Rroxscaffold_3G00239090

Retroviral aspartyl protease

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000094
Physical Location & Seq
Reverse (-)
28529944 .. 28531311
1368 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00239090.1

Sequence Viewer

Length: 681 bp
ATGGCACCATTTCGGATGGCACCAGCTGAACTTAAGGAGTTGAAAGAACAAATTGATGGTTTACTTGAACAGGGGTTCATTAGACCTAGTACTTCTCCTTGGGGTGCACCCGTGGTGTTTGCAAGGAAGAAGGATGGTTCGCTACGGTTGTGTGTGGATTATCGGCAGTTGAACAAGGTGACGATCAAGAATAGGTACCCTTTACCTAGGATTGATGACTTGTTTGACCAGCTTAGGGAAGCTACTGTGTTCTCGAAGATCGATTTGAGATCGGGATATCACCAGTTGAGGGTGAAGGATGATGATGTTCCTAAAACTGCTTTTAGGACCAGGTATGGACATTTTGAGTTTGTTGTCATGCCTTTTGGTCTAACCAATGCACCTGCTGCCTTTATGGACTTGATGAATCGTATGTTCAGTCCGTACTTGGATAAGTTCGTGGTGGTGTTCGTGGATGATATCTTGATTTATTCCAAGACGTTGGAGGACCATGATATGCATCTACGGATTGTGCTACAGATTTTGAGAGAAAAGGAGTTGTTTGCGAAATTCGAGAAGTGCGAATTTTGGCAAAGGGAGGTCAAGTTCCTTGGTCATGTAGTTTCGAAGGATGGAGTCTCTGTGGATCCTTCTAAAGTTGAAGCGGTGATGAACTGGGGCCAACCCACTACGGTTACTTGA
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
RVP_2 RVT_1 Retrotrans_gag zf-CCHC

Protein Analysis

226

Amino Acids

26.28

Weight (kDa)

8.44

Isoelectric Point (pI)

36.65

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_1 PF00078 42 - 200 6.5e-40 Reverse transcriptase (RNA-dependent DNA polymerase)
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: OG0000094)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G42190
fragaria_vesca FvH4_1g22371 FvH4_1g23261 FvH4_1g27933 FvH4_1g27934 FvH4_1g29231 FvH4_2g02781 FvH4_2g08031 FvH4_2g08581 FvH4_3g06961 FvH4_3g06962 FvH4_3g13531 FvH4_3g14391 FvH4_3g14392 FvH4_3g18622 FvH4_3g18964 FvH4_3g26314 FvH4_3g28781 FvH4_3g30771 FvH4_3g30772 FvH4_3g31752 FvH4_3g32803 FvH4_3g35751 FvH4_3g35752 FvH4_4g02151 FvH4_4g02642 FvH4_4g05523 FvH4_4g05524 FvH4_4g06574 FvH4_4g06722 FvH4_4g08644 FvH4_4g08645 FvH4_4g08646 FvH4_4g08851 FvH4_4g08971 FvH4_4g09081 FvH4_4g09243 FvH4_4g09244 FvH4_4g09283 FvH4_4g10021 FvH4_4g10032 FvH4_4g10033 FvH4_4g10182 FvH4_4g10361 FvH4_4g12502 FvH4_4g12503 FvH4_4g13341 FvH4_4g13942 FvH4_4g13943 FvH4_4g13944 FvH4_4g14432 FvH4_4g14822 FvH4_4g14823 FvH4_4g15291 FvH4_4g15292 FvH4_4g15293 FvH4_4g15471 FvH4_4g15583 FvH4_4g15584 FvH4_4g15585 FvH4_4g15586 FvH4_4g15587 FvH4_4g15591 FvH4_4g15592 FvH4_4g15593 FvH4_4g16179 FvH4_4g18131 FvH4_4g21031 FvH4_4g22021 FvH4_4g22021 FvH4_4g22042 FvH4_5g03402 FvH4_5g07411 FvH4_5g13881 FvH4_5g15792 FvH4_5g24682 FvH4_5g24911 FvH4_5g25322 FvH4_5g25641 FvH4_5g36692 FvH4_5g38072 FvH4_5g38171 FvH4_6g05202 FvH4_6g08531 FvH4_6g16342 FvH4_6g21771 FvH4_6g23303 FvH4_6g23961 FvH4_6g25381 FvH4_6g27021 FvH4_6g27022 FvH4_6g30091 FvH4_6g30092 FvH4_7g02051 FvH4_7g06031 FvH4_7g07031 FvH4_7g07581 FvH4_7g08381 FvH4_7g11551 FvH4_7g19711 FvH4_7g25621 FvH4_7g29722
malus_domestica MD06G1134500.v1.1 MD09G1067600.v1.1 MD13G1145500.v1.1 MD15G1166500.v1.1 MD16G1270000.v1.1
prunus_persica Prupe.7G030900_v2.0.a1
pyrus_communis pycom01g00710 pycom01g03760 pycom03g10770 pycom04g02180 pycom05g08050 pycom06g04140 pycom06g11110 pycom07g07550 pycom07g21570 pycom08g17240 pycom09g13900 pycom09g19570 pycom10g22300 pycom11g03210 pycom11g13750 pycom11g24890 pycom12561g00270 pycom12668g00020 pycom12g11280 pycom12g20720 pycom12g20730 pycom13g21410 pycom13g21660 pycom14g06010 pycom14g06370 pycom14g12800 pycom16g21440 pycom16g22530 pycom17g02030 pycom420g00170 pycom50g00020 pycom5153684g00110 pycom520g00860 pycom581g00060
rosa_chinensis RchiOBHm_Chr0c08g0498091 RchiOBHm_Chr0c08g0498101 RchiOBHm_Chr1g0326991 RchiOBHm_Chr2g0084311 RchiOBHm_Chr2g0090701 RchiOBHm_Chr2g0098591 RchiOBHm_Chr2g0109491 RchiOBHm_Chr2g0109501 RchiOBHm_Chr2g0130801 RchiOBHm_Chr2g0145931 RchiOBHm_Chr2g0168091 RchiOBHm_Chr3g0457081 RchiOBHm_Chr3g0457091 RchiOBHm_Chr3g0467781 RchiOBHm_Chr3g0467791 RchiOBHm_Chr3g0493771 RchiOBHm_Chr3g0494051 RchiOBHm_Chr3g0496881 RchiOBHm_Chr4g0401391 RchiOBHm_Chr4g0414861 RchiOBHm_Chr4g0424081 RchiOBHm_Chr5g0009611 RchiOBHm_Chr5g0049881 RchiOBHm_Chr5g0050351 RchiOBHm_Chr5g0053791 RchiOBHm_Chr5g0078031 RchiOBHm_Chr6g0256481 RchiOBHm_Chr6g0271231 RchiOBHm_Chr6g0286381 RchiOBHm_Chr7g0197101 RchiOBHm_Chr7g0221891 RchiOBHm_Chr7g0237801 RchiOBHm_Chr7g0237821
rosa_multiflora Rmu_sc0000509.1_g000034 Rmu_sc0004751.1_g000014 Rmu_sc0008546.1_g000002 Rmu_sc0009320.1_g000003 Rmu_sc0010661.1_g000006 Rmu_sc0029652.1_g000002
rosa_roxburghii Rroxscaffold_10G00433150 Rroxscaffold_15G00447630 Rroxscaffold_26G00447790 Rroxscaffold_29G00441810 Rroxscaffold_32G00442860 Rroxscaffold_33G00439800 Rroxscaffold_34G00443230 Rroxscaffold_3G00220560 Rroxscaffold_3G00227370 Rroxscaffold_3G00239080 Rroxscaffold_3G00239090 Rroxscaffold_3G00273190 Rroxscaffold_4G00323530 Rroxscaffold_4G00326840 Rroxscaffold_57G00443110 Rroxscaffold_5G00338590 Rroxscaffold_5G00347530 Rroxscaffold_68G00446990 Rroxscaffold_76G00448570 Rroxscaffold_90G00448860
rosa_rugosa Rorug06G0233600
rosa_samantha Rh3CG302700 Rh6DG286700
rosa_wichuraiana Rw0G002280 Rw0G004080 Rw0G011830 Rw1G003690 Rw1G008800 Rw1G009130 Rw1G009140 Rw1G009150 Rw1G009160 Rw1G009410 Rw1G009580 Rw1G012770 Rw1G015850 Rw1G026860 Rw2G003780 Rw2G006480 Rw2G016520 Rw2G016960 Rw2G018170 Rw2G025180 Rw2G025510 Rw2G025610 Rw2G025750 Rw2G025920 Rw2G029950 Rw2G046360 Rw2G046370 Rw2G046380 Rw3G009070 Rw3G025820 Rw3G027340 Rw3G027900 Rw3G028150 Rw3G029060 Rw4G002440 Rw4G005960 Rw4G007520 Rw4G011970 Rw4G011980 Rw4G012190 Rw4G012530 Rw4G018490 Rw4G026380 Rw5G003970 Rw5G030920 Rw5G031780 Rw5G031900 Rw5G033030 Rw5G033040 Rw5G036330 Rw5G039730 Rw5G048110 Rw6G006670 Rw6G007910 Rw6G009720 Rw6G010990 Rw6G012930 Rw6G012940 Rw6G013420 Rw6G014690 Rw6G015290 Rw6G015790 Rw6G015920 Rw6G036510 Rw7G016650 Rw7G023140 Rw7G028650 Rw7G036450 Rw7G036460 Rw7G036910

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 391
Acc36I ACCTGC 1 cut(s) 391
Acc65I GGTACC 1 cut(s) 195
AccB1I GGYRCC 3 cut(s) 4, 19, 195
AciI CCGC 1 cut(s) 644
AclWI GGATC 2 cut(s) 620, 633
AcsI RAATTY 2 cut(s) 548, 563
AfaI GTAC 3 cut(s) 91, 197, 425
AfiI CCNNNNNNNGG 2 cut(s) 235, 289
AflII CTTAAG 1 cut(s) 32
AgsI TTSAA 4 cut(s) 43, 68, 172, 641
AjnI CCWGG 1 cut(s) 329
AloI GAACNNNNNNTCC 2 cut(s) 569, 601
AluBI AGCT 3 cut(s) 26, 232, 242
AluI AGCT 3 cut(s) 26, 232, 242
Alw21I GWGCWC 1 cut(s) 109
Alw26I GTCTC 1 cut(s) 622
Alw44I GTGCAC 1 cut(s) 105
AlwI GGATC 2 cut(s) 620, 633
AoxI GGCC 1 cut(s) 658
ApaLI GTGCAC 1 cut(s) 105
ApeKI GCWGC 1 cut(s) 386
ApoI RAATTY 2 cut(s) 548, 563
Asp718I GGTACC 1 cut(s) 195
AspA2I CCTAGG 1 cut(s) 206
AspS9I GGNCC 3 cut(s) 327, 487, 658
AsuHPI GGTGA 4 cut(s) 190, 272, 304, 658
AsuII TTCGAA 1 cut(s) 605
AvaII GGWCC 2 cut(s) 327, 487
AvrII CCTAGG 1 cut(s) 206
BaeGI GKGCMC 1 cut(s) 109
BamHI GGATCC 1 cut(s) 625
BanI GGYRCC 3 cut(s) 4, 19, 195
Bbv12I GWGCWC 1 cut(s) 109
BbvI GCAGC 1 cut(s) 373
BccI CCATC 4 cut(s) 10, 50, 128, 605
BciT130I CCWGG 1 cut(s) 331
BcoDI GTCTC 1 cut(s) 622
BfaI CTAG 2 cut(s) 87, 207
BfmI CTRYAG 1 cut(s) 515
BfrI CTTAAG 1 cut(s) 32
BfuAI ACCTGC 1 cut(s) 391
BisI GCNGC 1 cut(s) 387
BlnI CCTAGG 1 cut(s) 206
BlsI GCNGC 1 cut(s) 388
BmcAI AGTACT 1 cut(s) 91
Bme1390I CCNGG 1 cut(s) 331
Bme18I GGWCC 2 cut(s) 327, 487
BmgT120I GGNCC 3 cut(s) 327, 487, 658
BmiI GGNNCC 5 cut(s) 6, 21, 197, 627, 659
BmrFI CCNGG 1 cut(s) 331
BmrI ACTGGG 1 cut(s) 664
BmsI GCATC 1 cut(s) 508
BmuI ACTGGG 1 cut(s) 664
Bpu10I CCTNAGC 1 cut(s) 233
Bpu14I TTCGAA 1 cut(s) 605
Bsa29I ATCGAT 1 cut(s) 261
BsaBI GATNNNNATC 1 cut(s) 498
BsaJI CCNNGG 4 cut(s) 98, 111, 206, 589
BsaXI ACNNNNNCTCC 4 cut(s) 569, 599, 606, 636
Bsc4I CCNNNNNNNGG 2 cut(s) 235, 289
Bse1I ACTGG 2 cut(s) 283, 659
Bse8I GATNNNNATC 1 cut(s) 498
BseBI CCWGG 1 cut(s) 331
BseCI ATCGAT 1 cut(s) 261
BseDI CCNNGG 4 cut(s) 98, 111, 206, 589
BseGI GGATG 5 cut(s) 21, 139, 304, 460, 616
BseJI GATNNNNATC 1 cut(s) 498
BseLI CCNNNNNNNGG 2 cut(s) 235, 289
BseNI ACTGG 2 cut(s) 283, 659
BseSI GKGCMC 1 cut(s) 109
BseXI GCAGC 1 cut(s) 373
BshFI GGCC 1 cut(s) 660
BshNI GGYRCC 3 cut(s) 4, 19, 195
BshVI ATCGAT 1 cut(s) 261
BsiHKAI GWGCWC 1 cut(s) 109
BslI CCNNNNNNNGG 2 cut(s) 235, 289
BsmAI GTCTC 1 cut(s) 622
BsnI GGCC 1 cut(s) 660
Bsp119I TTCGAA 1 cut(s) 605
Bsp1286I GDGCHC 1 cut(s) 109
Bsp143I GATC 4 cut(s) 183, 258, 269, 625
BspACI CCGC 1 cut(s) 644
BspANI GGCC 1 cut(s) 660
BspDI ATCGAT 1 cut(s) 261
BspLI GGNNCC 5 cut(s) 6, 21, 197, 627, 659
BspMI ACCTGC 1 cut(s) 391
BspPI GGATC 2 cut(s) 620, 633
BspT104I TTCGAA 1 cut(s) 605
BspT107I GGYRCC 3 cut(s) 4, 19, 195
BspTI CTTAAG 1 cut(s) 32
BsrI ACTGG 2 cut(s) 283, 659
BssECI CCNNGG 4 cut(s) 98, 111, 206, 589
BssMI GATC 4 cut(s) 183, 258, 269, 625
BssT1I CCWWGG 3 cut(s) 98, 206, 589
Bst2UI CCWGG 1 cut(s) 331
Bst4CI ACNGT 3 cut(s) 147, 247, 673
BstAFI CTTAAG 1 cut(s) 32
BstAPI GCANNNNNTGC 1 cut(s) 386
BstBI TTCGAA 1 cut(s) 605
BstDEI CTNAG 1 cut(s) 233
BstDSI CCRYGG 1 cut(s) 111
BstF5I GGATG 5 cut(s) 21, 139, 304, 460, 616
BstKTI GATC 4 cut(s) 186, 261, 272, 628
BstMAI GTCTC 1 cut(s) 622
BstMBI GATC 4 cut(s) 183, 258, 269, 625
BstMWI GCNNNNNNNGC 1 cut(s) 386
BstNI CCWGG 1 cut(s) 331
BstSCI CCNGG 1 cut(s) 329
BstSFI CTRYAG 1 cut(s) 515
BstSLI GKGCMC 1 cut(s) 109
BstV1I GCAGC 1 cut(s) 373
BstX2I RGATCY 1 cut(s) 625
BstXI CCANNNNNNTGG 1 cut(s) 481
BstYI RGATCY 1 cut(s) 625
Bsu15I ATCGAT 1 cut(s) 261
BsuRI GGCC 1 cut(s) 660
BsuTUI ATCGAT 1 cut(s) 261
BtgI CCRYGG 1 cut(s) 111
BtsCI GGATG 5 cut(s) 21, 139, 304, 460, 616
BveI ACCTGC 1 cut(s) 391
Cfr13I GGNCC 3 cut(s) 327, 487, 658
ClaI ATCGAT 1 cut(s) 261
CsiI ACCWGGT 1 cut(s) 329
Csp6I GTAC 3 cut(s) 90, 196, 424
CviAII CATG 3 cut(s) 358, 491, 596
CviJI RGCY 4 cut(s) 26, 232, 242, 660
CviKI_1 RGCY 4 cut(s) 26, 232, 242, 660
CviQI GTAC 3 cut(s) 90, 196, 424
DdeI CTNAG 1 cut(s) 233
DpnI GATC 4 cut(s) 185, 260, 271, 627
DpnII GATC 4 cut(s) 183, 258, 269, 625
Eco130I CCWWGG 3 cut(s) 98, 206, 589
Eco32I GATATC 2 cut(s) 278, 460
Eco47I GGWCC 2 cut(s) 327, 487
EcoRII CCWGG 1 cut(s) 329
EcoRV GATATC 2 cut(s) 278, 460
EcoT14I CCWWGG 3 cut(s) 98, 206, 589
EcoT22I ATGCAT 1 cut(s) 501
ErhI CCWWGG 3 cut(s) 98, 206, 589
FaeI CATG 3 cut(s) 361, 494, 599
FaiI YATR 7 cut(s) 336, 359, 395, 413, 492, 497, 597
FatI CATG 3 cut(s) 357, 490, 595
Fnu4HI GCNGC 1 cut(s) 387
FokI GGATG 5 cut(s) 28, 146, 311, 467, 623
Fsp4HI GCNGC 1 cut(s) 387
FspBI CTAG 2 cut(s) 87, 207
GluI GCNGC 1 cut(s) 387
HaeIII GGCC 1 cut(s) 660
Hin1II CATG 3 cut(s) 361, 494, 599
HinfI GANTC 2 cut(s) 406, 615
HphI GGTGA 4 cut(s) 190, 272, 304, 658
Hpy166II GTNNAC 2 cut(s) 62, 107
Hpy188I TCNGA 1 cut(s) 15
Hpy188III TCNNGA 5 cut(s) 187, 253, 273, 463, 553
Hpy8I GTNNAC 2 cut(s) 62, 107
HpyAV CCTTC 4 cut(s) 124, 289, 601, 639
HpyCH4III ACNGT 3 cut(s) 147, 247, 673
HpyCH4IV ACGT 1 cut(s) 479
HpyCH4V TGCA 4 cut(s) 107, 122, 380, 499
HpyF10VI GCNNNNNNNGC 1 cut(s) 386
HpyF3I CTNAG 1 cut(s) 233
HpySE526I ACGT 1 cut(s) 479
Hsp92II CATG 3 cut(s) 361, 494, 599
KpnI GGTACC 1 cut(s) 199
Kzo9I GATC 4 cut(s) 183, 258, 269, 625
LpnPI CCDG 8 cut(s) 36, 56, 242, 296, 316, 343, 396, 640
Lsp1109I GCAGC 1 cut(s) 373
LweI GCATC 1 cut(s) 508
MabI ACCWGGT 1 cut(s) 329
MaeI CTAG 2 cut(s) 87, 207
MaeII ACGT 1 cut(s) 479
MaeIII GTNAC 2 cut(s) 178, 673
MalI GATC 4 cut(s) 185, 260, 271, 627
MboI GATC 4 cut(s) 183, 258, 269, 625
MboII GAAGA 2 cut(s) 139, 268
MflI RGATCY 1 cut(s) 625
MhlI GDGCHC 1 cut(s) 109
MluCI AATT 3 cut(s) 51, 548, 563
MlyI GAGTC 1 cut(s) 624
MmeI TCCRAC 1 cut(s) 462
MnlI CCTC 3 cut(s) 282, 478, 571
Mph1103I ATGCAT 1 cut(s) 501
MseI TTAA 1 cut(s) 33
MspA1I CMGCKG 1 cut(s) 26
MspCI CTTAAG 1 cut(s) 32
MspR9I CCNGG 1 cut(s) 331
MvaI CCWGG 1 cut(s) 331
MwoI GCNNNNNNNGC 1 cut(s) 386
NdeII GATC 4 cut(s) 183, 258, 269, 625
NlaIII CATG 3 cut(s) 361, 494, 599
NlaIV GGNNCC 5 cut(s) 6, 21, 197, 627, 659
NmuCI GTSAC 1 cut(s) 178
NsiI ATGCAT 1 cut(s) 501
NspV TTCGAA 1 cut(s) 605
PaqCI CACCTGC 1 cut(s) 391
PcsI WCGNNNNNNNCGW 1 cut(s) 558
PfeI GAWTC 1 cut(s) 406
PkrI GCNGC 1 cut(s) 388
PleI GAGTC 1 cut(s) 623
PpsI GAGTC 1 cut(s) 623
Psp6I CCWGG 1 cut(s) 329
PspGI CCWGG 1 cut(s) 329
PspN4I GGNNCC 5 cut(s) 6, 21, 197, 627, 659
PspPI GGNCC 3 cut(s) 327, 487, 658
PsuI RGATCY 1 cut(s) 625
PvuII CAGCTG 1 cut(s) 26
RsaI GTAC 3 cut(s) 91, 197, 425
RsaNI GTAC 3 cut(s) 90, 196, 424
SaqAI TTAA 1 cut(s) 33
SatI GCNGC 1 cut(s) 387
Sau3AI GATC 4 cut(s) 183, 258, 269, 625
Sau96I GGNCC 3 cut(s) 327, 487, 658
ScaI AGTACT 1 cut(s) 91
SchI GAGTC 1 cut(s) 624
ScrFI CCNGG 1 cut(s) 331
SduI GDGCHC 1 cut(s) 109
SexAI ACCWGGT 1 cut(s) 329
SfaNI GCATC 1 cut(s) 508
SfcI CTRYAG 1 cut(s) 515
SfuI TTCGAA 1 cut(s) 605
SinI GGWCC 2 cut(s) 327, 487
SmlI CTYRAG 1 cut(s) 32
SmoI CTYRAG 1 cut(s) 32
Sse9I AATT 3 cut(s) 51, 548, 563
SsiI CCGC 1 cut(s) 644
SspMI CTAG 2 cut(s) 87, 207
StyD4I CCNGG 1 cut(s) 329
StyI CCWWGG 3 cut(s) 98, 206, 589
TaaI ACNGT 3 cut(s) 147, 247, 673
TaiI ACGT 1 cut(s) 482
TaqI TCGA 4 cut(s) 254, 261, 552, 605
TasI AATT 3 cut(s) 51, 548, 563
TatI WGTACW 1 cut(s) 89
TfiI GAWTC 1 cut(s) 406
Tru1I TTAA 1 cut(s) 33
Tru9I TTAA 1 cut(s) 33
TseFI GTSAC 1 cut(s) 178
TseI GCWGC 1 cut(s) 386
Tsp45I GTSAC 1 cut(s) 178
TspDTI ATGAA 3 cut(s) 67, 419, 665
TspGWI ACGGA 2 cut(s) 411, 520
Vha464I CTTAAG 1 cut(s) 32
VneI GTGCAC 1 cut(s) 105
VpaK11BI GGWCC 2 cut(s) 327, 487
XapI RAATTY 2 cut(s) 548, 563
XmaJI CCTAGG 1 cut(s) 206
XspI CTAG 2 cut(s) 87, 207
ZrmI AGTACT 1 cut(s) 91
Zsp2I ATGCAT 1 cut(s) 501
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.