RchiOBHm_Chr4g0403481

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000370
Physical Location & Seq
Forward (+)
22707989 .. 22708534
546 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ37521

Sequence Viewer

Length: 441 bp
ATGTTTGAGAATGATGTGGAGGCATCAAATGTTGAGTTGCCTGTTCCACCTGTGGTGGAGGTTGCTAATGTTGTAGATCCTACTCGTTTGTCGAAGTTGGCAAAGGAGATTTCGAGATTGGGAGGAGTTCCATTTCAGGGAGGTACGGATCACATGTTGGCAGACCAATGGATTGAGAATATGAAGACCTACTTCGAGATGGTCGTCTGTGACGACATTGAGAAGAGGAAGATTTCCACATTTATGCTCCAAGGCGATGCACGGGTGTGGTGGAATGGCACACAGAGGGTGATGGACGTGTCCACCATGACCTGGAATGAGTTTGTGGAACTGTTCAGGAAGAAGTACTTTCCGCCTTCAGTGAGGGAGCAGATGGAAAGGGAATTCATCTCGTTAGTCCAAGGGACTAAGAGTGTGAGGGAATGGATGCTGAGAGCTTAG
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 Retrotrans_gag zf-CCHC

Protein Analysis

146

Amino Acids

17.02

Weight (kDa)

5.12

Isoelectric Point (pI)

37.73

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 78 - 144 5.6e-14 Retrotransposon gag 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 312
AciI CCGC 1 cut(s) 353
AclWI GGATC 2 cut(s) 71, 156
AcsI RAATTY 1 cut(s) 383
AcuI CTGAAG 1 cut(s) 342
AfaI GTAC 2 cut(s) 145, 347
AfiI CCNNNNNNNGG 2 cut(s) 137, 312
AflIII ACRYGT 2 cut(s) 153, 297
AjiI CACGTC 1 cut(s) 298
AjnI CCWGG 1 cut(s) 311
AleI CACNNNNGTG 1 cut(s) 265
AluBI AGCT 1 cut(s) 437
AluI AGCT 1 cut(s) 437
AlwI GGATC 2 cut(s) 71, 156
ApoI RAATTY 1 cut(s) 383
AsuHPI GGTGA 1 cut(s) 301
BbsI GAAGAC 1 cut(s) 191
BccI CCATC 3 cut(s) 193, 286, 367
BciT130I CCWGG 1 cut(s) 313
BmcAI AGTACT 1 cut(s) 347
Bme1390I CCNGG 1 cut(s) 313
BmgBI CACGTC 1 cut(s) 298
BmrFI CCNGG 1 cut(s) 313
BmsI GCATC 3 cut(s) 32, 247, 417
BpiI GAAGAC 1 cut(s) 191
BsaJI CCNNGG 2 cut(s) 250, 400
Bsc4I CCNNNNNNNGG 2 cut(s) 137, 312
BseBI CCWGG 1 cut(s) 313
BseDI CCNNGG 2 cut(s) 250, 400
BseGI GGATG 1 cut(s) 432
BseLI CCNNNNNNNGG 2 cut(s) 137, 312
BseMII CTCAG 1 cut(s) 422
BseRI GAGGAG 1 cut(s) 138
BslFI GGGAC 1 cut(s) 418
BslI CCNNNNNNNGG 2 cut(s) 137, 312
BsmFI GGGAC 1 cut(s) 418
Bsp143I GATC 2 cut(s) 76, 148
BspACI CCGC 1 cut(s) 353
BspCNI CTCAG 1 cut(s) 423
BspPI GGATC 2 cut(s) 71, 156
BssECI CCNNGG 2 cut(s) 250, 400
BssMI GATC 2 cut(s) 76, 148
BssT1I CCWWGG 2 cut(s) 250, 400
Bst2UI CCWGG 1 cut(s) 313
Bst4CI ACNGT 1 cut(s) 333
Bst6I CTCTTC 1 cut(s) 218
BstDEI CTNAG 3 cut(s) 408, 431, 438
BstF5I GGATG 1 cut(s) 432
BstKTI GATC 2 cut(s) 79, 151
BstMBI GATC 2 cut(s) 76, 148
BstNI CCWGG 1 cut(s) 313
BstNSI RCATGY 1 cut(s) 157
BstSCI CCNGG 1 cut(s) 311
BstV2I GAAGAC 1 cut(s) 191
BstX2I RGATCY 1 cut(s) 76
BstYI RGATCY 1 cut(s) 76
BtgZI GCGATG 1 cut(s) 270
BtrI CACGTC 1 cut(s) 298
BtsCI GGATG 1 cut(s) 432
BtsIMutI CAGTG 1 cut(s) 366
Csp6I GTAC 2 cut(s) 144, 346
CviAII CATG 2 cut(s) 154, 307
CviJI RGCY 1 cut(s) 437
CviKI_1 RGCY 1 cut(s) 437
CviQI GTAC 2 cut(s) 144, 346
DdeI CTNAG 3 cut(s) 408, 431, 438
DpnI GATC 2 cut(s) 78, 150
DpnII GATC 2 cut(s) 76, 148
Eam1104I CTCTTC 1 cut(s) 218
EarI CTCTTC 1 cut(s) 218
EciI GGCGGA 1 cut(s) 342
Eco130I CCWWGG 2 cut(s) 250, 400
Eco57I CTGAAG 1 cut(s) 342
EcoRI GAATTC 1 cut(s) 383
EcoRII CCWGG 1 cut(s) 311
EcoT14I CCWWGG 2 cut(s) 250, 400
ErhI CCWWGG 2 cut(s) 250, 400
FaeI CATG 2 cut(s) 157, 310
FaiI YATR 4 cut(s) 155, 182, 245, 308
FalI AAGNNNNNCTT 4 cut(s) 176, 208, 332, 364
FaqI GGGAC 1 cut(s) 418
FatI CATG 2 cut(s) 153, 306
Hin1II CATG 2 cut(s) 157, 310
HphI GGTGA 1 cut(s) 301
Hpy166II GTNNAC 1 cut(s) 303
Hpy188III TCNNGA 3 cut(s) 114, 196, 337
Hpy8I GTNNAC 1 cut(s) 303
HpyAV CCTTC 1 cut(s) 366
HpyCH4III ACNGT 1 cut(s) 333
HpyCH4IV ACGT 1 cut(s) 297
HpyCH4V TGCA 1 cut(s) 260
HpyF3I CTNAG 3 cut(s) 408, 431, 438
HpySE526I ACGT 1 cut(s) 297
Hsp92II CATG 2 cut(s) 157, 310
Kzo9I GATC 2 cut(s) 76, 148
LmnI GCTCC 2 cut(s) 252, 367
LpnPI CCDG 6 cut(s) 54, 63, 122, 298, 322, 325
LweI GCATC 3 cut(s) 32, 247, 417
MaeII ACGT 1 cut(s) 297
MaeIII GTNAC 1 cut(s) 209
MalI GATC 2 cut(s) 78, 150
MboI GATC 2 cut(s) 76, 148
MboII GAAGA 4 cut(s) 196, 235, 241, 352
MflI RGATCY 1 cut(s) 76
MluCI AATT 1 cut(s) 383
MnlI CCTC 8 cut(s) 13, 52, 116, 134, 219, 279, 357, 411
MslI CAYNNNNRTG 2 cut(s) 242, 265
MspR9I CCNGG 1 cut(s) 313
MvaI CCWGG 1 cut(s) 313
NdeII GATC 2 cut(s) 76, 148
NlaIII CATG 2 cut(s) 157, 310
NmuCI GTSAC 1 cut(s) 209
NspI RCATGY 1 cut(s) 157
OliI CACNNNNGTG 1 cut(s) 265
PciI ACATGT 1 cut(s) 153
PcsI WCGNNNNNNNCGW 2 cut(s) 201, 210
PflMI CCANNNNNTGG 1 cut(s) 312
PscI ACATGT 1 cut(s) 153
Psp6I CCWGG 1 cut(s) 311
PspGI CCWGG 1 cut(s) 311
PsuI RGATCY 1 cut(s) 76
RsaI GTAC 2 cut(s) 145, 347
RsaNI GTAC 2 cut(s) 144, 346
RseI CAYNNNNRTG 2 cut(s) 242, 265
Sau3AI GATC 2 cut(s) 76, 148
ScaI AGTACT 1 cut(s) 347
ScrFI CCNGG 1 cut(s) 313
SetI ASST 7 cut(s) 52, 63, 145, 191, 300, 314, 439
SfaNI GCATC 3 cut(s) 32, 247, 417
SmiMI CAYNNNNRTG 2 cut(s) 242, 265
Sse9I AATT 1 cut(s) 383
SsiI CCGC 1 cut(s) 353
StyD4I CCNGG 1 cut(s) 311
StyI CCWWGG 2 cut(s) 250, 400
TaaI ACNGT 1 cut(s) 333
TaiI ACGT 1 cut(s) 300
TaqI TCGA 3 cut(s) 92, 113, 195
TasI AATT 1 cut(s) 383
TatI WGTACW 1 cut(s) 345
TscAI CASTG 1 cut(s) 366
TseFI GTSAC 1 cut(s) 209
Tsp45I GTSAC 1 cut(s) 209
TspDTI ATGAA 2 cut(s) 197, 376
TspGWI ACGGA 1 cut(s) 161
TspRI CASTG 1 cut(s) 366
Van91I CCANNNNNTGG 1 cut(s) 312
XapI RAATTY 1 cut(s) 383
XceI RCATGY 1 cut(s) 157
ZrmI AGTACT 1 cut(s) 347
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.