(s)	308
AciI	CCGC	2 cut(s)	668, 820
AclWI	GGATC	2 cut(s)	297, 426
AcsI	RAATTY	2 cut(s)	88, 770
AcuI	CTGAAG	2 cut(s)	462, 639
AfaI	GTAC	2 cut(s)	358, 818
AfiI	CCNNNNNNNGG	1 cut(s)	414
AgsI	TTSAA	5 cut(s)	49, 173, 204, 386, 716
AloI	GAACNNNNNNTCC	2 cut(s)	550, 582
AluBI	AGCT	4 cut(s)	32, 260, 463, 543
AluI	AGCT	4 cut(s)	32, 260, 463, 543
Alw26I	GTCTC	2 cut(s)	524, 681
AlwI	GGATC	2 cut(s)	297, 426
ApeKI	GCWGC	2 cut(s)	182, 665
ApoI	RAATTY	2 cut(s)	88, 770
AseI	ATTAAT	1 cut(s)	222
Asp700I	GAANNNNTTC	2 cut(s)	133, 609
AsuHPI	GGTGA	1 cut(s)	383
BbvI	GCAGC	2 cut(s)	169, 652
BccI	CCATC	2 cut(s)	554, 577
BcoDI	GTCTC	2 cut(s)	524, 681
BfaI	CTAG	1 cut(s)	257
BisI	GCNGC	3 cut(s)	183, 666, 669
BlpI	GCTNAGC	1 cut(s)	892
BlsI	GCNGC	3 cut(s)	184, 667, 670
BmsI	GCATC	5 cut(s)	14, 698, 732, 761, 793
Bpu1102I	GCTNAGC	1 cut(s)	892
BsaAI	YACGTR	1 cut(s)	216
BsaI	GGTCTC	1 cut(s)	681
BsaJI	CCNNGG	2 cut(s)	312, 808
Bsc4I	CCNNNNNNNGG	1 cut(s)	414
Bse1I	ACTGG	1 cut(s)	771
BseDI	CCNNGG	2 cut(s)	312, 808
BseGI	GGATG	3 cut(s)	526, 546, 784
BseLI	CCNNNNNNNGG	1 cut(s)	414
BseMII	CTCAG	1 cut(s)	426
BseNI	ACTGG	1 cut(s)	771
BseXI	GCAGC	2 cut(s)	169, 652
BsgI	GTGCAG	1 cut(s)	638
BslI	CCNNNNNNNGG	1 cut(s)	414
BsmAI	GTCTC	2 cut(s)	524, 681
BsmI	GAATGC	1 cut(s)	255
Bso31I	GGTCTC	1 cut(s)	681
Bsp143I	GATC	2 cut(s)	289, 418
Bsp1720I	GCTNAGC	1 cut(s)	892
Bsp19I	CCATGG	1 cut(s)	808
BspACI	CCGC	2 cut(s)	668, 820
BspCNI	CTCAG	1 cut(s)	427
BspPI	GGATC	2 cut(s)	297, 426
BspTNI	GGTCTC	1 cut(s)	681
BsrI	ACTGG	1 cut(s)	771
BssECI	CCNNGG	2 cut(s)	312, 808
BssMI	GATC	2 cut(s)	289, 418
BssNAI	GTATAC	1 cut(s)	309
BssT1I	CCWWGG	2 cut(s)	312, 808
Bst1107I	GTATAC	1 cut(s)	309
Bst6I	CTCTTC	3 cut(s)	519, 570, 640
BstAPI	GCANNNNNTGC	1 cut(s)	665
BstBAI	YACGTR	1 cut(s)	216
BstDEI	CTNAG	5 cut(s)	261, 276, 327, 435, 892
BstDSI	CCRYGG	1 cut(s)	808
BstF5I	GGATG	3 cut(s)	526, 546, 784
BstKTI	GATC	2 cut(s)	292, 421
BstMAI	GTCTC	2 cut(s)	524, 681
BstMBI	GATC	2 cut(s)	289, 418
BstMWI	GCNNNNNNNGC	3 cut(s)	323, 665, 819
BstV1I	GCAGC	2 cut(s)	169, 652
BstZ17I	GTATAC	1 cut(s)	309
BtgI	CCRYGG	1 cut(s)	808
BtsCI	GGATG	3 cut(s)	526, 546, 784
BtsIMutI	CAGTG	2 cut(s)	695, 764
Csp6I	GTAC	2 cut(s)	357, 817
CviAII	CATG	5 cut(s)	186, 702, 736, 809, 824
CviQI	GTAC	2 cut(s)	357, 817
DdeI	CTNAG	5 cut(s)	261, 276, 327, 435, 892
DpnI	GATC	2 cut(s)	291, 420
DpnII	GATC	2 cut(s)	289, 418
Eam1104I	CTCTTC	3 cut(s)	519, 570, 640
EarI	CTCTTC	3 cut(s)	519, 570, 640
Eco130I	CCWWGG	2 cut(s)	312, 808
Eco31I	GGTCTC	1 cut(s)	681
Eco57I	CTGAAG	2 cut(s)	462, 639
EcoT14I	CCWWGG	2 cut(s)	312, 808
ErhI	CCWWGG	2 cut(s)	312, 808
FaeI	CATG	5 cut(s)	189, 705, 739, 812, 827
FatI	CATG	5 cut(s)	185, 701, 735, 808, 823
FauNDI	CATATG	1 cut(s)	76
FblI	GTMKAC	1 cut(s)	308
Fnu4HI	GCNGC	3 cut(s)	183, 666, 669
FokI	GGATG	3 cut(s)	533, 533, 771
Fsp4HI	GCNGC	3 cut(s)	183, 666, 669
FspBI	CTAG	1 cut(s)	257
GluI	GCNGC	3 cut(s)	183, 666, 669
Hin1II	CATG	5 cut(s)	189, 705, 739, 812, 827
HinfI	GANTC	4 cut(s)	20, 352, 578, 777
HphI	GGTGA	1 cut(s)	383
Hpy166II	GTNNAC	2 cut(s)	309, 817
Hpy188III	TCNNGA	3 cut(s)	126, 518, 529
Hpy8I	GTNNAC	2 cut(s)	309, 817
Hpy99I	CGWCG	1 cut(s)	646
HpyAV	CCTTC	1 cut(s)	560
HpyCH4IV	ACGT	3 cut(s)	215, 272, 490
HpyCH4V	TGCA	6 cut(s)	11, 185, 253, 428, 619, 784
HpyF10VI	GCNNNNNNNGC	3 cut(s)	323, 665, 819
HpyF3I	CTNAG	5 cut(s)	261, 276, 327, 435, 892
HpySE526I	ACGT	3 cut(s)	215, 272, 490
Hsp92II	CATG	5 cut(s)	189, 705, 739, 812, 827
Kzo9I	GATC	2 cut(s)	289, 418
LmnI	GCTCC	1 cut(s)	548
LpnPI	CCDG	4 cut(s)	111, 377, 453, 752
Lsp1109I	GCAGC	2 cut(s)	169, 652
LweI	GCATC	5 cut(s)	14, 698, 732, 761, 793
MaeI	CTAG	1 cut(s)	257
MaeII	ACGT	3 cut(s)	215, 272, 490
MaeIII	GTNAC	1 cut(s)	594
MalI	GATC	2 cut(s)	291, 420
MboI	GATC	2 cut(s)	289, 418
MboII	GAAGA	7 cut(s)	97, 455, 494, 506, 557, 617, 627
MfeI	CAATTG	1 cut(s)	338
MluCI	AATT	9 cut(s)	44, 58, 88, 173, 199, 226, 319, 338, 770
MlyI	GAGTC	1 cut(s)	786
MmeI	TCCRAC	1 cut(s)	824
MnlI	CCTC	2 cut(s)	324, 522
MroXI	GAANNNNTTC	2 cut(s)	133, 609
MseI	TTAA	4 cut(s)	222, 431, 588, 872
MslI	CAYNNNNRTG	4 cut(s)	700, 706, 734, 740
MunI	CAATTG	1 cut(s)	338
Mva1269I	GAATGC	1 cut(s)	255
MwoI	GCNNNNNNNGC	3 cut(s)	323, 665, 819
NcoI	CCATGG	1 cut(s)	808
NdeI	CATATG	1 cut(s)	76
NdeII	GATC	2 cut(s)	289, 418
NlaIII	CATG	5 cut(s)	189, 705, 739, 812, 827
NmeAIII	GCCGAG	1 cut(s)	429
PctI	GAATGC	1 cut(s)	255
PdmI	GAANNNNTTC	2 cut(s)	133, 609
PfeI	GAWTC	3 cut(s)	20, 352, 578
PflMI	CCANNNNNTGG	1 cut(s)	414
PkrI	GCNGC	3 cut(s)	184, 667, 670
PleI	GAGTC	1 cut(s)	785
PpsI	GAGTC	1 cut(s)	785
Ppu21I	YACGTR	1 cut(s)	216
PshBI	ATTAAT	1 cut(s)	222
PsiI	TTATAA	1 cut(s)	471
RsaI	GTAC	2 cut(s)	358, 818
RsaNI	GTAC	2 cut(s)	357, 817
RseI	CAYNNNNRTG	4 cut(s)	700, 706, 734, 740
SaqAI	TTAA	4 cut(s)	222, 431, 588, 872
SatI	GCNGC	3 cut(s)	183, 666, 669
Sau3AI	GATC	2 cut(s)	289, 418
SchI	GAGTC	1 cut(s)	786
SfaNI	GCATC	5 cut(s)	14, 698, 732, 761, 793
SmiMI	CAYNNNNRTG	4 cut(s)	700, 706, 734, 740
Sse9I	AATT	9 cut(s)	44, 58, 88, 173, 199, 226, 319, 338, 770
SsiI	CCGC	2 cut(s)	668, 820
SspI	AATATT	1 cut(s)	852
SspMI	CTAG	1 cut(s)	257
StyI	CCWWGG	2 cut(s)	312, 808
TaiI	ACGT	3 cut(s)	218, 275, 493
TaqI	TCGA	3 cut(s)	528, 556, 726
TasI	AATT	9 cut(s)	44, 58, 88, 173, 199, 226, 319, 338, 770
TauI	GCSGC	1 cut(s)	671
TfiI	GAWTC	3 cut(s)	20, 352, 578
Tru1I	TTAA	4 cut(s)	222, 431, 588, 872
Tru9I	TTAA	4 cut(s)	222, 431, 588, 872
TscAI	CASTG	2 cut(s)	702, 771
TseI	GCWGC	2 cut(s)	182, 665
TspDTI	ATGAA	5 cut(s)	98, 209, 414, 542, 627
TspGWI	ACGGA	1 cut(s)	527
TspRI	CASTG	2 cut(s)	702, 771
Van91I	CCANNNNNTGG	1 cut(s)	414
VspI	ATTAAT	1 cut(s)	222
XapI	RAATTY	2 cut(s)	88, 770
XcmI	CCANNNNNNNNNTGG	1 cut(s)	795
XmiI	GTMKAC	1 cut(s)	308
XmnI	GAANNNNTTC	2 cut(s)	133, 609
XspI	CTAG	1 cut(s)	257

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