MD16G1243200.v1.1

RNA helicase SDE3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr16
OG0000595
Physical Location & Seq
Forward (+)
26386654 .. 26387349
696 bp
Loading structure...
UTR
Exon/CDS
Intron
MD16G1243200.v1.1.491

Sequence Viewer

Length: 696 bp
ATGATCTTACCTGTTATACAGGGCTTTATATATCGCGTCGTCAAGAGCAGTGTTGTTTTAGTAGAATTTGAGGATGACTTTTATGTTCATCATTATTTGACCCGAAAATATGATGTCAGCTTCTCATTCAATAGAGTCTGTTTGCAAAGAGCTCATCAAGCTGTACAAAATGCATCGGATGCTTTGTTTAGGAACTTCATCTTTCCTGAGTCTGTTTCGCGTACGAACATTCCCACTGCACCAGCGCTGCTGTGCCCTGGTCATAAACTTGATGCCAATCAATTATCTGCAGTTCGTCACATTTTAAGCATTCGTGGCTCACCACCTTACCTATTGGTTGGCCAGCTGTGTGTTAAAAAGAGCGGTTCACCACCTTACCTATTGCCTGGCCAGTTCTGGGATGAAAAGACCAATTTTAGGCTATCGAGAACTGGAGTGGTGGTTAGTGAAGCAGTGCACCAGTTATGTCAAACTTCACACGGAAATAGGATCCTTGTATGTGCTCCTAGCAACCTCTGTTGTGATGGGCTTATGAGAAGCTTGTTGAAATGGATTCCTGAGTCAGACATGTTTCGAGTGAATGCTGCATTCCGCGAGAAGGAGGAGGTACCTGAAGACATCCTCCCGTCATGCCTTTACAAAGAGACTTACACTTCTCTTGTCCTCCGACGGAGGAACTTTGTGAATTCAGAGTGA
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
No domains found.

Protein Analysis

232

Amino Acids

26.31

Weight (kDa)

8.79

Isoelectric Point (pI)

54.2

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000595)

Species Orthologous Gene IDs
fragaria_vesca FvH4_4g37100 FvH4_4g37100 FvH4_4g37100
malus_domestica MD13G1238300.v1.1 MD16G1243100.v1.1 MD16G1243200.v1.1
prunus_persica Prupe.1G070100_v2.0.a1 Prupe.1G070200_v2.0.a1 Prupe.1G070300_v2.0.a1 Prupe.1G070300_v2.0.a1
pyrus_communis pycom13g21070 pycom16g20390 pycom16g20400
rosa_chinensis RchiOBHm_Chr1g0318071 RchiOBHm_Chr1g0318111 RchiOBHm_Chr4g0446861 RchiOBHm_Chr4g0446881 RchiOBHm_Chr4g0446891
rosa_laevigata RLG00000005623 RLG00000005624 RLG00000009337 RLG00000030560 RLG00000030566
rosa_multiflora Rmu_co8177450.1_g000001 Rmu_sc0001753.1_g000012 Rmu_sc0001753.1_g000013 Rmu_sc0001753.1_g000014 Rmu_sc0001753.1_g000015 Rmu_sc0011424.1_g000009 Rmu_sc0011424.1_g000020 Rmu_sc0034555.1_g000001 Rmu_ssc0000008.1_g000002
rosa_roxburghii Rroxscaffold_4G00329530 Rroxscaffold_4G00329590 Rroxscaffold_4G00329800 Rroxscaffold_4G00329810 Rroxscaffold_4G00329860 Rroxscaffold_4G00329910 Rroxscaffold_4G00330030 Rroxscaffold_5G00343610 Rroxscaffold_5G00348280 Rroxscaffold_5G00387220 Rroxscaffold_5G00387230
rosa_rugosa Rorug01G0019100 Rorug01G0019100 Rorug01G0019500 Rorug01G0019600 Rorug04G0010100 Rorug04G0375200 Rorug04G0375300 Rorug04G0375400 Rorug04G0375500 Rorug04G0375600 Rorug04G0375700
rosa_samantha Rh1AG030700 Rh1AG030900 Rh1BG026900 Rh1CG029500 Rh1CG029700 Rh1DG040500 Rh4AG088100 Rh4AG436700 Rh4AG436800 Rh4AG436900 Rh4BG084700 Rh4BG445800 Rh4BG445900 Rh4BG446100 Rh4CG096300 Rh4CG463100 Rh4CG463200 Rh4CG463400 Rh4DG444500 Rh4DG444600 Rh4DG444700
rosa_wichuraiana Rw1G002420 Rw1G002440 Rw1G002480 Rw4G037360 Rw4G037370 Rw4G037380

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 607
AccB1I GGYRCC 1 cut(s) 607
AccBSI CCGCTC 1 cut(s) 363
AccII CGCG 3 cut(s) 36, 220, 594
AciI CCGC 2 cut(s) 363, 592
AclWI GGATC 2 cut(s) 484, 497
AcoI YGGCCR 2 cut(s) 340, 388
AcsI RAATTY 2 cut(s) 65, 685
AcuI CTGAAG 1 cut(s) 633
AfaI GTAC 3 cut(s) 165, 223, 609
AfeI AGCGCT 1 cut(s) 246
AfiI CCNNNNNNNGG 3 cut(s) 397, 417, 598
AflIII ACRYGT 1 cut(s) 567
AgsI TTSAA 2 cut(s) 130, 547
AjnI CCWGG 2 cut(s) 256, 385
AluBI AGCT 5 cut(s) 120, 152, 161, 346, 540
AluI AGCT 5 cut(s) 120, 152, 161, 346, 540
Alw21I GWGCWC 3 cut(s) 154, 459, 505
Alw26I GTCTC 1 cut(s) 638
Alw44I GTGCAC 1 cut(s) 455
AlwI GGATC 2 cut(s) 484, 497
Aor51HI AGCGCT 1 cut(s) 246
AoxI GGCC 2 cut(s) 340, 388
ApaLI GTGCAC 1 cut(s) 455
ApeKI GCWGC 2 cut(s) 247, 584
ApoI RAATTY 2 cut(s) 65, 685
Asp718I GGTACC 1 cut(s) 607
AspLEI GCGC 1 cut(s) 247
AsuHPI GGTGA 2 cut(s) 312, 360
BaeGI GKGCMC 2 cut(s) 257, 459
BalI TGGCCA 2 cut(s) 342, 390
BamHI GGATCC 1 cut(s) 489
BanI GGYRCC 1 cut(s) 607
BanII GRGCYC 1 cut(s) 154
BbsI GAAGAC 1 cut(s) 621
Bbv12I GWGCWC 3 cut(s) 154, 459, 505
BbvI GCAGC 2 cut(s) 234, 571
BccI CCATC 1 cut(s) 518
BciT130I CCWGG 2 cut(s) 258, 387
BcoDI GTCTC 1 cut(s) 638
BfaI CTAG 1 cut(s) 507
BfmI CTRYAG 1 cut(s) 288
BfoI RGCGCY 1 cut(s) 248
BisI GCNGC 2 cut(s) 248, 585
BlsI GCNGC 2 cut(s) 249, 586
Bme1390I CCNGG 2 cut(s) 258, 387
BmiI GGNNCC 2 cut(s) 491, 609
BmrFI CCNGG 2 cut(s) 258, 387
BmsI GCATC 3 cut(s) 169, 182, 262
BpiI GAAGAC 1 cut(s) 621
BpmI CTGGAG 1 cut(s) 453
BsaBI GATNNNNATC 1 cut(s) 276
BsaJI CCNNGG 1 cut(s) 256
BsaXI ACNNNNNCTCC 2 cut(s) 426, 456
Bsc4I CCNNNNNNNGG 3 cut(s) 397, 417, 598
Bse1I ACTGG 3 cut(s) 391, 436, 460
Bse8I GATNNNNATC 1 cut(s) 276
BseBI CCWGG 2 cut(s) 258, 387
BseDI CCNNGG 1 cut(s) 256
BseGI GGATG 4 cut(s) 79, 184, 406, 618
BseJI GATNNNNATC 1 cut(s) 276
BseLI CCNNNNNNNGG 3 cut(s) 397, 417, 598
BseMII CTCAG 2 cut(s) 198, 549
BseNI ACTGG 3 cut(s) 391, 436, 460
BseRI GAGGAG 1 cut(s) 617
BseSI GKGCMC 2 cut(s) 257, 459
BseXI GCAGC 2 cut(s) 234, 571
BsgI GTGCAG 1 cut(s) 222
Bsh1236I CGCG 3 cut(s) 36, 220, 594
BshFI GGCC 2 cut(s) 342, 390
BshNI GGYRCC 1 cut(s) 607
BsiHKAI GWGCWC 3 cut(s) 154, 459, 505
BsiWI CGTACG 1 cut(s) 221
BslI CCNNNNNNNGG 3 cut(s) 397, 417, 598
BsmAI GTCTC 1 cut(s) 638
BsmI GAATGC 3 cut(s) 309, 586, 587
BsnI GGCC 2 cut(s) 342, 390
Bsp1286I GDGCHC 4 cut(s) 154, 257, 459, 505
Bsp1407I TGTACA 1 cut(s) 163
Bsp143I GATC 2 cut(s) 3, 489
BspACI CCGC 2 cut(s) 363, 592
BspANI GGCC 2 cut(s) 342, 390
BspCNI CTCAG 2 cut(s) 199, 550
BspFNI CGCG 3 cut(s) 36, 220, 594
BspLI GGNNCC 2 cut(s) 491, 609
BspMAI CTGCAG 1 cut(s) 292
BspPI GGATC 2 cut(s) 484, 497
BspT107I GGYRCC 1 cut(s) 607
BsrBI CCGCTC 1 cut(s) 363
BsrGI TGTACA 1 cut(s) 163
BsrI ACTGG 3 cut(s) 391, 436, 460
BssECI CCNNGG 1 cut(s) 256
BssMI GATC 2 cut(s) 3, 489
Bst2UI CCWGG 2 cut(s) 258, 387
BstAPI GCANNNNNTGC 1 cut(s) 179
BstAUI TGTACA 1 cut(s) 163
BstC8I GCNNGC 1 cut(s) 344
BstDEI CTNAG 2 cut(s) 207, 558
BstF5I GGATG 4 cut(s) 79, 184, 406, 618
BstFNI CGCG 3 cut(s) 36, 220, 594
BstH2I RGCGCY 1 cut(s) 248
BstHHI GCGC 1 cut(s) 247
BstKTI GATC 2 cut(s) 6, 492
BstMAI GTCTC 1 cut(s) 638
BstMBI GATC 2 cut(s) 3, 489
BstMWI GCNNNNNNNGC 3 cut(s) 158, 179, 315
BstNI CCWGG 2 cut(s) 258, 387
BstNSI RCATGY 1 cut(s) 571
BstSCI CCNGG 2 cut(s) 256, 385
BstSFI CTRYAG 1 cut(s) 288
BstSLI GKGCMC 2 cut(s) 257, 459
BstUI CGCG 3 cut(s) 36, 220, 594
BstV1I GCAGC 2 cut(s) 234, 571
BstV2I GAAGAC 1 cut(s) 621
BstX2I RGATCY 1 cut(s) 489
BstYI RGATCY 1 cut(s) 489
BsuRI GGCC 2 cut(s) 342, 390
BtsCI GGATG 4 cut(s) 79, 184, 406, 618
BtsI GCAGTG 3 cut(s) 55, 234, 459
BtsIMutI CAGTG 3 cut(s) 55, 234, 459
Cac8I GCNNGC 1 cut(s) 344
CfoI GCGC 1 cut(s) 247
CseI GACGC 1 cut(s) 25
Csp6I GTAC 3 cut(s) 164, 222, 608
CviAII CATG 2 cut(s) 568, 630
CviQI GTAC 3 cut(s) 164, 222, 608
DdeI CTNAG 2 cut(s) 207, 558
DpnI GATC 2 cut(s) 5, 491
DpnII GATC 2 cut(s) 3, 489
EaeI YGGCCR 2 cut(s) 340, 388
Ecl136II GAGCTC 1 cut(s) 152
Eco24I GRGCYC 1 cut(s) 154
Eco47III AGCGCT 1 cut(s) 246
Eco53kI GAGCTC 1 cut(s) 152
Eco57I CTGAAG 1 cut(s) 633
EcoICRI GAGCTC 1 cut(s) 152
EcoRI GAATTC 1 cut(s) 685
EcoRII CCWGG 2 cut(s) 256, 385
EcoT22I ATGCAT 1 cut(s) 175
EcoT38I GRGCYC 1 cut(s) 154
FaeI CATG 2 cut(s) 571, 633
FatI CATG 2 cut(s) 567, 629
Fnu4HI GCNGC 2 cut(s) 248, 585
FokI GGATG 4 cut(s) 86, 191, 413, 605
FriOI GRGCYC 1 cut(s) 154
Fsp4HI GCNGC 2 cut(s) 248, 585
FspBI CTAG 1 cut(s) 507
GlaI GCGC 1 cut(s) 246
GluI GCNGC 2 cut(s) 248, 585
GsuI CTGGAG 1 cut(s) 453
HaeII RGCGCY 1 cut(s) 248
HaeIII GGCC 2 cut(s) 342, 390
HgaI GACGC 1 cut(s) 25
HhaI GCGC 1 cut(s) 247
Hin1II CATG 2 cut(s) 571, 633
Hin6I GCGC 1 cut(s) 245
HinP1I GCGC 1 cut(s) 245
HindIII AAGCTT 1 cut(s) 538
HinfI GANTC 4 cut(s) 135, 209, 553, 560
HphI GGTGA 2 cut(s) 312, 360
Hpy166II GTNNAC 2 cut(s) 368, 457
Hpy188I TCNGA 4 cut(s) 178, 565, 668, 691
Hpy188III TCNNGA 4 cut(s) 43, 206, 426, 557
Hpy8I GTNNAC 2 cut(s) 368, 457
Hpy99I CGWCG 2 cut(s) 41, 672
HpyAV CCTTC 1 cut(s) 592
HpyCH4V TGCA 6 cut(s) 145, 173, 239, 290, 457, 587
HpyF10VI GCNNNNNNNGC 3 cut(s) 158, 179, 315
HpyF3I CTNAG 2 cut(s) 207, 558
Hsp92II CATG 2 cut(s) 571, 633
HspAI GCGC 1 cut(s) 245
KpnI GGTACC 1 cut(s) 611
Kzo9I GATC 2 cut(s) 3, 489
LmnI GCTCC 1 cut(s) 508
Lsp1109I GCAGC 2 cut(s) 234, 571
LweI GCATC 3 cut(s) 169, 182, 262
MaeI CTAG 1 cut(s) 507
MaeIII GTNAC 1 cut(s) 296
MalI GATC 2 cut(s) 5, 491
MbiI CCGCTC 1 cut(s) 363
MboI GATC 2 cut(s) 3, 489
MboII GAAGA 1 cut(s) 626
MflI RGATCY 1 cut(s) 489
MhlI GDGCHC 4 cut(s) 154, 257, 459, 505
MlsI TGGCCA 2 cut(s) 342, 390
MluCI AATT 4 cut(s) 65, 281, 412, 685
MluNI TGGCCA 2 cut(s) 342, 390
MlyI GAGTC 3 cut(s) 144, 218, 569
MmeI TCCRAC 1 cut(s) 691
MnlI CCTC 7 cut(s) 64, 524, 595, 598, 632, 666, 674
Mox20I TGGCCA 2 cut(s) 342, 390
Mph1103I ATGCAT 1 cut(s) 175
MscI TGGCCA 2 cut(s) 342, 390
MseI TTAA 2 cut(s) 305, 354
Msp20I TGGCCA 2 cut(s) 342, 390
MspA1I CMGCKG 1 cut(s) 346
MspR9I CCNGG 2 cut(s) 258, 387
Mva1269I GAATGC 3 cut(s) 309, 586, 587
MvaI CCWGG 2 cut(s) 258, 387
MvnI CGCG 3 cut(s) 36, 220, 594
MwoI GCNNNNNNNGC 3 cut(s) 158, 179, 315
NdeII GATC 2 cut(s) 3, 489
NlaIII CATG 2 cut(s) 571, 633
NlaIV GGNNCC 2 cut(s) 491, 609
NmuCI GTSAC 1 cut(s) 296
NsiI ATGCAT 1 cut(s) 175
NspI RCATGY 1 cut(s) 571
PciI ACATGT 1 cut(s) 567
PctI GAATGC 3 cut(s) 309, 586, 587
PfeI GAWTC 1 cut(s) 553
Pfl23II CGTACG 1 cut(s) 221
PkrI GCNGC 2 cut(s) 249, 586
PleI GAGTC 3 cut(s) 143, 217, 568
PpsI GAGTC 3 cut(s) 143, 217, 568
PscI ACATGT 1 cut(s) 567
Psp124BI GAGCTC 1 cut(s) 154
Psp6I CCWGG 2 cut(s) 256, 385
PspGI CCWGG 2 cut(s) 256, 385
PspLI CGTACG 1 cut(s) 221
PspN4I GGNNCC 2 cut(s) 491, 609
PstI CTGCAG 1 cut(s) 292
PsuI RGATCY 1 cut(s) 489
PvuII CAGCTG 1 cut(s) 346
RsaI GTAC 3 cut(s) 165, 223, 609
RsaNI GTAC 3 cut(s) 164, 222, 608
SacI GAGCTC 1 cut(s) 154
SaqAI TTAA 2 cut(s) 305, 354
SatI GCNGC 2 cut(s) 248, 585
Sau3AI GATC 2 cut(s) 3, 489
SchI GAGTC 3 cut(s) 144, 218, 569
ScrFI CCNGG 2 cut(s) 258, 387
SduI GDGCHC 4 cut(s) 154, 257, 459, 505
SfaNI GCATC 3 cut(s) 169, 182, 262
SfcI CTRYAG 1 cut(s) 288
Sse9I AATT 4 cut(s) 65, 281, 412, 685
SsiI CCGC 2 cut(s) 363, 592
SspMI CTAG 1 cut(s) 507
SstI GAGCTC 1 cut(s) 154
StyD4I CCNGG 2 cut(s) 256, 385
TaqI TCGA 2 cut(s) 425, 574
TasI AATT 4 cut(s) 65, 281, 412, 685
TatI WGTACW 1 cut(s) 163
TfiI GAWTC 1 cut(s) 553
Tru1I TTAA 2 cut(s) 305, 354
Tru9I TTAA 2 cut(s) 305, 354
TscAI CASTG 3 cut(s) 55, 241, 459
TseFI GTSAC 1 cut(s) 296
TseI GCWGC 2 cut(s) 247, 584
Tsp45I GTSAC 1 cut(s) 296
TspDTI ATGAA 3 cut(s) 77, 187, 417
TspGWI ACGGA 2 cut(s) 495, 685
TspRI CASTG 3 cut(s) 55, 241, 459
VneI GTGCAC 1 cut(s) 455
XapI RAATTY 2 cut(s) 65, 685
XceI RCATGY 1 cut(s) 571
XspI CTAG 1 cut(s) 507
Zsp2I ATGCAT 1 cut(s) 175
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.