Rroxscaffold_1G00041340

Pfam:UBN2

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0000106
Physical Location & Seq
Reverse (-)
59180831 .. 59183195
2365 bp
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UTR
Exon/CDS
Intron
Rroxscaffold_1G00041340.1

Sequence Viewer

Length: 645 bp
ATGAAAAAGAAAAGAAATTTGAAGAATTTTTCTAGAGGAGGAGATAGACCCAAATATTGGGCAAATAAAAAAGATATAAAGGAGAAAAGAAATTATTCTCCATGTGGAATTTGCCACAAAAATAATCATCGAGAAATAGATTGTTGGTTTCGGGGAAAACCAGAATGCCGAAACTGCAACAAGTTTGGTCATATTGAGGAAAATTGTTTCCTCAAGAAAAATCACCGAGCAGACTTTTCAGAAGAAAATGAGCAAGATGATAATCTCTTCTATGCATGTCACTCGGCGATTGAAGAGAAAAATAAGAAGTGGTACGTGGATAGCGACTGCAGCAATCACATGTCGGGAGACAAAACCATTTTCTCCAAACTTAGTACTTTCCGAAAGTCTCAAGTGAAACTAGGAAATGGAGAAATGGTGAAAACTGAAGGAAAAGAAGTCAAGAAGAAAAATATTGGCCTAGAAAAAAAGCAGCTGAAGACTCTACCACGTCAAGCAAGTAAAGAAGGGAGTTCAAATCCTCCACAACTAAAAAGTTGTGAAGTTGCAATGAAGAAGAAAGCCGGAGGAAGGCCATGGAAAAAGAAAGCAAGAGCGAGAACACCTTTGCCAAGGCACTTCCAAGATCGAGACTTGAATTACTAA
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
DUF4219 Retrotran_gag_2 zf-CCHC

Protein Analysis

214

Amino Acids

25.07

Weight (kDa)

9.8

Isoelectric Point (pI)

54.46

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pol_BBD PF22936 104 - 146 2.6e-11 Pol polyprotein, beta-barrel 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
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Orthologous Genes (Group: OG0000106)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G20980 AT3G21000
fragaria_vesca FvH4_1g15931 FvH4_1g15931 FvH4_1g18381 FvH4_1g18382 FvH4_1g22571 FvH4_1g24950 FvH4_1g29372 FvH4_2g03582 FvH4_2g09851 FvH4_2g13112 FvH4_2g20843 FvH4_2g22701 FvH4_2g22702 FvH4_2g23403 FvH4_2g40201 FvH4_3g03542 FvH4_3g03543 FvH4_3g04761 FvH4_3g10464 FvH4_3g12741 FvH4_3g15781 FvH4_3g30981 FvH4_4g00985 FvH4_4g07035 FvH4_4g08192 FvH4_4g08211 FvH4_4g08553 FvH4_4g14242 FvH4_4g14243 FvH4_4g14641 FvH4_4g14843 FvH4_4g14844 FvH4_4g15061 FvH4_4g16281 FvH4_4g19152 FvH4_4g26451 FvH4_5g06442 FvH4_5g22521 FvH4_5g24301 FvH4_5g38641 FvH4_6g02393 FvH4_6g12782 FvH4_6g13871 FvH4_6g19391 FvH4_6g20105 FvH4_6g21292 FvH4_6g23581 FvH4_6g29153 FvH4_6g29691 FvH4_6g30871 FvH4_6g33351 FvH4_6g37042 FvH4_6g38781 FvH4_6g40340 FvH4_7g11221 FvH4_7g23352 FvH4_7g23352 FvH4_7g31212 FvH4_7g32172 FvH4_7g32173 FvH4_7g33701
malus_domestica MD03G1006900.v1.1 MD04G1039100.v1.1 MD04G1239100.v1.1 MD05G1048700.v1.1 MD08G1001800.v1.1 MD09G1165800.v1.1 MD11G1065200.v1.1 MD11G1138200.v1.1 MD14G1033300.v1.1 MD14G1173900.v1.1 MD15G1218200.v1.1 MD16G1034000.v1.1
prunus_persica Prupe.1G219500_v2.0.a1 Prupe.2G169400_v2.0.a1 Prupe.4G109700_v2.0.a1 Prupe.7G022000_v2.0.a1
pyrus_communis pycom01g02000 pycom02g13350 pycom03g01010 pycom04g05000 pycom04g06100 pycom05g05580 pycom05g09950 pycom05g13280 pycom05g26610 pycom06g05940 pycom06g07760 pycom07g06120 pycom07g24780 pycom08g08820 pycom09g03600 pycom09g07200 pycom10g01280 pycom10g06730 pycom10g08410 pycom10g25520 pycom11g00470 pycom11g05250 pycom11g25180 pycom12g08050 pycom13g14760 pycom13g28170 pycom15g14310 pycom15g19880 pycom15g24230 pycom15g33640 pycom16g02150 pycom16g16240 pycom16g20050 pycom16g21090 pycom17g06100
rosa_chinensis RchiOBHm_Chr1g0322161 RchiOBHm_Chr1g0326341 RchiOBHm_Chr1g0357701 RchiOBHm_Chr1g0379861 RchiOBHm_Chr1g0383421 RchiOBHm_Chr2g0093981 RchiOBHm_Chr2g0139051 RchiOBHm_Chr2g0145501 RchiOBHm_Chr3g0450971 RchiOBHm_Chr3g0451441 RchiOBHm_Chr3g0457411 RchiOBHm_Chr4g0436261 RchiOBHm_Chr5g0051431 RchiOBHm_Chr5g0064031 RchiOBHm_Chr5g0073141 RchiOBHm_Chr5g0080061 RchiOBHm_Chr7g0200561 RchiOBHm_Chr7g0235911
rosa_laevigata RLG00000000145 RLG00000000429 RLG00000020339 RLG00000035212
rosa_multiflora Rmu_co7977988.1_g000001 Rmu_co8037866.1_g000001 Rmu_co8243895.1_g000001 Rmu_co8363787.1_g000001 Rmu_co8381003.1_g000001 Rmu_sc0000263.1_g000006 Rmu_sc0000349.1_g000002 Rmu_sc0000455.1_g000031 Rmu_sc0000936.1_g000022 Rmu_sc0001035.1_g000023 Rmu_sc0001169.1_g000019 Rmu_sc0001250.1_g000026 Rmu_sc0002200.1_g000051 Rmu_sc0002230.1_g000027 Rmu_sc0002591.1_g000039 Rmu_sc0003182.1_g000003 Rmu_sc0003441.1_g000068 Rmu_sc0003722.1_g000018 Rmu_sc0003764.1_g000007 Rmu_sc0006014.1_g000016 Rmu_sc0012582.1_g000002 Rmu_sc0013519.1_g000002 Rmu_sc0014550.1_g000005 Rmu_sc0014857.1_g000007 Rmu_sc0019855.1_g000001 Rmu_sc0030839.1_g000001 Rmu_sc0031308.1_g000001
rosa_roxburghii Rroxscaffold_1G00011290 Rroxscaffold_1G00041340 Rroxscaffold_1G00053780 Rroxscaffold_1G00059130 Rroxscaffold_1G00061580 Rroxscaffold_2G00080940 Rroxscaffold_2G00109540 Rroxscaffold_3G00228400 Rroxscaffold_3G00237710 Rroxscaffold_4G00285210 Rroxscaffold_4G00299600 Rroxscaffold_4G00324940 Rroxscaffold_4G00330580 Rroxscaffold_5G00333000 Rroxscaffold_5G00347920 Rroxscaffold_5G00375310 Rroxscaffold_6G00394760 Rroxscaffold_6G00406260 Rroxscaffold_7G00165690 Rroxscaffold_7G00187680
rosa_rugosa Rorug01G0050200 Rorug02G0273800 Rorug06G0490600 Rorug06G0490600 Rorug06G0490700
rosa_samantha Rh1AG348400 Rh5AG222600 Rh6DG000500 Rh6DG194500 Rh7BG452700
rosa_wichuraiana Rw0G003060 Rw0G010530 Rw0G012970 Rw0G022560 Rw0G023390 Rw1G001270 Rw1G001530 Rw1G006070 Rw1G008210 Rw1G022090 Rw1G023320 Rw2G003790 Rw2G004140 Rw2G005280 Rw2G006460 Rw2G019620 Rw2G019840 Rw2G022530 Rw2G023280 Rw2G024990 Rw2G042380 Rw2G051390 Rw3G001640 Rw3G016720 Rw3G017100 Rw3G020890 Rw3G020900 Rw3G021100 Rw4G004820 Rw4G014950 Rw4G030920 Rw4G031400 Rw5G008500 Rw5G017950 Rw5G020170 Rw5G030160 Rw5G033050 Rw5G034640 Rw5G043920 Rw6G005060 Rw6G005540 Rw6G006720 Rw6G008460 Rw6G008670 Rw6G014780 Rw6G019100 Rw6G019350 Rw6G026310 Rw7G016810 Rw7G019180 Rw7G022890 Rw7G025880 Rw7G026390 Rw7G028340 Rw7G034850 Rw7G035170 Rw7G035420 Rw7G037990 Rw7G041560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 57
AcsI RAATTY 3 cut(s) 16, 25, 108
AcuI CTGAAG 2 cut(s) 447, 497
AfaI GTAC 2 cut(s) 314, 376
AfiI CCNNNNNNNGG 2 cut(s) 57, 570
AflIII ACRYGT 1 cut(s) 339
AgsI TTSAA 4 cut(s) 22, 293, 516, 637
AjiI CACGTC 1 cut(s) 491
AluBI AGCT 1 cut(s) 475
AluI AGCT 1 cut(s) 475
Alw26I GTCTC 3 cut(s) 342, 393, 624
AoxI GGCC 2 cut(s) 457, 572
ApeKI GCWGC 2 cut(s) 330, 472
ApoI RAATTY 3 cut(s) 16, 25, 108
Asp700I GAANNNNTTC 1 cut(s) 94
AsuHPI GGTGA 2 cut(s) 215, 430
BbsI GAAGAC 1 cut(s) 485
BbvI GCAGC 2 cut(s) 342, 484
BcgI CGANNNNNNTGC 2 cut(s) 264, 298
BcoDI GTCTC 3 cut(s) 342, 393, 624
BfaI CTAG 3 cut(s) 33, 401, 461
BfmI CTRYAG 1 cut(s) 328
BisI GCNGC 2 cut(s) 331, 473
BlsI GCNGC 2 cut(s) 332, 474
BmcAI AGTACT 1 cut(s) 376
BmgBI CACGTC 1 cut(s) 491
BpiI GAAGAC 1 cut(s) 485
BpuEI CTTGAG 2 cut(s) 197, 375
BsaAI YACGTR 1 cut(s) 316
BsaBI GATNNNNATC 1 cut(s) 261
BsaJI CCNNGG 2 cut(s) 575, 611
BsaXI ACNNNNNCTCC 2 cut(s) 402, 432
Bsc4I CCNNNNNNNGG 2 cut(s) 57, 570
Bse3DI GCAATG 1 cut(s) 555
Bse8I GATNNNNATC 1 cut(s) 261
BseDI CCNNGG 2 cut(s) 575, 611
BseJI GATNNNNATC 1 cut(s) 261
BseLI CCNNNNNNNGG 2 cut(s) 57, 570
BseMI GCAATG 1 cut(s) 555
BseRI GAGGAG 2 cut(s) 51, 54
BseXI GCAGC 2 cut(s) 342, 484
BshFI GGCC 2 cut(s) 459, 574
BsiSI CCGG 1 cut(s) 564
BslI CCNNNNNNNGG 2 cut(s) 57, 570
BsmAI GTCTC 3 cut(s) 342, 393, 624
BsmI GAATGC 1 cut(s) 170
BsnI GGCC 2 cut(s) 459, 574
Bsp143I GATC 1 cut(s) 625
Bsp19I CCATGG 1 cut(s) 575
BspANI GGCC 2 cut(s) 459, 574
BspMAI CTGCAG 1 cut(s) 332
BsrDI GCAATG 1 cut(s) 555
BssECI CCNNGG 2 cut(s) 575, 611
BssMI GATC 1 cut(s) 625
BssT1I CCWWGG 2 cut(s) 575, 611
Bst6I CTCTTC 2 cut(s) 272, 288
BstBAI YACGTR 1 cut(s) 316
BstDEI CTNAG 1 cut(s) 371
BstDSI CCRYGG 1 cut(s) 575
BstKTI GATC 1 cut(s) 628
BstMAI GTCTC 3 cut(s) 342, 393, 624
BstMBI GATC 1 cut(s) 625
BstMWI GCNNNNNNNGC 2 cut(s) 174, 330
BstNSI RCATGY 2 cut(s) 279, 343
BstSFI CTRYAG 1 cut(s) 328
BstV1I GCAGC 2 cut(s) 342, 484
BstV2I GAAGAC 1 cut(s) 485
BsuRI GGCC 2 cut(s) 459, 574
BtgI CCRYGG 1 cut(s) 575
BtrI CACGTC 1 cut(s) 491
Csp6I GTAC 2 cut(s) 313, 375
CviAII CATG 4 cut(s) 102, 276, 340, 576
CviJI RGCY 4 cut(s) 459, 475, 563, 574
CviKI_1 RGCY 4 cut(s) 459, 475, 563, 574
CviQI GTAC 2 cut(s) 313, 375
DdeI CTNAG 1 cut(s) 371
DpnI GATC 1 cut(s) 627
DpnII GATC 1 cut(s) 625
Eam1104I CTCTTC 2 cut(s) 272, 288
EarI CTCTTC 2 cut(s) 272, 288
Eco130I CCWWGG 2 cut(s) 575, 611
Eco57I CTGAAG 2 cut(s) 447, 497
EcoT14I CCWWGG 2 cut(s) 575, 611
EcoT22I ATGCAT 1 cut(s) 277
ErhI CCWWGG 2 cut(s) 575, 611
FaeI CATG 4 cut(s) 105, 279, 343, 579
FaiI YATR 7 cut(s) 77, 103, 192, 273, 277, 341, 577
FatI CATG 4 cut(s) 101, 275, 339, 575
Fnu4HI GCNGC 2 cut(s) 331, 473
Fsp4HI GCNGC 2 cut(s) 331, 473
FspBI CTAG 3 cut(s) 33, 401, 461
GluI GCNGC 2 cut(s) 331, 473
HaeIII GGCC 2 cut(s) 459, 574
HapII CCGG 1 cut(s) 564
Hin1II CATG 4 cut(s) 105, 279, 343, 579
HinfI GANTC 1 cut(s) 481
HpaII CCGG 1 cut(s) 564
HphI GGTGA 2 cut(s) 215, 430
Hpy188I TCNGA 2 cut(s) 241, 383
Hpy188III TCNNGA 6 cut(s) 33, 131, 214, 345, 442, 629
HpyAV CCTTC 3 cut(s) 422, 500, 564
HpyCH4IV ACGT 2 cut(s) 315, 490
HpyCH4V TGCA 4 cut(s) 177, 275, 330, 548
HpyF10VI GCNNNNNNNGC 2 cut(s) 174, 330
HpyF3I CTNAG 1 cut(s) 371
HpySE526I ACGT 2 cut(s) 315, 490
Hsp92II CATG 4 cut(s) 105, 279, 343, 579
Kzo9I GATC 1 cut(s) 625
LpnPI CCDG 2 cut(s) 174, 577
Lsp1109I GCAGC 2 cut(s) 342, 484
MaeI CTAG 3 cut(s) 33, 401, 461
MaeII ACGT 2 cut(s) 315, 490
MaeIII GTNAC 1 cut(s) 278
MalI GATC 1 cut(s) 627
MboI GATC 1 cut(s) 625
MboII GAAGA 8 cut(s) 34, 254, 259, 305, 457, 490, 565, 568
MluCI AATT 6 cut(s) 16, 25, 91, 108, 202, 637
MlyI GAGTC 1 cut(s) 475
MnlI CCTC 6 cut(s) 29, 32, 190, 221, 531, 560
Mph1103I ATGCAT 1 cut(s) 277
MroXI GAANNNNTTC 1 cut(s) 94
MspA1I CMGCKG 1 cut(s) 475
MspI CCGG 1 cut(s) 564
Mva1269I GAATGC 1 cut(s) 170
MwoI GCNNNNNNNGC 2 cut(s) 174, 330
NcoI CCATGG 1 cut(s) 575
NdeII GATC 1 cut(s) 625
NlaIII CATG 4 cut(s) 105, 279, 343, 579
NmeAIII GCCGAG 1 cut(s) 263
NmuCI GTSAC 1 cut(s) 278
NsiI ATGCAT 1 cut(s) 277
NspI RCATGY 2 cut(s) 279, 343
PciI ACATGT 1 cut(s) 339
PcsI WCGNNNNNNNCGW 1 cut(s) 321
PctI GAATGC 1 cut(s) 170
PdmI GAANNNNTTC 1 cut(s) 94
PflMI CCANNNNNTGG 1 cut(s) 57
PkrI GCNGC 2 cut(s) 332, 474
PleI GAGTC 1 cut(s) 475
PpsI GAGTC 1 cut(s) 475
Ppu21I YACGTR 1 cut(s) 316
PscI ACATGT 1 cut(s) 339
PstI CTGCAG 1 cut(s) 332
PvuII CAGCTG 1 cut(s) 475
RsaI GTAC 2 cut(s) 314, 376
RsaNI GTAC 2 cut(s) 313, 375
SatI GCNGC 2 cut(s) 331, 473
Sau3AI GATC 1 cut(s) 625
ScaI AGTACT 1 cut(s) 376
SchI GAGTC 1 cut(s) 475
SetI ASST 4 cut(s) 318, 477, 493, 607
SfcI CTRYAG 1 cut(s) 328
SmlI CTYRAG 2 cut(s) 212, 390
SmoI CTYRAG 2 cut(s) 212, 390
Sse9I AATT 6 cut(s) 16, 25, 91, 108, 202, 637
SspI AATATT 2 cut(s) 56, 454
SspMI CTAG 3 cut(s) 33, 401, 461
StyI CCWWGG 2 cut(s) 575, 611
TaiI ACGT 2 cut(s) 318, 493
TaqI TCGA 2 cut(s) 130, 628
TasI AATT 6 cut(s) 16, 25, 91, 108, 202, 637
TatI WGTACW 1 cut(s) 374
TseFI GTSAC 1 cut(s) 278
TseI GCWGC 2 cut(s) 330, 472
Tsp45I GTSAC 1 cut(s) 278
TspDTI ATGAA 2 cut(s) 17, 566
Van91I CCANNNNNTGG 1 cut(s) 57
XapI RAATTY 3 cut(s) 16, 25, 108
XbaI TCTAGA 1 cut(s) 32
XceI RCATGY 2 cut(s) 279, 343
XmnI GAANNNNTTC 1 cut(s) 94
XspI CTAG 3 cut(s) 33, 401, 461
ZrmI AGTACT 1 cut(s) 376
Zsp2I ATGCAT 1 cut(s) 277
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.