Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr15

Orthogroup ID

OG0004066

Physical Location & Seq

Genomic Coordinates Forward (+)

323132 .. 324473

Gene Structure 1342 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD15G1005400.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 969 bp

ATGGTTGAATCTGAAATTGGTGAAAAATTTAGGGTTCTTCCCGGAAATGCTGGCTGTGATAATTTGATTTCTGAGACCAGAAATGAAGTTAGCCTTAGCATTAATGAAGAAATTAAGGTTCTTACGGAGAATGCTGGGGTTGATAATTCGAATTCTGAACTCAAAACTGAAATTAGCATTAGTATTAATAACAATGAGGTTACTGAAATTGAGGTTGAGAATAATCGAGTGGTCCCCAATGAGGCAGAGGCTGCTGATTTGAATTCGGAGTCACTAGATGATACGAATGTTAGTTTTGGTGAAGAGAAGGCTAATGAAAAAGAGAATACAGAGGAAGGAAGTGGAAAAGGAAATGGGTTTTGTTATGGTGAGAAGGAGAGGGAAAGGTTCAACAAAATTTTGAATAGTTATGAGGGGACTCATAACTTCCACAACTTCACCACCAGAACTAAAGCTGTAGACCCCGCTGCTCAGCGCTACATTATTTCATTCAATGCGAACACCACGGTTACAGTTGAGGGTATGGAATTCGTTAAGTGTGAGGTTGTGGGGCAGAGCTTCATGCTTCATCAGATTAGGAAGATGATCGGGCTTGCGGTGGCAATCTTCAGGGGATGTGCTCCAGAGTCATTGCTCGAAAGAGCATTGCAAAAGGATGTTAACATCAATGTGCCGACAGCTCCTGAAGTTGGATTGTACTTGGATGAGTGCTTCTTTTCGTCATATAACCAGAAATGGGGAGACAGTCATGAAGAGCTGTCAATGAAAGGCTATGAACAAGAGGCAGAAGACTTCAAGATGAAGCATATATACACTCACATAGCATCCACCGAGCATAAAGAAGGTGTTGTGGGTCTCTGGTTGCACTCCCTCAACCACCGTAACTATCCGGATTTAGGTCCTGCTGAGAACAATGGAAATACCAGCAACGGAATAAGTGCTGATACGGGTAATGTCGTTGCTGAGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000049 GO:0000959 GO:0000963 GO:0001522 GO:0002153 GO:0003674 GO:0003676 GO:0003723 GO:0003727 GO:0003824 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0006139 GO:0006396 GO:0006399 GO:0006400 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009451 GO:0009982 GO:0009987 GO:0010467 GO:0016070 GO:0016071 GO:0016556 GO:0016853 GO:0016866 GO:0031119 GO:0031974 GO:0034470 GO:0034641 GO:0034660 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043412 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044429 GO:0044444 GO:0044446 GO:0044464 GO:0046483 GO:0070013 GO:0070525 GO:0070900 GO:0070902 GO:0071704 GO:0090304 GO:0090646 GO:0097159 GO:0140053 GO:1900864 GO:1901360 GO:1901363 GO:1990481

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_1

Protein Analysis

323

Amino Acids

35.78

Weight (kDa)

4.69

Isoelectric Point (pI)

34.21

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_1	PF01416	135 - 239	2.4e-14	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

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Orthologous Genes (Group: OG0004066)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G20370 AT1G76120 AT1G76120
fragaria_vesca	FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_4g09040 FvH4_5g07491
malus_domestica	MD15G1005300.v1.1 MD15G1005400.v1.1
prunus_persica	Prupe.1G357900_v2.0.a1
pyrus_communis	pycom08g00460 pycom15g00380 pycom15g00390
rosa_chinensis	RchiOBHm_Chr6g0303831
rosa_laevigata	RLG00000011040
rosa_multiflora	Rmu_co8307379.1_g000001 Rmu_sc0012878.1_g000001 Rmu_sc0022895.1_g000001
rosa_roxburghii	Rroxscaffold_7G00164370
rosa_rugosa	Rorug06G0325200
rosa_samantha	Rh6AG439500 Rh6BG463500 Rh6CG451800 Rh6DG438700
rosa_wichuraiana	Rw6G038050

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	459
AccIII	TCCGGA	1 cut(s)	889
AciI	CCGC	2 cut(s)	465, 596
AcsI	RAATTY	5 cut(s)	26, 151, 262, 396, 527
AcuI	CTGAAG	2 cut(s)	592, 705
AfaI	GTAC	1 cut(s)	698
AfeI	AGCGCT	1 cut(s)	476
AfiI	CCNNNNNNNGG	4 cut(s)	241, 689, 736, 896
AgsI	TTSAA	6 cut(s)	8, 262, 391, 403, 493, 796
AjuI	GAANNNNNNNTTGG	1 cut(s)	32
AluBI	AGCT	4 cut(s)	455, 558, 680, 757
AluI	AGCT	4 cut(s)	455, 558, 680, 757
Alw21I	GWGCWC	1 cut(s)	622
Alw26I	GTCTC	3 cut(s)	68, 735, 860
AlwNI	CAGNNNCTG	2 cut(s)	251, 683
Aor13HI	TCCGGA	1 cut(s)	889
Aor51HI	AGCGCT	1 cut(s)	476
ApeKI	GCWGC	2 cut(s)	251, 467
ApoI	RAATTY	5 cut(s)	26, 151, 262, 396, 527
AseI	ATTAAT	2 cut(s)	102, 186
AspLEI	GCGC	1 cut(s)	477
AspS9I	GGNCC	2 cut(s)	232, 899
AsuC2I	CCSGG	1 cut(s)	42
AsuHPI	GGTGA	4 cut(s)	32, 311, 380, 430
AsuII	TTCGAA	1 cut(s)	149
AvaII	GGWCC	2 cut(s)	232, 899
BaeI	ACNNNNGTAYC	2 cut(s)	273, 306
BarI	GAAGNNNNNNTAC	2 cut(s)	794, 826
BbsI	GAAGAC	1 cut(s)	795
Bbv12I	GWGCWC	1 cut(s)	622
BbvI	GCAGC	2 cut(s)	238, 454
BcnI	CCSGG	1 cut(s)	42
BcoDI	GTCTC	3 cut(s)	68, 735, 860
BfaI	CTAG	1 cut(s)	275
BfmI	CTRYAG	1 cut(s)	456
BfoI	RGCGCY	1 cut(s)	478
BisI	GCNGC	2 cut(s)	252, 468
BlpI	GCTNAGC	1 cut(s)	471
BlsI	GCNGC	2 cut(s)	253, 469
Bme1390I	CCNGG	1 cut(s)	42
Bme18I	GGWCC	2 cut(s)	232, 899
BmgT120I	GGNCC	2 cut(s)	232, 899
BmiI	GGNNCC	1 cut(s)	234
BmrFI	CCNGG	1 cut(s)	42
BmsI	GCATC	1 cut(s)	833
BpiI	GAAGAC	1 cut(s)	795
BpmI	CTGGAG	1 cut(s)	606
Bpu10I	CCTNAGC	1 cut(s)	95
Bpu1102I	GCTNAGC	1 cut(s)	471
Bpu14I	TTCGAA	1 cut(s)	149
BpuMI	CCSGG	1 cut(s)	42
BsaI	GGTCTC	2 cut(s)	68, 860
BsaJI	CCNNGG	1 cut(s)	504
BsaWI	WCCGGW	1 cut(s)	889
Bsc4I	CCNNNNNNNGG	4 cut(s)	241, 689, 736, 896
Bse3DI	GCAATG	2 cut(s)	629, 644
BseAI	TCCGGA	1 cut(s)	889
BseDI	CCNNGG	1 cut(s)	504
BseGI	GGATG	4 cut(s)	620, 661, 709, 824
BseLI	CCNNNNNNNGG	4 cut(s)	241, 689, 736, 896
BseMI	GCAATG	2 cut(s)	629, 644
BseMII	CTCAG	4 cut(s)	63, 485, 897, 954
BseXI	GCAGC	2 cut(s)	238, 454
BseYI	CCCAGC	1 cut(s)	134
BsiHKAI	GWGCWC	1 cut(s)	622
BsiSI	CCGG	2 cut(s)	42, 890
BslFI	GGGAC	2 cut(s)	218, 430
BslI	CCNNNNNNNGG	4 cut(s)	241, 689, 736, 896
BsmAI	GTCTC	3 cut(s)	68, 735, 860
BsmFI	GGGAC	2 cut(s)	218, 430
BsmI	GAATGC	1 cut(s)	136
Bso31I	GGTCTC	2 cut(s)	68, 860
Bsp119I	TTCGAA	1 cut(s)	149
Bsp1286I	GDGCHC	1 cut(s)	622
Bsp13I	TCCGGA	1 cut(s)	889
Bsp143I	GATC	1 cut(s)	585
Bsp1720I	GCTNAGC	1 cut(s)	471
BspACI	CCGC	2 cut(s)	465, 596
BspCNI	CTCAG	4 cut(s)	64, 484, 898, 955
BspEI	TCCGGA	1 cut(s)	889
BspHI	TCATGA	1 cut(s)	748
BspLI	GGNNCC	1 cut(s)	234
BspQI	GCTCTTC	1 cut(s)	747
BspT104I	TTCGAA	1 cut(s)	149
BspTNI	GGTCTC	2 cut(s)	68, 860
BsrDI	GCAATG	2 cut(s)	629, 644
BssECI	CCNNGG	1 cut(s)	504
BssMI	GATC	1 cut(s)	585
Bst4CI	ACNGT	4 cut(s)	508, 514, 746, 881
Bst6I	CTCTTC	2 cut(s)	297, 747
BstAPI	GCANNNNNTGC	1 cut(s)	251
BstBI	TTCGAA	1 cut(s)	149
BstC8I	GCNNGC	2 cut(s)	52, 594
BstDEI	CTNAG	5 cut(s)	72, 95, 471, 906, 963
BstDSI	CCRYGG	1 cut(s)	504
BstF5I	GGATG	4 cut(s)	620, 661, 709, 824
BstH2I	RGCGCY	1 cut(s)	478
BstHHI	GCGC	1 cut(s)	477
BstKTI	GATC	1 cut(s)	588
BstMAI	GTCTC	3 cut(s)	68, 735, 860
BstMBI	GATC	1 cut(s)	585
BstMWI	GCNNNNNNNGC	1 cut(s)	251
BstSCI	CCNGG	1 cut(s)	40
BstSFI	CTRYAG	1 cut(s)	456
BstV1I	GCAGC	2 cut(s)	238, 454
BstV2I	GAAGAC	1 cut(s)	795
BtgI	CCRYGG	1 cut(s)	504
BtsCI	GGATG	4 cut(s)	620, 661, 709, 824
Cac8I	GCNNGC	2 cut(s)	52, 594
CaiI	CAGNNNCTG	2 cut(s)	251, 683
CciI	TCATGA	1 cut(s)	748
CfoI	GCGC	1 cut(s)	477
Cfr13I	GGNCC	2 cut(s)	232, 899
Csp6I	GTAC	1 cut(s)	697
CviAII	CATG	2 cut(s)	562, 749
CviQI	GTAC	1 cut(s)	697
DdeI	CTNAG	5 cut(s)	72, 95, 471, 906, 963
DpnI	GATC	1 cut(s)	587
DpnII	GATC	1 cut(s)	585
Eam1104I	CTCTTC	2 cut(s)	297, 747
EarI	CTCTTC	2 cut(s)	297, 747
Eco31I	GGTCTC	2 cut(s)	68, 860
Eco47I	GGWCC	2 cut(s)	232, 899
Eco47III	AGCGCT	1 cut(s)	476
Eco57I	CTGAAG	2 cut(s)	592, 705
EcoO109I	RGGNCCY	1 cut(s)	899
EcoRI	GAATTC	3 cut(s)	151, 262, 527
FaeI	CATG	2 cut(s)	565, 752
FalI	AAGNNNNNCTT	2 cut(s)	78, 110
FaqI	GGGAC	2 cut(s)	218, 430
FatI	CATG	2 cut(s)	561, 748
FauI	CCCGC	1 cut(s)	472
FblI	GTMKAC	1 cut(s)	459
Fnu4HI	GCNGC	2 cut(s)	252, 468
FokI	GGATG	4 cut(s)	627, 668, 716, 811
Fsp4HI	GCNGC	2 cut(s)	252, 468
FspBI	CTAG	1 cut(s)	275
GlaI	GCGC	1 cut(s)	476
GluI	GCNGC	2 cut(s)	252, 468
GsaI	CCCAGC	1 cut(s)	138
GsuI	CTGGAG	1 cut(s)	606
HaeII	RGCGCY	1 cut(s)	478
HapII	CCGG	2 cut(s)	42, 890
HhaI	GCGC	1 cut(s)	477
Hin1II	CATG	2 cut(s)	565, 752
Hin6I	GCGC	1 cut(s)	475
HinP1I	GCGC	1 cut(s)	475
HincII	GTYRAC	1 cut(s)	661
HindII	GTYRAC	1 cut(s)	661
HinfI	GANTC	4 cut(s)	8, 269, 418, 626
HpaI	GTTAAC	1 cut(s)	661
HpaII	CCGG	2 cut(s)	42, 890
HphI	GGTGA	4 cut(s)	32, 311, 380, 430
Hpy166II	GTNNAC	2 cut(s)	460, 661
Hpy188I	TCNGA	5 cut(s)	13, 73, 157, 268, 573
Hpy188III	TCNNGA	5 cut(s)	623, 683, 749, 796, 890
Hpy8I	GTNNAC	2 cut(s)	460, 661
HpyAV	CCTTC	4 cut(s)	301, 329, 367, 836
HpyCH4III	ACNGT	4 cut(s)	508, 514, 746, 881
HpyCH4V	TGCA	2 cut(s)	649, 865
HpyF10VI	GCNNNNNNNGC	1 cut(s)	251
HpyF3I	CTNAG	5 cut(s)	72, 95, 471, 906, 963
Hsp92II	CATG	2 cut(s)	565, 752
HspAI	GCGC	1 cut(s)	475
Kpn2I	TCCGGA	1 cut(s)	889
KspAI	GTTAAC	1 cut(s)	661
Kzo9I	GATC	1 cut(s)	585
LguI	GCTCTTC	1 cut(s)	747
LmnI	GCTCC	2 cut(s)	625, 685
Lsp1109I	GCAGC	2 cut(s)	238, 454
LweI	GCATC	1 cut(s)	833
MaeI	CTAG	1 cut(s)	275
MaeIII	GTNAC	4 cut(s)	199, 270, 508, 881
MalI	GATC	1 cut(s)	587
MboI	GATC	1 cut(s)	585
MboII	GAAGA	7 cut(s)	29, 119, 314, 592, 598, 764, 800
MhlI	GDGCHC	1 cut(s)	622
MlyI	GAGTC	3 cut(s)	278, 412, 635
MmeI	TCCRAC	1 cut(s)	670
MroI	TCCGGA	1 cut(s)	889
MseI	TTAA	5 cut(s)	102, 114, 186, 534, 660
MslI	CAYNNNNRTG	1 cut(s)	668
MspA1I	CMGCKG	1 cut(s)	467
MspI	CCGG	2 cut(s)	42, 890
MspR9I	CCNGG	1 cut(s)	42
Mva1269I	GAATGC	1 cut(s)	136
MwoI	GCNNNNNNNGC	1 cut(s)	251
NciI	CCSGG	1 cut(s)	42
NdeII	GATC	1 cut(s)	585
NlaIII	CATG	2 cut(s)	565, 752
NlaIV	GGNNCC	1 cut(s)	234
NmuCI	GTSAC	1 cut(s)	270
NspV	TTCGAA	1 cut(s)	149
PagI	TCATGA	1 cut(s)	748
PciSI	GCTCTTC	1 cut(s)	747
PctI	GAATGC	1 cut(s)	136
PfeI	GAWTC	1 cut(s)	8
PfoI	TCCNGGA	1 cut(s)	40
PkrI	GCNGC	2 cut(s)	253, 469
PleI	GAGTC	3 cut(s)	277, 412, 634
PpsI	GAGTC	3 cut(s)	277, 412, 634
PpuMI	RGGWCCY	1 cut(s)	899
PshBI	ATTAAT	2 cut(s)	102, 186
Psp5II	RGGWCCY	1 cut(s)	899
PspFI	CCCAGC	1 cut(s)	134
PspN4I	GGNNCC	1 cut(s)	234
PspPI	GGNCC	2 cut(s)	232, 899
PspPPI	RGGWCCY	1 cut(s)	899
PstNI	CAGNNNCTG	2 cut(s)	251, 683
RsaI	GTAC	1 cut(s)	698
RsaNI	GTAC	1 cut(s)	697
RseI	CAYNNNNRTG	1 cut(s)	668
SapI	GCTCTTC	1 cut(s)	747
SaqAI	TTAA	5 cut(s)	102, 114, 186, 534, 660
SatI	GCNGC	2 cut(s)	252, 468
Sau3AI	GATC	1 cut(s)	585
Sau96I	GGNCC	2 cut(s)	232, 899
SchI	GAGTC	3 cut(s)	278, 412, 635
ScrFI	CCNGG	1 cut(s)	42
SduI	GDGCHC	1 cut(s)	622
SfaNI	GCATC	1 cut(s)	833
SfcI	CTRYAG	1 cut(s)	456
SfuI	TTCGAA	1 cut(s)	149
SinI	GGWCC	2 cut(s)	232, 899
SmiMI	CAYNNNNRTG	1 cut(s)	668
SsiI	CCGC	2 cut(s)	465, 596
SspMI	CTAG	1 cut(s)	275
StyD4I	CCNGG	1 cut(s)	40
TaaI	ACNGT	4 cut(s)	508, 514, 746, 881
TaqI	TCGA	3 cut(s)	149, 226, 636
TatI	WGTACW	1 cut(s)	696
TfiI	GAWTC	1 cut(s)	8
Tru1I	TTAA	5 cut(s)	102, 114, 186, 534, 660
Tru9I	TTAA	5 cut(s)	102, 114, 186, 534, 660
TseFI	GTSAC	1 cut(s)	270
TseI	GCWGC	2 cut(s)	251, 467
Tsp45I	GTSAC	1 cut(s)	270
TspGWI	ACGGA	2 cut(s)	140, 945
VpaK11BI	GGWCC	2 cut(s)	232, 899
VspI	ATTAAT	2 cut(s)	102, 186
XapI	RAATTY	5 cut(s)	26, 151, 262, 396, 527
XmiI	GTMKAC	1 cut(s)	459
XspI	CTAG	1 cut(s)	275

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