MD00G1047200.v1.1

Protein ROOT HAIR DEFECTIVE 3 homolog

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr00
OG0000525
Physical Location & Seq
Reverse (-)
8779619 .. 8781834
2216 bp
Loading structure...
UTR
Exon/CDS
Intron
MD00G1047200.v1.1.491

Sequence Viewer

Length: 978 bp
ATGGTTGCTACGGTTCGGTGTGAAGAGATTGCCAACCAGAAATTCAAACAGTTGGTCCACGATGAGGTATGTGGTCATTTATCTCCACATATGAGAAAAAAACTTTCTTCGTCTTTAAGCGGTCCTGTAGAGGCTCTACTGGAAACTGGTGCGAAAGACACCTGGGCTTCGATACGAAAACTACTTAATCGTGAGACCAAAGTTGCAGTATCGGAGTTCTCAACTGCAGTTGCCAATTTTGAGTTGGACAATGAAACGTCTCTGAAGCTTTTGTTGACCATGGCTGCCATTCGCTTGGATGAGAAGCCAGATAATATTGAAAATGTCCTAGTTTCTTCTCTGGTGGACAGGACTGTTACTGTTTCATCTTCACAAAATAGGAAACTAGGACCTCCTACAGATCCTCTTGCCTCAAGCTCTTGGCAAGAGGTACCATTTATTTATGGGTTTGGTTTTTATGTAAAATTTTTCTATGATGAGACTCCCTTCTTATTAAGGTTAACTCTAAACTATGTTTCTTCAAAGGATACCTTAATTACCCCAGTACAGTGCAAGTCATTGTCAAAGCAGTTCAAAGCAGAGACCGAATATATCGTCACTCAAGCTATTTCGGCACAGGAGGCTCACAAGCGGAGTAACAACTGGTTACCTCCTCCATGGGCTATAATGGCGATGATCATTCTTGGTTTTAACGAATTTATGATGCTTTTAAAGAACCCTCTCTACCTCATGGTTCTATTTGTTGGATTTTTACTTTCAAAGGCCTTATGGGTACAGATGGACATTACAGGACAGTTCCAGCATGGCGCTCTGTCCGGAATACTGTCTATCTCATCAAGGTTTCTTCCAACCGTCATGAATCTTCTAAGAAAACTCGCAGAAGAAGCTCAGGGGAATCAAACACCGGAAGCACAAAGGCGGCTAGTTCTCTTTCTTCTCAGAGTTATAGAAATGAAACACCTCAGCCAAATCCAGTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005783 GO:0012505 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RHD3

Protein Analysis

326

Amino Acids

36.7

Weight (kDa)

8.65

Isoelectric Point (pI)

34.82

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Sey1_3HB PF20428 26 - 86 4.2e-09 Sey1 three-helix bundle domain
Sey1_3HB PF20428 85 - 144 2.3e-06 Sey1 three-helix bundle domain
Sey1_3HB PF20428 170 - 295 2.1e-33 Sey1 three-helix bundle domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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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: OG0000525)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G45160
fragaria_vesca FvH4_3g11890
malus_domestica MD00G1023300.v1.1 MD00G1023500.v1.1 MD00G1046300.v1.1 MD00G1046400.v1.1 MD00G1047200.v1.1 MD05G1180600.v1.1 MD05G1256900.v1.1 MD05G1257200.v1.1 MD05G1257300.v1.1 MD05G1257400.v1.1 MD05G1257900.v1.1 MD05G1258000.v1.1 MD10G1213100.v1.1 MD10G1237400.v1.1
prunus_persica Prupe.4G106400_v2.0.a1 Prupe.4G106400_v2.0.a1 Prupe.4G106900_v2.0.a1 Prupe.4G113800_v2.0.a1 Prupe.4G113800_v2.0.a1 Prupe.4G113800_v2.0.a1 Prupe.I001700_v2.0.a1
pyrus_communis pycom05g23620 pycom05g23630 pycom05g23880 pycom05g24090 pycom05g24270 pycom10g19870
rosa_chinensis RchiOBHm_Chr5g0019311 RchiOBHm_Chr5g0019391 RchiOBHm_Chr5g0019401 RchiOBHm_Chr7g0226131 RchiOBHm_Chr7g0226141 RchiOBHm_Chr7g0226161
rosa_laevigata RLG00000001766 RLG00000001767 RLG00000032437 RLG00000032441 RLG00000032445
rosa_multiflora Rmu_sc0001350.1_g000022 Rmu_sc0001350.1_g000031 Rmu_sc0002141.1_g000028 Rmu_sc0002759.1_g000037 Rmu_sc0002759.1_g000039 Rmu_sc0005292.1_g000004 Rmu_sc0005292.1_g000050
rosa_roxburghii Rroxscaffold_1G00058650 Rroxscaffold_1G00058670 Rroxscaffold_1G00074270 Rroxscaffold_2G00108890 Rroxscaffold_2G00125570
rosa_rugosa Rorug05G0050100 Rorug05G0050200 Rorug05G0050300 Rorug05G0050500 Rorug05G0050600 Rorug05G0050700
rosa_samantha Rh5AG140700 Rh5AG141000 Rh5AG141300 Rh5AG390000 Rh5BG139700 Rh5BG139800 Rh5BG139900 Rh5BG140000 Rh5CG151000 Rh5CG151500 Rh5CG151600 Rh5DG140200 Rh5DG140400 Rh5DG140600 Rh7AG368100 Rh7AG381400 Rh7AG381700 Rh7CG386400 Rh7CG400900 Rh7CG401200 Rh7DG380400 Rh7DG380500
rosa_wichuraiana Rw5G012510 Rw5G012530 Rw5G012540 Rw7G031980 Rw7G031990

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 430
AccB1I GGYRCC 1 cut(s) 430
AccIII TCCGGA 1 cut(s) 815
AciI CCGC 3 cut(s) 120, 631, 919
AclWI GGATC 1 cut(s) 395
AcsI RAATTY 3 cut(s) 41, 464, 695
AcuI CTGAAG 1 cut(s) 284
AfaI GTAC 3 cut(s) 432, 546, 774
AfiI CCNNNNNNNGG 1 cut(s) 64
AgsI TTSAA 5 cut(s) 46, 320, 522, 574, 759
AjnI CCWGG 1 cut(s) 161
AjuI GAANNNNNNNTTGG 2 cut(s) 26, 58
AluBI AGCT 4 cut(s) 268, 417, 605, 887
AluI AGCT 4 cut(s) 268, 417, 605, 887
Alw26I GTCTC 4 cut(s) 188, 264, 473, 575
AlwI GGATC 1 cut(s) 395
Aor13HI TCCGGA 1 cut(s) 815
AoxI GGCC 1 cut(s) 762
ApeKI GCWGC 1 cut(s) 284
ApoI RAATTY 3 cut(s) 41, 464, 695
ArsI GACNNNNNNTTYG 4 cut(s) 39, 71, 579, 611
Asp718I GGTACC 1 cut(s) 430
AspLEI GCGC 1 cut(s) 809
AspS9I GGNCC 3 cut(s) 55, 122, 389
AvaII GGWCC 3 cut(s) 55, 122, 389
BanI GGYRCC 1 cut(s) 430
BbvCI CCTCAGC 1 cut(s) 962
BbvI GCAGC 1 cut(s) 271
BccI CCATC 1 cut(s) 772
BciT130I CCWGG 1 cut(s) 163
BciVI GTATCC 1 cut(s) 520
BclI TGATCA 1 cut(s) 675
BcoDI GTCTC 4 cut(s) 188, 264, 473, 575
BfaI CTAG 3 cut(s) 329, 386, 923
BfmI CTRYAG 3 cut(s) 126, 225, 396
BfoI RGCGCY 1 cut(s) 810
BfuI GTATCC 1 cut(s) 520
BisI GCNGC 2 cut(s) 285, 920
BlsI GCNGC 2 cut(s) 286, 921
Bme1390I CCNGG 1 cut(s) 163
Bme18I GGWCC 3 cut(s) 55, 122, 389
BmgT120I GGNCC 3 cut(s) 55, 122, 389
BmiI GGNNCC 1 cut(s) 432
BmrFI CCNGG 1 cut(s) 163
BmrI ACTGGG 1 cut(s) 536
BmsI GCATC 1 cut(s) 693
BmuI ACTGGG 1 cut(s) 536
Bpu10I CCTNAGC 2 cut(s) 888, 962
BpuEI CTTGAG 2 cut(s) 397, 585
BsaI GGTCTC 2 cut(s) 188, 575
BsaJI CCNNGG 3 cut(s) 162, 279, 656
BsaWI WCCGGW 2 cut(s) 815, 904
Bsc4I CCNNNNNNNGG 1 cut(s) 64
Bse1I ACTGG 5 cut(s) 144, 151, 542, 647, 973
BseAI TCCGGA 1 cut(s) 815
BseBI CCWGG 1 cut(s) 163
BseDI CCNNGG 3 cut(s) 162, 279, 656
BseGI GGATG 1 cut(s) 304
BseLI CCNNNNNNNGG 1 cut(s) 64
BseMII CTCAG 3 cut(s) 902, 952, 976
BseNI ACTGG 5 cut(s) 144, 151, 542, 647, 973
BseRI GAGGAG 1 cut(s) 642
BseXI GCAGC 1 cut(s) 271
BshFI GGCC 1 cut(s) 764
BshNI GGYRCC 1 cut(s) 430
BsiSI CCGG 2 cut(s) 816, 905
BslI CCNNNNNNNGG 1 cut(s) 64
BsmAI GTCTC 4 cut(s) 188, 264, 473, 575
BsmBI CGTCTC 1 cut(s) 264
BsnI GGCC 1 cut(s) 764
Bso31I GGTCTC 2 cut(s) 188, 575
Bsp13I TCCGGA 1 cut(s) 815
Bsp143I GATC 2 cut(s) 400, 675
Bsp19I CCATGG 2 cut(s) 279, 656
BspACI CCGC 3 cut(s) 120, 631, 919
BspANI GGCC 1 cut(s) 764
BspCNI CTCAG 3 cut(s) 901, 951, 975
BspEI TCCGGA 1 cut(s) 815
BspHI TCATGA 1 cut(s) 855
BspLI GGNNCC 1 cut(s) 432
BspMAI CTGCAG 1 cut(s) 229
BspPI GGATC 1 cut(s) 395
BspT107I GGYRCC 1 cut(s) 430
BspTNI GGTCTC 2 cut(s) 188, 575
BsrI ACTGG 5 cut(s) 144, 151, 542, 647, 973
BssECI CCNNGG 3 cut(s) 162, 279, 656
BssMI GATC 2 cut(s) 400, 675
BssT1I CCWWGG 2 cut(s) 279, 656
Bst2UI CCWGG 1 cut(s) 163
Bst4CI ACNGT 8 cut(s) 13, 51, 355, 361, 549, 795, 825, 853
Bst6I CTCTTC 1 cut(s) 18
BstDEI CTNAG 4 cut(s) 866, 888, 938, 962
BstDSI CCRYGG 2 cut(s) 279, 656
BstEII GGTNACC 1 cut(s) 645
BstF5I GGATG 1 cut(s) 304
BstH2I RGCGCY 1 cut(s) 810
BstHHI GCGC 1 cut(s) 809
BstKTI GATC 2 cut(s) 403, 678
BstMAI GTCTC 4 cut(s) 188, 264, 473, 575
BstMBI GATC 2 cut(s) 400, 675
BstMWI GCNNNNNNNGC 4 cut(s) 611, 620, 668, 884
BstNI CCWGG 1 cut(s) 163
BstPI GGTNACC 1 cut(s) 645
BstSCI CCNGG 1 cut(s) 161
BstSFI CTRYAG 3 cut(s) 126, 225, 396
BstV1I GCAGC 1 cut(s) 271
BstX2I RGATCY 1 cut(s) 400
BstXI CCANNNNNNTGG 1 cut(s) 295
BstYI RGATCY 1 cut(s) 400
BsuI GTATCC 1 cut(s) 520
BsuRI GGCC 1 cut(s) 764
BtgI CCRYGG 2 cut(s) 279, 656
BtgZI GCGATG 1 cut(s) 686
BtsCI GGATG 1 cut(s) 304
BtsIMutI CAGTG 1 cut(s) 554
CciI TCATGA 1 cut(s) 855
CfoI GCGC 1 cut(s) 809
Cfr13I GGNCC 3 cut(s) 55, 122, 389
Csp6I GTAC 3 cut(s) 431, 545, 773
CviAII CATG 5 cut(s) 280, 657, 730, 803, 856
CviQI GTAC 3 cut(s) 431, 545, 773
DdeI CTNAG 4 cut(s) 866, 888, 938, 962
DpnI GATC 2 cut(s) 402, 677
DpnII GATC 2 cut(s) 400, 675
DraI TTTAAA 1 cut(s) 711
Eam1104I CTCTTC 1 cut(s) 18
EarI CTCTTC 1 cut(s) 18
Eco130I CCWWGG 2 cut(s) 279, 656
Eco147I AGGCCT 1 cut(s) 764
Eco31I GGTCTC 2 cut(s) 188, 575
Eco47I GGWCC 3 cut(s) 55, 122, 389
Eco57I CTGAAG 1 cut(s) 284
Eco91I GGTNACC 1 cut(s) 645
EcoO109I RGGNCCY 1 cut(s) 389
EcoO65I GGTNACC 1 cut(s) 645
EcoRII CCWGG 1 cut(s) 161
EcoT14I CCWWGG 2 cut(s) 279, 656
ErhI CCWWGG 2 cut(s) 279, 656
Esp3I CGTCTC 1 cut(s) 264
FaeI CATG 5 cut(s) 283, 660, 733, 806, 859
FalI AAGNNNNNCTT 2 cut(s) 515, 547
FatI CATG 5 cut(s) 279, 656, 729, 802, 855
FauNDI CATATG 1 cut(s) 90
FbaI TGATCA 1 cut(s) 675
Fnu4HI GCNGC 2 cut(s) 285, 920
FokI GGATG 1 cut(s) 311
Fsp4HI GCNGC 2 cut(s) 285, 920
FspBI CTAG 3 cut(s) 329, 386, 923
GlaI GCGC 1 cut(s) 808
GluI GCNGC 2 cut(s) 285, 920
HaeII RGCGCY 1 cut(s) 810
HaeIII GGCC 1 cut(s) 764
HapII CCGG 2 cut(s) 816, 905
HhaI GCGC 1 cut(s) 809
Hin1II CATG 5 cut(s) 283, 660, 733, 806, 859
Hin6I GCGC 1 cut(s) 807
HinP1I GCGC 1 cut(s) 807
HincII GTYRAC 2 cut(s) 276, 501
HindII GTYRAC 2 cut(s) 276, 501
HindIII AAGCTT 1 cut(s) 266
HinfI GANTC 3 cut(s) 481, 859, 895
HpaI GTTAAC 1 cut(s) 501
HpaII CCGG 2 cut(s) 816, 905
Hpy166II GTNNAC 4 cut(s) 58, 276, 346, 501
Hpy188I TCNGA 3 cut(s) 214, 264, 941
Hpy188III TCNNGA 3 cut(s) 191, 816, 856
Hpy8I GTNNAC 4 cut(s) 58, 276, 346, 501
HpyAV CCTTC 1 cut(s) 496
HpyCH4III ACNGT 8 cut(s) 13, 51, 355, 361, 549, 795, 825, 853
HpyCH4IV ACGT 1 cut(s) 257
HpyCH4V TGCA 3 cut(s) 206, 227, 552
HpyF10VI GCNNNNNNNGC 4 cut(s) 611, 620, 668, 884
HpyF3I CTNAG 4 cut(s) 866, 888, 938, 962
HpySE526I ACGT 1 cut(s) 257
Hsp92II CATG 5 cut(s) 283, 660, 733, 806, 859
HspAI GCGC 1 cut(s) 807
Kpn2I TCCGGA 1 cut(s) 815
KpnI GGTACC 1 cut(s) 434
Ksp22I TGATCA 1 cut(s) 675
KspAI GTTAAC 1 cut(s) 501
Kzo9I GATC 2 cut(s) 400, 675
Lsp1109I GCAGC 1 cut(s) 271
LweI GCATC 1 cut(s) 693
MaeI CTAG 3 cut(s) 329, 386, 923
MaeII ACGT 1 cut(s) 257
MaeIII GTNAC 4 cut(s) 355, 595, 635, 645
MalI GATC 2 cut(s) 402, 677
MboI GATC 2 cut(s) 400, 675
MboII GAAGA 9 cut(s) 35, 99, 327, 360, 510, 836, 854, 893, 926
MflI RGATCY 1 cut(s) 400
MluCI AATT 5 cut(s) 41, 235, 464, 534, 695
MlyI GAGTC 1 cut(s) 475
MmeI TCCRAC 3 cut(s) 225, 724, 872
MroI TCCGGA 1 cut(s) 815
MseI TTAA 7 cut(s) 116, 186, 494, 500, 533, 690, 710
MspI CCGG 2 cut(s) 816, 905
MspR9I CCNGG 1 cut(s) 163
MvaI CCWGG 1 cut(s) 163
MwoI GCNNNNNNNGC 4 cut(s) 611, 620, 668, 884
NcoI CCATGG 2 cut(s) 279, 656
NdeI CATATG 1 cut(s) 90
NdeII GATC 2 cut(s) 400, 675
NlaIII CATG 5 cut(s) 283, 660, 733, 806, 859
NlaIV GGNNCC 1 cut(s) 432
NmuCI GTSAC 1 cut(s) 595
PagI TCATGA 1 cut(s) 855
PceI AGGCCT 1 cut(s) 764
PfeI GAWTC 2 cut(s) 859, 895
PkrI GCNGC 2 cut(s) 286, 921
PleI GAGTC 1 cut(s) 475
PpsI GAGTC 1 cut(s) 475
PpuMI RGGWCCY 1 cut(s) 389
Psp5II RGGWCCY 1 cut(s) 389
Psp6I CCWGG 1 cut(s) 161
PspEI GGTNACC 1 cut(s) 645
PspGI CCWGG 1 cut(s) 161
PspN4I GGNNCC 1 cut(s) 432
PspPI GGNCC 3 cut(s) 55, 122, 389
PspPPI RGGWCCY 1 cut(s) 389
PsrI GAACNNNNNNTAC 2 cut(s) 707, 739
PstI CTGCAG 1 cut(s) 229
PsuI RGATCY 1 cut(s) 400
RsaI GTAC 3 cut(s) 432, 546, 774
RsaNI GTAC 3 cut(s) 431, 545, 773
SaqAI TTAA 7 cut(s) 116, 186, 494, 500, 533, 690, 710
SatI GCNGC 2 cut(s) 285, 920
Sau3AI GATC 2 cut(s) 400, 675
Sau96I GGNCC 3 cut(s) 55, 122, 389
SchI GAGTC 1 cut(s) 475
ScrFI CCNGG 1 cut(s) 163
SfaNI GCATC 1 cut(s) 693
SfcI CTRYAG 3 cut(s) 126, 225, 396
SinI GGWCC 3 cut(s) 55, 122, 389
SmlI CTYRAG 2 cut(s) 412, 600
SmoI CTYRAG 2 cut(s) 412, 600
Sse9I AATT 5 cut(s) 41, 235, 464, 534, 695
SseBI AGGCCT 1 cut(s) 764
SsiI CCGC 3 cut(s) 120, 631, 919
SspI AATATT 1 cut(s) 316
SspMI CTAG 3 cut(s) 329, 386, 923
StuI AGGCCT 1 cut(s) 764
StyD4I CCNGG 1 cut(s) 161
StyI CCWWGG 2 cut(s) 279, 656
TaaI ACNGT 8 cut(s) 13, 51, 355, 361, 549, 795, 825, 853
TaiI ACGT 1 cut(s) 260
TaqI TCGA 1 cut(s) 170
TaqII GACCGA 1 cut(s) 599
TasI AATT 5 cut(s) 41, 235, 464, 534, 695
TatI WGTACW 1 cut(s) 544
TauI GCSGC 1 cut(s) 922
TfiI GAWTC 2 cut(s) 859, 895
Tru1I TTAA 7 cut(s) 116, 186, 494, 500, 533, 690, 710
Tru9I TTAA 7 cut(s) 116, 186, 494, 500, 533, 690, 710
TscAI CASTG 1 cut(s) 554
TseFI GTSAC 1 cut(s) 595
TseI GCWGC 1 cut(s) 284
Tsp45I GTSAC 1 cut(s) 595
TspDTI ATGAA 4 cut(s) 267, 354, 872, 968
TspRI CASTG 1 cut(s) 554
VpaK11BI GGWCC 3 cut(s) 55, 122, 389
XapI RAATTY 3 cut(s) 41, 464, 695
XcmI CCANNNNNNNNNTGG 1 cut(s) 241
XspI CTAG 3 cut(s) 329, 386, 923
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.