Rh2DG337800

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2D
OG0000370
Physical Location & Seq
Reverse (-)
43480022 .. 43483364
3343 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2DG337800.1

Sequence Viewer

Length: 543 bp
ATGGAACTCATGGAATGGGCTGCCTTCAAAGAGAAATTTCTGGAAAGATATTTTCCACAAGTTGAGAAAGACAAGAAAGAACTAGAGTTTATTCAACTTACTCAAGGAAAGATGACTGTAATTGAGTATGAGACCAAATTCACTAAACTTTCTCGTTTTGCTCCACATATGGTGGATACAGACTATAAAAAGGCAAGACGGTTCATTGGAGGACTAAATTCGAACATTCGAAGAATGGTCACTTCACGTGGAATCACGTACGAAGAAGCTGTGGACAAAGCCTTAACTCATGAGGAGGAAAATCAAAAGTACCGCCTAGAGAAGGAACGAGAGAATAGCTTCCGAGGAAAAAGAAGCCATCCAGTGCCTAACCAGAAAGGTGGACAACCATGGGAGCAGCAAAAACGGAGAGACGCATTTCAAAAGACAACAACATCAACTCAAAAAGGAAAGGAGGTGGCAAGAGGCCCAATTCGTTGTTTCAACTGTGGAGGAATGGGGCACATGTCTAATGCTTGTCCAAAGCCACGCCGCCTTCCATGA
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

180

Amino Acids

21.19

Weight (kDa)

9.78

Isoelectric Point (pI)

43.73

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 4 - 103 3.8e-06 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 5 - 73 2.5e-15 Retrotransposon gag protein
zf-CCHC PF00098 159 - 175 2e-06 Zinc knuckle
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: 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)
AciI CCGC 2 cut(s) 313, 532
AcsI RAATTY 3 cut(s) 35, 137, 217
AcvI CACGTG 1 cut(s) 248
AfaI GTAC 2 cut(s) 260, 311
AfiI CCNNNNNNNGG 1 cut(s) 322
AflIII ACRYGT 1 cut(s) 504
AgsI TTSAA 4 cut(s) 28, 95, 422, 484
AluBI AGCT 2 cut(s) 269, 339
AluI AGCT 2 cut(s) 269, 339
Alw26I GTCTC 2 cut(s) 125, 405
AoxI GGCC 1 cut(s) 466
ApeKI GCWGC 2 cut(s) 20, 397
ApoI RAATTY 3 cut(s) 35, 137, 217
Asp700I GAANNNNTTC 1 cut(s) 338
AspS9I GGNCC 1 cut(s) 467
AsuII TTCGAA 2 cut(s) 221, 229
BaeGI GKGCMC 1 cut(s) 504
BbrPI CACGTG 1 cut(s) 248
BbvI GCAGC 2 cut(s) 7, 409
BccI CCATC 1 cut(s) 366
BciVI GTATCC 1 cut(s) 169
BcoDI GTCTC 2 cut(s) 125, 405
BfaI CTAG 2 cut(s) 83, 317
BfuI GTATCC 1 cut(s) 169
BisI GCNGC 3 cut(s) 21, 398, 532
BlsI GCNGC 3 cut(s) 22, 399, 533
BmgT120I GGNCC 1 cut(s) 467
Bpu14I TTCGAA 2 cut(s) 221, 229
BpuEI CTTGAG 1 cut(s) 87
BsaAI YACGTR 2 cut(s) 248, 258
BsaI GGTCTC 1 cut(s) 125
BsaJI CCNNGG 2 cut(s) 343, 389
Bsc4I CCNNNNNNNGG 1 cut(s) 322
Bse1I ACTGG 1 cut(s) 362
BseDI CCNNGG 2 cut(s) 343, 389
BseGI GGATG 1 cut(s) 358
BseLI CCNNNNNNNGG 1 cut(s) 322
BseNI ACTGG 1 cut(s) 362
BseRI GAGGAG 1 cut(s) 308
BseSI GKGCMC 1 cut(s) 504
BseXI GCAGC 2 cut(s) 7, 409
BshFI GGCC 1 cut(s) 468
BsiWI CGTACG 1 cut(s) 258
BslI CCNNNNNNNGG 1 cut(s) 322
BsmAI GTCTC 2 cut(s) 125, 405
BsmBI CGTCTC 1 cut(s) 405
BsnI GGCC 1 cut(s) 468
Bso31I GGTCTC 1 cut(s) 125
Bsp119I TTCGAA 2 cut(s) 221, 229
Bsp1286I GDGCHC 1 cut(s) 504
Bsp19I CCATGG 1 cut(s) 389
BspACI CCGC 2 cut(s) 313, 532
BspANI GGCC 1 cut(s) 468
BspHI TCATGA 1 cut(s) 289
BspT104I TTCGAA 2 cut(s) 221, 229
BspTNI GGTCTC 1 cut(s) 125
BsrI ACTGG 1 cut(s) 362
BssECI CCNNGG 2 cut(s) 343, 389
BssT1I CCWWGG 1 cut(s) 389
Bst4CI ACNGT 3 cut(s) 118, 201, 488
BstBAI YACGTR 2 cut(s) 248, 258
BstBI TTCGAA 2 cut(s) 221, 229
BstDSI CCRYGG 1 cut(s) 389
BstENI CCTNNNNNAGG 1 cut(s) 320
BstF5I GGATG 1 cut(s) 358
BstMAI GTCTC 2 cut(s) 125, 405
BstNSI RCATGY 1 cut(s) 508
BstSLI GKGCMC 1 cut(s) 504
BstV1I GCAGC 2 cut(s) 7, 409
BstXI CCANNNNNNTGG 1 cut(s) 380
BsuI GTATCC 1 cut(s) 169
BsuRI GGCC 1 cut(s) 468
BtgI CCRYGG 1 cut(s) 389
BtsCI GGATG 1 cut(s) 358
BtsIMutI CAGTG 1 cut(s) 369
CciI TCATGA 1 cut(s) 289
Cfr13I GGNCC 1 cut(s) 467
CseI GACGC 1 cut(s) 422
Csp6I GTAC 2 cut(s) 259, 310
CviAII CATG 5 cut(s) 10, 290, 390, 505, 540
CviJI RGCY 7 cut(s) 20, 269, 281, 339, 357, 468, 526
CviKI_1 RGCY 7 cut(s) 20, 269, 281, 339, 357, 468, 526
CviQI GTAC 2 cut(s) 259, 310
Eco130I CCWWGG 1 cut(s) 389
Eco31I GGTCTC 1 cut(s) 125
Eco72I CACGTG 1 cut(s) 248
EcoNI CCTNNNNNAGG 1 cut(s) 320
EcoT14I CCWWGG 1 cut(s) 389
ErhI CCWWGG 1 cut(s) 389
Esp3I CGTCTC 1 cut(s) 405
FaeI CATG 5 cut(s) 13, 293, 393, 508, 543
FaiI YATR 9 cut(s) 11, 129, 168, 170, 186, 291, 391, 506, 541
FatI CATG 5 cut(s) 9, 289, 389, 504, 539
FauNDI CATATG 1 cut(s) 168
Fnu4HI GCNGC 3 cut(s) 21, 398, 532
FokI GGATG 1 cut(s) 345
Fsp4HI GCNGC 3 cut(s) 21, 398, 532
FspBI CTAG 2 cut(s) 83, 317
GluI GCNGC 3 cut(s) 21, 398, 532
HaeIII GGCC 1 cut(s) 468
HgaI GACGC 1 cut(s) 422
Hin1II CATG 5 cut(s) 13, 293, 393, 508, 543
HinfI GANTC 1 cut(s) 252
Hpy166II GTNNAC 2 cut(s) 274, 383
Hpy188I TCNGA 1 cut(s) 344
Hpy188III TCNNGA 2 cut(s) 41, 290
Hpy8I GTNNAC 2 cut(s) 274, 383
HpyAV CCTTC 2 cut(s) 34, 316
HpyCH4III ACNGT 3 cut(s) 118, 201, 488
HpyCH4IV ACGT 2 cut(s) 247, 257
HpySE526I ACGT 2 cut(s) 247, 257
Hsp92II CATG 5 cut(s) 13, 293, 393, 508, 543
LmnI GCTCC 2 cut(s) 166, 394
LpnPI CCDG 3 cut(s) 26, 375, 386
Lsp1109I GCAGC 2 cut(s) 7, 409
MaeI CTAG 2 cut(s) 83, 317
MaeII ACGT 2 cut(s) 247, 257
MaeIII GTNAC 1 cut(s) 238
MboII GAAGA 2 cut(s) 243, 275
MhlI GDGCHC 1 cut(s) 504
MluCI AATT 5 cut(s) 35, 120, 137, 217, 471
MnlI CCTC 7 cut(s) 203, 286, 289, 338, 448, 458, 485
MroXI GAANNNNTTC 1 cut(s) 338
MseI TTAA 1 cut(s) 284
NcoI CCATGG 1 cut(s) 389
NdeI CATATG 1 cut(s) 168
NlaIII CATG 5 cut(s) 13, 293, 393, 508, 543
NmuCI GTSAC 1 cut(s) 238
NspI RCATGY 1 cut(s) 508
NspV TTCGAA 2 cut(s) 221, 229
PagI TCATGA 1 cut(s) 289
PciI ACATGT 1 cut(s) 504
PdmI GAANNNNTTC 1 cut(s) 338
PfeI GAWTC 1 cut(s) 252
Pfl23II CGTACG 1 cut(s) 258
PkrI GCNGC 3 cut(s) 22, 399, 533
PmaCI CACGTG 1 cut(s) 248
PmlI CACGTG 1 cut(s) 248
Ppu21I YACGTR 2 cut(s) 248, 258
PscI ACATGT 1 cut(s) 504
PspCI CACGTG 1 cut(s) 248
PspLI CGTACG 1 cut(s) 258
PspPI GGNCC 1 cut(s) 467
RsaI GTAC 2 cut(s) 260, 311
RsaNI GTAC 2 cut(s) 259, 310
SaqAI TTAA 1 cut(s) 284
SatI GCNGC 3 cut(s) 21, 398, 532
Sau96I GGNCC 1 cut(s) 467
SduI GDGCHC 1 cut(s) 504
SetI ASST 6 cut(s) 250, 260, 271, 341, 382, 459
SfuI TTCGAA 2 cut(s) 221, 229
SmlI CTYRAG 1 cut(s) 102
SmoI CTYRAG 1 cut(s) 102
Sse9I AATT 5 cut(s) 35, 120, 137, 217, 471
SsiI CCGC 2 cut(s) 313, 532
SspMI CTAG 2 cut(s) 83, 317
StyI CCWWGG 1 cut(s) 389
TaaI ACNGT 3 cut(s) 118, 201, 488
TaiI ACGT 2 cut(s) 250, 260
TaqI TCGA 2 cut(s) 221, 229
TasI AATT 5 cut(s) 35, 120, 137, 217, 471
TauI GCSGC 1 cut(s) 534
TfiI GAWTC 1 cut(s) 252
Tru1I TTAA 1 cut(s) 284
Tru9I TTAA 1 cut(s) 284
TscAI CASTG 1 cut(s) 369
TseFI GTSAC 1 cut(s) 238
TseI GCWGC 2 cut(s) 20, 397
Tsp45I GTSAC 1 cut(s) 238
TspDTI ATGAA 1 cut(s) 193
TspGWI ACGGA 1 cut(s) 421
TspRI CASTG 1 cut(s) 369
XagI CCTNNNNNAGG 1 cut(s) 320
XapI RAATTY 3 cut(s) 35, 137, 217
XceI RCATGY 1 cut(s) 508
XmnI GAANNNNTTC 1 cut(s) 338
XspI CTAG 2 cut(s) 83, 317
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.