Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr16

Orthogroup ID

OG0006793

Physical Location & Seq

Genomic Coordinates Reverse (-)

10395608 .. 10397678

Gene Structure 2071 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD16G1135500.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 972 bp

ATGAGTAGTGCTGCAGTTGTGAGTAGTGCTGCAGTTGTAGTAGCCCTTCCTTCTCCCCCTAATCTTAACGGGTCTCTCTTTTCTCCAACTCCCATTAATAGCAGCTCGAACAAAAAGGATGGAATTGGAGAGCAAATGGTAATGAAGGAGACAGGGGATGGTGGGTACAAGTGGCGTTTGGTGATTGCTTATGACGGCACCCGTTATGCAGGATGGCAATATCAGAGTTCACCACCTACCGTACAGTGCTTTGTGGAGAAAGCTCTAACGACCGCTACGAAGCTGGAAAGGAACGATCTTCATTTCGTTGGTGCAAGTAGGACGGATAAAGGAGTACATGCCTGGGGTCAGGTTGCACACTTTGTCACACCTTTCGACTATGACAGCATTGAAAGCATTCACGCTGCTCTCAACGGTCTTCTTCCTGATGATATCCGAGTTAGGGAGATCAGCCCTGCAATGCCTGAATTCCATGCTCGTTTTTCAGCGAAAAGCAAGATTTATCATTACAAAATACATAACGACACATTCATGGATCCATTTCAGCGCCAATATGCTTACCATAGATATTTTATTGGAAAGCATGATTTCTCTGCTTTTGTCAATGCTTCCCAGAAGGAACAAGTGCGTGATCCAGTGAAGGATATATTCCGTTTTGATGTCATTGAATTGGGAGTTCTTTTACGGCTAGAAGTTGAAGGCTCCGGCTTCTTATACAGACAAGTCCGGAACATGGTTGCTCTGCTTATTCAAATTGGAAGGGAAGCACTTCCTCCTGATATTGTTCCCAAGATATTGGCAACACGAGATCGGAGAGTGCTTGCCAAATATACCATGTTTGCTCCACCCCACGGGCTTTGTCTTGCGACGGTCAAGTACAACGAGGAGCATCTACGGCTTCCATCCGGTTCCTTCGCAACCAGTTTTGGTATGCATTATACTATTGGCTCATGTAAGCTTCCATTCTACTAA

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

PseudoU_synth_1

Protein Analysis

324

Amino Acids

36.27

Weight (kDa)

8.95

Isoelectric Point (pI)

50.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_1	PF01416	62 - 161	1e-08	tRNA pseudouridine synthase
PseudoU_synth_1	PF01416	189 - 294	3.7e-24	tRNA pseudouridine synthase

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: OG0006793)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G06950
fragaria_vesca	FvH4_4g21570 FvH4_4g21570 FvH4_4g21570
malus_domestica	MD13G1140300.v1.1 MD16G1135500.v1.1
prunus_persica	Prupe.1G104700_v2.0.a1 Prupe.1G104700_v2.0.a1 Prupe.1G104700_v2.0.a1 Prupe.1G104700_v2.0.a1
pyrus_communis	pycom13g12200 pycom16g11950
rosa_chinensis	RchiOBHm_Chr4g0427681
rosa_laevigata	RLG00000007217
rosa_multiflora	Rmu_sc0003399.1_g000003 Rmu_sc0016038.1_g000001
rosa_roxburghii	Rroxscaffold_5G00369310
rosa_rugosa	Rorug04G0219100 Rorug04G0219200 Rorug04G0219300 Rorug04G0219400
rosa_samantha	Rh4AG275600 Rh4BG281600 Rh4CG297100 Rh4DG279000
rosa_wichuraiana	Rw4G023920

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	197
AccIII	TCCGGA	1 cut(s)	726
AciI	CCGC	1 cut(s)	273
AclWI	GGATC	3 cut(s)	530, 543, 626
AcsI	RAATTY	1 cut(s)	467
AfaI	GTAC	4 cut(s)	167, 243, 336, 878
AfiI	CCNNNNNNNGG	3 cut(s)	442, 733, 851
AgsI	TTSAA	4 cut(s)	392, 668, 698, 752
AjnI	CCWGG	1 cut(s)	341
AluBI	AGCT	4 cut(s)	105, 263, 283, 958
AluI	AGCT	4 cut(s)	105, 263, 283, 958
Alw26I	GTCTC	2 cut(s)	78, 143
AlwI	GGATC	3 cut(s)	530, 543, 626
Aor13HI	TCCGGA	1 cut(s)	726
ApeKI	GCWGC	4 cut(s)	11, 29, 102, 404
ApoI	RAATTY	1 cut(s)	467
AseI	ATTAAT	1 cut(s)	96
Asp700I	GAANNNNTTC	2 cut(s)	396, 768
AspLEI	GCGC	1 cut(s)	549
AsuHPI	GGTGA	2 cut(s)	193, 222
BamHI	GGATCC	1 cut(s)	535
BanI	GGYRCC	1 cut(s)	197
BarI	GAAGNNNNNNTAC	2 cut(s)	30, 62
BauI	CACGAG	1 cut(s)	804
BbsI	GAAGAC	1 cut(s)	410
BbvI	GCAGC	3 cut(s)	16, 114, 391
BccI	CCATC	4 cut(s)	113, 152, 207, 910
BceAI	ACGGC	3 cut(s)	211, 701, 911
BciT130I	CCWGG	1 cut(s)	343
BcoDI	GTCTC	2 cut(s)	78, 143
BfaI	CTAG	1 cut(s)	689
BfmI	CTRYAG	2 cut(s)	12, 30
BfoI	RGCGCY	1 cut(s)	550
BisI	GCNGC	4 cut(s)	12, 30, 103, 405
BlsI	GCNGC	4 cut(s)	13, 31, 104, 406
Bme1390I	CCNGG	1 cut(s)	343
BmiI	GGNNCC	4 cut(s)	199, 537, 703, 910
BmrFI	CCNGG	1 cut(s)	343
BmsI	GCATC	1 cut(s)	898
BpiI	GAAGAC	1 cut(s)	410
BsaI	GGTCTC	1 cut(s)	78
BsaJI	CCNNGG	2 cut(s)	342, 850
BsaWI	WCCGGW	2 cut(s)	726, 905
Bsc4I	CCNNNNNNNGG	3 cut(s)	442, 733, 851
Bse1I	ACTGG	2 cut(s)	635, 921
Bse3DI	GCAATG	1 cut(s)	465
BseAI	TCCGGA	1 cut(s)	726
BseBI	CCWGG	1 cut(s)	343
BseDI	CCNNGG	2 cut(s)	342, 850
BseGI	GGATG	4 cut(s)	124, 163, 218, 902
BseLI	CCNNNNNNNGG	3 cut(s)	442, 733, 851
BseMI	GCAATG	1 cut(s)	465
BseNI	ACTGG	2 cut(s)	635, 921
BseRI	GAGGAG	1 cut(s)	899
BseXI	GCAGC	3 cut(s)	16, 114, 391
Bsh1285I	CGRYCG	1 cut(s)	273
BshNI	GGYRCC	1 cut(s)	197
BsiEI	CGRYCG	1 cut(s)	273
BsiSI	CCGG	3 cut(s)	705, 727, 906
BslI	CCNNNNNNNGG	3 cut(s)	442, 733, 851
BsmAI	GTCTC	2 cut(s)	78, 143
BsmI	GAATGC	1 cut(s)	396
Bso31I	GGTCTC	1 cut(s)	78
Bsp13I	TCCGGA	1 cut(s)	726
Bsp143I	GATC	5 cut(s)	295, 447, 535, 631, 808
BspACI	CCGC	1 cut(s)	273
BspEI	TCCGGA	1 cut(s)	726
BspLI	GGNNCC	4 cut(s)	199, 537, 703, 910
BspMAI	CTGCAG	2 cut(s)	16, 34
BspPI	GGATC	3 cut(s)	530, 543, 626
BspT107I	GGYRCC	1 cut(s)	197
BspTNI	GGTCTC	1 cut(s)	78
BsrDI	GCAATG	1 cut(s)	465
BsrI	ACTGG	2 cut(s)	635, 921
BssECI	CCNNGG	2 cut(s)	342, 850
BssMI	GATC	5 cut(s)	295, 447, 535, 631, 808
BssSI	CACGAG	1 cut(s)	804
Bst2BI	CACGAG	1 cut(s)	804
Bst2UI	CCWGG	1 cut(s)	343
Bst4CI	ACNGT	4 cut(s)	241, 246, 416, 871
BstC8I	GCNNGC	1 cut(s)	822
BstDSI	CCRYGG	1 cut(s)	850
BstF5I	GGATG	4 cut(s)	124, 163, 218, 902
BstH2I	RGCGCY	1 cut(s)	550
BstHHI	GCGC	1 cut(s)	549
BstKTI	GATC	5 cut(s)	298, 450, 538, 634, 811
BstMAI	GTCTC	2 cut(s)	78, 143
BstMBI	GATC	5 cut(s)	295, 447, 535, 631, 808
BstMCI	CGRYCG	1 cut(s)	273
BstMWI	GCNNNNNNNGC	2 cut(s)	393, 895
BstNI	CCWGG	1 cut(s)	343
BstNSI	RCATGY	1 cut(s)	341
BstSCI	CCNGG	1 cut(s)	341
BstSFI	CTRYAG	2 cut(s)	12, 30
BstV1I	GCAGC	3 cut(s)	16, 114, 391
BstV2I	GAAGAC	1 cut(s)	410
BstX2I	RGATCY	1 cut(s)	535
BstXI	CCANNNNNNTGG	1 cut(s)	796
BstYI	RGATCY	1 cut(s)	535
BtgI	CCRYGG	1 cut(s)	850
BtsCI	GGATG	4 cut(s)	124, 163, 218, 902
BtsIMutI	CAGTG	2 cut(s)	251, 642
Cac8I	GCNNGC	1 cut(s)	822
CfoI	GCGC	1 cut(s)	549
Csp6I	GTAC	4 cut(s)	166, 242, 335, 877
CspCI	CAANNNNNGTGG	2 cut(s)	839, 874
CviAII	CATG	7 cut(s)	338, 473, 532, 584, 733, 835, 951
CviQI	GTAC	4 cut(s)	166, 242, 335, 877
DpnI	GATC	5 cut(s)	297, 449, 537, 633, 810
DpnII	GATC	5 cut(s)	295, 447, 535, 631, 808
Eco31I	GGTCTC	1 cut(s)	78
Eco32I	GATATC	1 cut(s)	433
EcoRI	GAATTC	1 cut(s)	467
EcoRII	CCWGG	1 cut(s)	341
EcoRV	GATATC	1 cut(s)	433
EcoT22I	ATGCAT	1 cut(s)	936
FaeI	CATG	7 cut(s)	341, 476, 535, 587, 736, 838, 954
FatI	CATG	7 cut(s)	337, 472, 531, 583, 732, 834, 950
Fnu4HI	GCNGC	4 cut(s)	12, 30, 103, 405
FokI	GGATG	4 cut(s)	131, 170, 225, 889
Fsp4HI	GCNGC	4 cut(s)	12, 30, 103, 405
FspBI	CTAG	1 cut(s)	689
GlaI	GCGC	1 cut(s)	548
GluI	GCNGC	4 cut(s)	12, 30, 103, 405
HaeII	RGCGCY	1 cut(s)	550
HapII	CCGG	3 cut(s)	705, 727, 906
HhaI	GCGC	1 cut(s)	549
Hin1II	CATG	7 cut(s)	341, 476, 535, 587, 736, 838, 954
Hin6I	GCGC	1 cut(s)	547
HinP1I	GCGC	1 cut(s)	547
HindIII	AAGCTT	1 cut(s)	956
HpaII	CCGG	3 cut(s)	705, 727, 906
HphI	GGTGA	2 cut(s)	193, 222
Hpy166II	GTNNAC	1 cut(s)	230
Hpy188I	TCNGA	3 cut(s)	225, 437, 813
Hpy188III	TCNNGA	3 cut(s)	425, 727, 776
Hpy8I	GTNNAC	1 cut(s)	230
Hpy99I	CGWCG	1 cut(s)	871
HpyAV	CCTTC	8 cut(s)	56, 60, 139, 610, 634, 692, 753, 922
HpyCH4III	ACNGT	4 cut(s)	241, 246, 416, 871
HpyCH4V	TGCA	7 cut(s)	14, 32, 209, 314, 356, 458, 934
HpyF10VI	GCNNNNNNNGC	2 cut(s)	393, 895
Hsp92II	CATG	7 cut(s)	341, 476, 535, 587, 736, 838, 954
HspAI	GCGC	1 cut(s)	547
Kpn2I	TCCGGA	1 cut(s)	726
Kzo9I	GATC	5 cut(s)	295, 447, 535, 631, 808
LmnI	GCTCC	3 cut(s)	707, 847, 886
Lsp1109I	GCAGC	3 cut(s)	16, 114, 391
LweI	GCATC	1 cut(s)	898
MaeI	CTAG	1 cut(s)	689
MaeIII	GTNAC	1 cut(s)	364
MalI	GATC	5 cut(s)	297, 449, 537, 633, 810
MboI	GATC	5 cut(s)	295, 447, 535, 631, 808
MboII	GAAGA	3 cut(s)	290, 410, 413
MflI	RGATCY	1 cut(s)	535
MluCI	AATT	4 cut(s)	123, 467, 668, 753
MmeI	TCCRAC	1 cut(s)	110
MnlI	CCTC	2 cut(s)	783, 877
Mph1103I	ATGCAT	1 cut(s)	936
MroI	TCCGGA	1 cut(s)	726
MroXI	GAANNNNTTC	2 cut(s)	396, 768
MseI	TTAA	2 cut(s)	66, 96
MslI	CAYNNNNRTG	1 cut(s)	530
MspI	CCGG	3 cut(s)	705, 727, 906
MspR9I	CCNGG	1 cut(s)	343
Mva1269I	GAATGC	1 cut(s)	396
MvaI	CCWGG	1 cut(s)	343
MwoI	GCNNNNNNNGC	2 cut(s)	393, 895
NdeII	GATC	5 cut(s)	295, 447, 535, 631, 808
NlaIII	CATG	7 cut(s)	341, 476, 535, 587, 736, 838, 954
NlaIV	GGNNCC	4 cut(s)	199, 537, 703, 910
NmuCI	GTSAC	1 cut(s)	364
NsiI	ATGCAT	1 cut(s)	936
NspI	RCATGY	1 cut(s)	341
PcsI	WCGNNNNNNNCGW	1 cut(s)	275
PctI	GAATGC	1 cut(s)	396
PdmI	GAANNNNTTC	2 cut(s)	396, 768
PkrI	GCNGC	4 cut(s)	13, 31, 104, 406
PshBI	ATTAAT	1 cut(s)	96
Psp6I	CCWGG	1 cut(s)	341
PspGI	CCWGG	1 cut(s)	341
PspN4I	GGNNCC	4 cut(s)	199, 537, 703, 910
PstI	CTGCAG	2 cut(s)	16, 34
PsuI	RGATCY	1 cut(s)	535
RsaI	GTAC	4 cut(s)	167, 243, 336, 878
RsaNI	GTAC	4 cut(s)	166, 242, 335, 877
RseI	CAYNNNNRTG	1 cut(s)	530
SaqAI	TTAA	2 cut(s)	66, 96
SatI	GCNGC	4 cut(s)	12, 30, 103, 405
Sau3AI	GATC	5 cut(s)	295, 447, 535, 631, 808
ScrFI	CCNGG	1 cut(s)	343
SetI	ASST	7 cut(s)	107, 238, 265, 285, 354, 373, 960
SfaNI	GCATC	1 cut(s)	898
SfcI	CTRYAG	2 cut(s)	12, 30
SmiMI	CAYNNNNRTG	1 cut(s)	530
Sse9I	AATT	4 cut(s)	123, 467, 668, 753
SsiI	CCGC	1 cut(s)	273
SspMI	CTAG	1 cut(s)	689
StyD4I	CCNGG	1 cut(s)	341
TaaI	ACNGT	4 cut(s)	241, 246, 416, 871
TaqI	TCGA	2 cut(s)	107, 375
TasI	AATT	4 cut(s)	123, 467, 668, 753
TatI	WGTACW	2 cut(s)	334, 876
Tru1I	TTAA	2 cut(s)	66, 96
Tru9I	TTAA	2 cut(s)	66, 96
TscAI	CASTG	2 cut(s)	251, 642
TseFI	GTSAC	1 cut(s)	364
TseI	GCWGC	4 cut(s)	11, 29, 102, 404
Tsp45I	GTSAC	1 cut(s)	364
TspDTI	ATGAA	3 cut(s)	158, 290, 520
TspGWI	ACGGA	2 cut(s)	338, 641
TspRI	CASTG	2 cut(s)	251, 642
VspI	ATTAAT	1 cut(s)	96
XapI	RAATTY	1 cut(s)	467
XceI	RCATGY	1 cut(s)	341
XmnI	GAANNNNTTC	2 cut(s)	396, 768
XspI	CTAG	1 cut(s)	689
Zsp2I	ATGCAT	1 cut(s)	936

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