Rh5BG434100

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5B
OG0000278
Physical Location & Seq
Forward (+)
69819349 .. 69819654
306 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5BG434100.1

Sequence Viewer

Length: 306 bp
ATGACGACGAAGTACGAAATAGAAAAGTTCAATAGGAACAATTTTTTATTGTGGAAAATGAGAATAAAAGCAGTTTTGAGAAAAGATAACTACTTGGCAGCAATTAGAGATAGGCCTGAGAAGATCACTGACGATGGCAAGTGGAACGAGATGGATGGCAATGCTATTGCTAATCTGCACCTAGCACTAGCCAATGAAGTATTTTCAAGTGTGGCGGAGAAGAAGATGGGAAAAGAGATATGGGATACACTCACAAAATTGTACGAGGCCAAATCACTACACAACAAAATCATCTTGAAGAGATAG
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 zf-CCHC

Protein Analysis

101

Amino Acids

11.91

Weight (kDa)

9.62

Isoelectric Point (pI)

33.6

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 17 - 101 4.3e-10 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
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Orthologous Genes (Group: OG0000278)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G29785
fragaria_vesca FvH4_1g10046 FvH4_1g17351 FvH4_1g18441 FvH4_1g24222 FvH4_2g00141 FvH4_2g05931 FvH4_2g06671 FvH4_2g14030 FvH4_2g15291 FvH4_2g22611 FvH4_2g22612 FvH4_2g26380 FvH4_2g39202 FvH4_2g39202 FvH4_3g06691 FvH4_3g08580 FvH4_3g20502 FvH4_3g20503 FvH4_3g22421 FvH4_3g42580 FvH4_4g02061 FvH4_4g06794 FvH4_4g08661 FvH4_4g11771 FvH4_4g14601 FvH4_4g14721 FvH4_4g20921 FvH4_4g33601 FvH4_4g33602 FvH4_5g07492 FvH4_5g20321 FvH4_5g21591 FvH4_5g30343 FvH4_5g37875 FvH4_6g04372 FvH4_6g04373 FvH4_6g04373 FvH4_6g21377 FvH4_6g23760 FvH4_6g29471 FvH4_6g43142 FvH4_7g14351 FvH4_7g14352 FvH4_7g22582 FvH4_7g22583 FvH4_7g22584
malus_domestica MD00G1179400.v1.1 MD01G1170500.v1.1 MD03G1286700.v1.1 MD04G1054600.v1.1 MD04G1071700.v1.1 MD04G1193900.v1.1 MD08G1054300.v1.1 MD08G1217500.v1.1 MD09G1034600.v1.1 MD09G1098100.v1.1 MD10G1018300.v1.1 MD10G1220000.v1.1 MD10G1250300.v1.1 MD12G1014400.v1.1 MD15G1021000.v1.1 MD16G1112200.v1.1
prunus_persica Prupe.1G188900_v2.0.a1 Prupe.1G258000_v2.0.a1 Prupe.4G233400_v2.0.a1
pyrus_communis pycom01g10100 pycom02g01340 pycom03g19700 pycom05g01320 pycom07g16000 pycom07g16520 pycom11g26500 pycom13g09380 pycom13g13960 pycom14g08180 pycom14g16810 pycom16g09590
rosa_chinensis RchiOBHm_Chr1g0319891 RchiOBHm_Chr1g0333711 RchiOBHm_Chr2g0115331 RchiOBHm_Chr2g0143411 RchiOBHm_Chr2g0167631 RchiOBHm_Chr3g0448581 RchiOBHm_Chr3g0494991 RchiOBHm_Chr4g0442471 RchiOBHm_Chr6g0262311 RchiOBHm_Chr6g0301831 RchiOBHm_Chr6g0301841 RchiOBHm_Chr7g0183451
rosa_roxburghii Rroxscaffold_1G00039280 Rroxscaffold_1G00047670 Rroxscaffold_1G00066330 Rroxscaffold_2G00107510 Rroxscaffold_3G00255410 Rroxscaffold_4G00301460 Rroxscaffold_5G00352730 Rroxscaffold_7G00166350 Rroxscaffold_7G00166360 Rroxscaffold_7G00203820
rosa_rugosa Rorug03G0240500 Rorug05G0191700 Rorug06G0310200
rosa_samantha Rh2BG287000 Rh4CG073500 Rh4CG176200 Rh4CG191400 Rh5BG356100 Rh5BG434100 Rh6AG110600 Rh6AG421900 Rh6AG422000 Rh6AG422100 Rh6BG428600 Rh6BG428700 Rh6BG428800 Rh6CG435200 Rh6CG435300 Rh6CG435400 Rh6DG422000 Rh6DG422100 Rh6DG422200 Rh7BG190500 Rh7CG172800 Rh7CG225200
rosa_wichuraiana Rw2G044060 Rw6G036540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 215
AfaI GTAC 2 cut(s) 14, 263
AgsI TTSAA 3 cut(s) 31, 207, 298
AoxI GGCC 2 cut(s) 113, 267
ApeKI GCWGC 1 cut(s) 98
BbvI GCAGC 1 cut(s) 110
BccI CCATC 4 cut(s) 128, 145, 149, 220
BciVI GTATCC 1 cut(s) 238
BfaI CTAG 2 cut(s) 182, 188
BfuI GTATCC 1 cut(s) 238
BisI GCNGC 1 cut(s) 99
BlsI GCNGC 1 cut(s) 100
Bse3DI GCAATG 1 cut(s) 166
BseGI GGATG 1 cut(s) 160
BseMI GCAATG 1 cut(s) 166
BseMII CTCAG 1 cut(s) 108
BseXI GCAGC 1 cut(s) 110
BsgI GTGCAG 1 cut(s) 161
BshFI GGCC 2 cut(s) 115, 269
BsnI GGCC 2 cut(s) 115, 269
Bsp143I GATC 1 cut(s) 123
BspACI CCGC 1 cut(s) 215
BspANI GGCC 2 cut(s) 115, 269
BspCNI CTCAG 1 cut(s) 109
BsrDI GCAATG 1 cut(s) 166
BssMI GATC 1 cut(s) 123
Bst6I CTCTTC 1 cut(s) 293
BstDEI CTNAG 1 cut(s) 117
BstF5I GGATG 1 cut(s) 160
BstKTI GATC 1 cut(s) 126
BstMBI GATC 1 cut(s) 123
BstV1I GCAGC 1 cut(s) 110
BsuI GTATCC 1 cut(s) 238
BsuRI GGCC 2 cut(s) 115, 269
BtsCI GGATG 1 cut(s) 160
BtsIMutI CAGTG 1 cut(s) 126
Csp6I GTAC 2 cut(s) 13, 262
CviJI RGCY 3 cut(s) 115, 191, 269
CviKI_1 RGCY 3 cut(s) 115, 191, 269
CviQI GTAC 2 cut(s) 13, 262
DdeI CTNAG 1 cut(s) 117
DpnI GATC 1 cut(s) 125
DpnII GATC 1 cut(s) 123
Eam1104I CTCTTC 1 cut(s) 293
EarI CTCTTC 1 cut(s) 293
EciI GGCGGA 1 cut(s) 230
Eco147I AGGCCT 1 cut(s) 115
FaiI YATR 1 cut(s) 241
Fnu4HI GCNGC 1 cut(s) 99
FokI GGATG 1 cut(s) 167
Fsp4HI GCNGC 1 cut(s) 99
FspBI CTAG 2 cut(s) 182, 188
GluI GCNGC 1 cut(s) 99
HaeIII GGCC 2 cut(s) 115, 269
Hpy188III TCNNGA 1 cut(s) 295
Hpy99I CGWCG 1 cut(s) 10
HpyCH4V TGCA 1 cut(s) 178
HpyF3I CTNAG 1 cut(s) 117
Kzo9I GATC 1 cut(s) 123
LpnPI CCDG 1 cut(s) 129
Lsp1109I GCAGC 1 cut(s) 110
MaeI CTAG 2 cut(s) 182, 188
MalI GATC 1 cut(s) 125
MboI GATC 1 cut(s) 123
MboII GAAGA 3 cut(s) 133, 232, 235
MluCI AATT 3 cut(s) 40, 102, 257
MnlI CCTC 1 cut(s) 259
NdeII GATC 1 cut(s) 123
PceI AGGCCT 1 cut(s) 115
PkrI GCNGC 1 cut(s) 100
RsaI GTAC 2 cut(s) 14, 263
RsaNI GTAC 2 cut(s) 13, 262
SatI GCNGC 1 cut(s) 99
Sau3AI GATC 1 cut(s) 123
SetI ASST 1 cut(s) 183
SgeI CNNG 8 cut(s) 106, 128, 151, 160, 194, 200, 219, 277
Sse9I AATT 3 cut(s) 40, 102, 257
SseBI AGGCCT 1 cut(s) 115
SsiI CCGC 1 cut(s) 215
SspMI CTAG 2 cut(s) 182, 188
StuI AGGCCT 1 cut(s) 115
TasI AATT 3 cut(s) 40, 102, 257
TscAI CASTG 1 cut(s) 133
TseI GCWGC 1 cut(s) 98
TspDTI ATGAA 1 cut(s) 210
TspRI CASTG 1 cut(s) 133
XspI CTAG 2 cut(s) 182, 188
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.