Rroxscaffold_1G00039340

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0000146
Physical Location & Seq
Forward (+)
56931761 .. 56932006
246 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00039340.1

Sequence Viewer

Length: 246 bp
ATGGCCGGACGTATAATTGAAGGCGAACAGTCAAATCCCGAGAAGGCAATGGTGCCATCCTCACAAGTCATCCATCACCACTACACCGTCCAACAAGACAACTCTGCGTTCCCAACAAGTGTTGTCTTGAATGAATCCAACTACACCATATGGGCTCCTCTCATGCAGATGCGCATTAGAGCACGAGGGAAGGTTGATTATTTGACCGGAGTAAAGGCCGAACCCGCCATGAATTCTGCAGTATGA
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
Retrotran_gag_2

Protein Analysis

81

Amino Acids

9.0

Weight (kDa)

6.82

Isoelectric Point (pI)

45.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 37 - 76 2.8e-06 gag-polypeptide of LTR copia-type
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: OG0000146)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g19561 FvH4_1g25371 FvH4_1g25961 FvH4_2g00352 FvH4_2g00861 FvH4_2g04952 FvH4_2g05413 FvH4_2g07531 FvH4_2g08961 FvH4_2g25141 FvH4_2g27292 FvH4_3g18164 FvH4_3g19921 FvH4_3g43870 FvH4_4g14441 FvH4_4g15581 FvH4_4g15582 FvH4_4g16890 FvH4_4g19782 FvH4_4g33444 FvH4_4g33921 FvH4_5g22281 FvH4_5g22282 FvH4_5g32571 FvH4_5g37451 FvH4_5g39631 FvH4_6g04721 FvH4_6g11661 FvH4_6g20571 FvH4_6g32791 FvH4_7g23184
prunus_persica Prupe.1G090900_v2.0.a1 Prupe.1G241200_v2.0.a1 Prupe.1G534100_v2.0.a1 Prupe.3G076700_v2.0.a1 Prupe.4G150800_v2.0.a1 Prupe.4G181800_v2.0.a1 Prupe.4G240900_v2.0.a1 Prupe.4G247600_v2.0.a1 Prupe.6G115900_v2.0.a1 Prupe.6G327500_v2.0.a1 Prupe.8G071700_v2.0.a1
pyrus_communis pycom06g11480 pycom10g08330 pycom15g04320 pycom15g04350 pycom15g12620 pycom2874g00060
rosa_chinensis RchiOBHm_Chr1g0317241 RchiOBHm_Chr1g0341801 RchiOBHm_Chr1g0341931 RchiOBHm_Chr1g0359621 RchiOBHm_Chr2g0113741 RchiOBHm_Chr2g0117261 RchiOBHm_Chr2g0138831 RchiOBHm_Chr2g0141421 RchiOBHm_Chr2g0145281 RchiOBHm_Chr2g0152991 RchiOBHm_Chr3g0448001 RchiOBHm_Chr3g0450981 RchiOBHm_Chr3g0455161 RchiOBHm_Chr3g0457401 RchiOBHm_Chr3g0460001 RchiOBHm_Chr4g0387431 RchiOBHm_Chr4g0388741 RchiOBHm_Chr4g0444201 RchiOBHm_Chr4g0444261 RchiOBHm_Chr5g0010221 RchiOBHm_Chr6g0271721 RchiOBHm_Chr6g0274641 RchiOBHm_Chr6g0294691 RchiOBHm_Chr7g0237031 RchiOBHm_Chr7g0238461 RchiOBHm_Chr7g0239981
rosa_laevigata RLG00000009017
rosa_multiflora Rmu_co7986768.1_g000001 Rmu_co8302239.1_g000001 Rmu_co8485799.1_g000001 Rmu_sc0000061.1_g000013 Rmu_sc0000303.1_g000034 Rmu_sc0000303.1_g000035 Rmu_sc0000315.1_g000017 Rmu_sc0000349.1_g000003 Rmu_sc0000498.1_g000068 Rmu_sc0000508.1_g000014 Rmu_sc0000602.1_g000001 Rmu_sc0000633.1_g000002 Rmu_sc0000638.1_g000030 Rmu_sc0000756.1_g000016 Rmu_sc0000756.1_g000017 Rmu_sc0000785.1_g000037 Rmu_sc0000795.1_g000017 Rmu_sc0000796.1_g000030 Rmu_sc0000863.1_g000023 Rmu_sc0000920.1_g000021 Rmu_sc0000960.1_g000015 Rmu_sc0000982.1_g000102 Rmu_sc0001036.1_g000008 Rmu_sc0001036.1_g000009 Rmu_sc0001643.1_g000029 Rmu_sc0001687.1_g000026 Rmu_sc0001708.1_g000037 Rmu_sc0001768.1_g000015 Rmu_sc0001790.1_g000022 Rmu_sc0002180.1_g000007 Rmu_sc0002211.1_g000006 Rmu_sc0002270.1_g000010 Rmu_sc0002404.1_g000031 Rmu_sc0002858.1_g000016 Rmu_sc0003063.1_g000028 Rmu_sc0003730.1_g000017 Rmu_sc0004087.1_g000020 Rmu_sc0004618.1_g000048 Rmu_sc0004724.1_g000005 Rmu_sc0005167.1_g000036 Rmu_sc0005781.1_g000003 Rmu_sc0005878.1_g000012 Rmu_sc0006011.1_g000003 Rmu_sc0006343.1_g000011 Rmu_sc0006573.1_g000007 Rmu_sc0006599.1_g000007 Rmu_sc0006803.1_g000014 Rmu_sc0006836.1_g000002 Rmu_sc0006849.1_g000002 Rmu_sc0007109.1_g000009 Rmu_sc0009268.1_g000016 Rmu_sc0009618.1_g000017 Rmu_sc0009674.1_g000009 Rmu_sc0010244.1_g000009 Rmu_sc0011151.1_g000004 Rmu_sc0011356.1_g000001 Rmu_sc0011674.1_g000002 Rmu_sc0011778.1_g000016 Rmu_sc0012342.1_g000001 Rmu_sc0012467.1_g000002 Rmu_sc0012574.1_g000003 Rmu_sc0012913.1_g000005 Rmu_sc0013612.1_g000020 Rmu_sc0014824.1_g000001 Rmu_sc0017869.1_g000002 Rmu_sc0018085.1_g000003 Rmu_sc0024789.1_g000001 Rmu_sc0025106.1_g000013 Rmu_sc0034502.1_g000001 Rmu_sc0034547.1_g000001 Rmu_sc0035094.1_g000001 Rmu_sc0035095.1_g000001 Rmu_ssc0000100.1_g000027 Rmu_ssc0000244.1_g000005 Rmu_ssc0000371.1_g000029 Rmu_ssc0000381.1_g000004
rosa_roxburghii Rroxscaffold_1G00015480 Rroxscaffold_1G00023580 Rroxscaffold_1G00039340 Rroxscaffold_1G00047080 Rroxscaffold_2G00095820 Rroxscaffold_2G00125200 Rroxscaffold_2G00128330 Rroxscaffold_3G00270860
rosa_rugosa Rorug06G0120700
rosa_samantha Rh3BG173100 Rh6AG089600 Rh7AG488100 Rh7DG389600
rosa_wichuraiana Rw0G001150 Rw0G001990 Rw0G002010 Rw0G019540 Rw1G013730 Rw1G024110 Rw1G029190 Rw2G018850 Rw2G021090 Rw2G022260 Rw2G023180 Rw2G027280 Rw3G010190 Rw3G020660 Rw3G029380 Rw4G002390 Rw4G002690 Rw4G033260 Rw5G011960 Rw5G023110 Rw5G025250 Rw5G028950 Rw5G033740 Rw5G033950 Rw5G037900 Rw6G009640 Rw6G011620 Rw6G027720 Rw7G010680 Rw7G042070

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 173
AccB1I GGYRCC 1 cut(s) 52
AciI CCGC 1 cut(s) 225
AcoI YGGCCR 1 cut(s) 3
AcsI RAATTY 1 cut(s) 232
AgsI TTSAA 2 cut(s) 20, 130
Alw21I GWGCWC 1 cut(s) 184
Ama87I CYCGRG 1 cut(s) 38
AoxI GGCC 2 cut(s) 3, 216
ApoI RAATTY 1 cut(s) 232
AspLEI GCGC 1 cut(s) 174
AsuHPI GGTGA 1 cut(s) 68
AvaI CYCGRG 1 cut(s) 38
BanI GGYRCC 1 cut(s) 52
BanII GRGCYC 1 cut(s) 157
BauI CACGAG 1 cut(s) 183
Bbv12I GWGCWC 1 cut(s) 184
BccI CCATC 2 cut(s) 64, 81
BfmI CTRYAG 1 cut(s) 237
BmeT110I CYCGRG 1 cut(s) 38
BmiI GGNNCC 2 cut(s) 54, 156
BmsI GCATC 1 cut(s) 159
BsaWI WCCGGW 1 cut(s) 206
Bse3DI GCAATG 1 cut(s) 54
BseGI GGATG 2 cut(s) 56, 69
BseMI GCAATG 1 cut(s) 54
BseRI GAGGAG 1 cut(s) 147
BshFI GGCC 2 cut(s) 5, 218
BshNI GGYRCC 1 cut(s) 52
BsiHKAI GWGCWC 1 cut(s) 184
BsiHKCI CYCGRG 1 cut(s) 38
BsiSI CCGG 2 cut(s) 6, 207
BsnI GGCC 2 cut(s) 5, 218
BsoBI CYCGRG 1 cut(s) 38
Bsp1286I GDGCHC 2 cut(s) 157, 184
BspACI CCGC 1 cut(s) 225
BspANI GGCC 2 cut(s) 5, 218
BspLI GGNNCC 2 cut(s) 54, 156
BspMAI CTGCAG 1 cut(s) 241
BspT107I GGYRCC 1 cut(s) 52
BsrDI GCAATG 1 cut(s) 54
BssSI CACGAG 1 cut(s) 183
Bst2BI CACGAG 1 cut(s) 183
Bst4CI ACNGT 2 cut(s) 30, 88
BstF5I GGATG 2 cut(s) 56, 69
BstHHI GCGC 1 cut(s) 174
BstMWI GCNNNNNNNGC 1 cut(s) 224
BstSFI CTRYAG 1 cut(s) 237
BsuRI GGCC 2 cut(s) 5, 218
BtsCI GGATG 2 cut(s) 56, 69
CfoI GCGC 1 cut(s) 174
CviAII CATG 2 cut(s) 163, 229
CviJI RGCY 3 cut(s) 5, 155, 218
CviKI_1 RGCY 3 cut(s) 5, 155, 218
EaeI YGGCCR 1 cut(s) 3
Eco24I GRGCYC 1 cut(s) 157
Eco88I CYCGRG 1 cut(s) 38
EcoRI GAATTC 1 cut(s) 232
EcoT38I GRGCYC 1 cut(s) 157
FaeI CATG 2 cut(s) 166, 232
FaiI YATR 6 cut(s) 14, 149, 151, 164, 230, 244
FatI CATG 2 cut(s) 162, 228
FauI CCCGC 1 cut(s) 232
FauNDI CATATG 1 cut(s) 149
FokI GGATG 2 cut(s) 43, 56
FriOI GRGCYC 1 cut(s) 157
FspAI RTGCGCAY 1 cut(s) 173
FspI TGCGCA 1 cut(s) 173
GlaI GCGC 1 cut(s) 173
HaeIII GGCC 2 cut(s) 5, 218
HapII CCGG 2 cut(s) 6, 207
HhaI GCGC 1 cut(s) 174
Hin1II CATG 2 cut(s) 166, 232
Hin6I GCGC 1 cut(s) 172
HinP1I GCGC 1 cut(s) 172
HinfI GANTC 1 cut(s) 134
HpaII CCGG 2 cut(s) 6, 207
HphI GGTGA 1 cut(s) 68
Hpy188III TCNNGA 2 cut(s) 38, 127
HpyAV CCTTC 3 cut(s) 14, 37, 184
HpyCH4III ACNGT 2 cut(s) 30, 88
HpyCH4IV ACGT 1 cut(s) 10
HpyCH4V TGCA 2 cut(s) 166, 239
HpyF10VI GCNNNNNNNGC 1 cut(s) 224
HpySE526I ACGT 1 cut(s) 10
Hsp92II CATG 2 cut(s) 166, 232
HspAI GCGC 1 cut(s) 172
LmnI GCTCC 1 cut(s) 160
LpnPI CCDG 2 cut(s) 19, 220
LweI GCATC 1 cut(s) 159
MaeII ACGT 1 cut(s) 10
MhlI GDGCHC 2 cut(s) 157, 184
MluCI AATT 2 cut(s) 15, 232
MmeI TCCRAC 2 cut(s) 115, 162
MnlI CCTC 3 cut(s) 70, 168, 179
MslI CAYNNNNRTG 1 cut(s) 167
MspI CCGG 2 cut(s) 6, 207
MwoI GCNNNNNNNGC 1 cut(s) 224
NdeI CATATG 1 cut(s) 149
NlaIII CATG 2 cut(s) 166, 232
NlaIV GGNNCC 2 cut(s) 54, 156
NsbI TGCGCA 1 cut(s) 173
PfeI GAWTC 1 cut(s) 134
PspN4I GGNNCC 2 cut(s) 54, 156
PstI CTGCAG 1 cut(s) 241
RseI CAYNNNNRTG 1 cut(s) 167
SduI GDGCHC 2 cut(s) 157, 184
SetI ASST 2 cut(s) 13, 195
SfaNI GCATC 1 cut(s) 159
SfcI CTRYAG 1 cut(s) 237
SmiMI CAYNNNNRTG 1 cut(s) 167
Sse9I AATT 2 cut(s) 15, 232
SsiI CCGC 1 cut(s) 225
TaaI ACNGT 2 cut(s) 30, 88
TaiI ACGT 1 cut(s) 13
TasI AATT 2 cut(s) 15, 232
TfiI GAWTC 1 cut(s) 134
TspDTI ATGAA 2 cut(s) 147, 245
XapI RAATTY 1 cut(s) 232
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.