Rh5BG480300

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5B
OG0000333
Physical Location & Seq
Forward (+)
76409136 .. 76410189
1054 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5BG480300.1

Sequence Viewer

Length: 717 bp
ATGGTATACCCAGAACTCAAGACCACCCACAGACTCGACTTTGGCGTCAACTTTCATATCTGGAGACAAAAAATAGGCTTCGTCCTCGTCGACAACAAGGTCAACTACGTCCTCACCGAGCCAAAACCCCCGGAAAAAGACGTCGCTGGCCACCAGAAGTGGATCCACGACGACTTCATCGCCCGGCACCTCATCATGGGAACCCTAAACGACCACGTGTACATGAGCTACGAGACACACGAGACTGCCAAGTCCCTCATGGACGCTCTCACCGCCACTTACACCCAACCCTCGATGACGAAGCGGATGTACAAGCTCCGCAACTACGTGGGGCACAAGATGGCCGAGGGCAAATCCATCCATGAGCATATTATGGAGATGACCTCGATGGCTTATGATCTCCAATGCGAGGGGTTGAAGATTCCGGAGGAAGTTCAGGCTGTGATGCTGATGAATAGCGTGCCGGAGAGTTGGGACGAGATGATGACCGTGGTGAGGTTGAACATGGATTTCGATAAGTCTAAGTCGGGTGAGCCAGATTTCGGTTTGCACAAGGTGAGCAGCAGGCTCAGGGAGATCGGGGCTTTGGAAAAGTTGTATCGGAGGCAGGAGGAGGAGGAGGAGGCCAAGCAGAGGAGGCCGCATTTCAATGGCCATTGCCATACTTGTGGAGAATATGGGCATCACCGTAATCACTGCACCATCGCCATGAAATAG
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

238

Amino Acids

27.88

Weight (kDa)

6.62

Isoelectric Point (pI)

49.71

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 166 1.2e-23 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: OG0000333)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G11910 AT3G11910 AT3G11910 AT3G11910 AT5G06600 AT5G06600 AT5G06600
fragaria_vesca FvH4_3g26930 FvH4_3g39132 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220
malus_domestica MD02G1261100.v1.1 MD03G1161100.v1.1 MD07G1059900.v1.1 MD11G1177100.v1.1 MD12G1047900.v1.1 MD12G1048000.v1.1 MD12G1048400.v1.1 MD12G1048500.v1.1 MD12G1048700.v1.1 MD12G1048800.v1.1 MD12G1056200.v1.1 MD14G1046300.v1.1 MD14G1046500.v1.1 MD15G1166900.v1.1
prunus_persica Prupe.2G066200_v2.0.a1 Prupe.2G066200_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1
pyrus_communis pycom02g22320 pycom03g11340 pycom07g04580 pycom11g14290 pycom11g15110 pycom12g04110 pycom12g04140 pycom12g04160 pycom12g04210 pycom12g04220 pycom12g04230 pycom12g04290 pycom12g04320 pycom12g04330 pycom12g04350 pycom12g04360 pycom14g03880 pycom14g03900 pycom16g18750
rosa_chinensis RchiOBHm_Chr1g0324111 RchiOBHm_Chr1g0324241 RchiOBHm_Chr3g0477691 RchiOBHm_Chr5g0049371 RchiOBHm_Chr5g0070531
rosa_laevigata RLG00000008612 RLG00000023698 RLG00000034613 RLG00000036139
rosa_multiflora Rmu_co8271779.1_g000001 Rmu_sc0006187.1_g000014
rosa_roxburghii Rroxscaffold_1G00010670 Rroxscaffold_1G00030450 Rroxscaffold_1G00031950 Rroxscaffold_1G00031970 Rroxscaffold_1G00032320 Rroxscaffold_1G00055490 Rroxscaffold_2G00083610 Rroxscaffold_2G00084480 Rroxscaffold_2G00115610 Rroxscaffold_3G00261320 Rroxscaffold_4G00312220 Rroxscaffold_4G00325820 Rroxscaffold_5G00339170 Rroxscaffold_5G00364030 Rroxscaffold_6G00403750
rosa_rugosa Rorug03G0162700 Rorug03G0162800 Rorug03G0162900 Rorug05G0247700 Rorug05G0406600 Rorug05G0406800
rosa_samantha Rh1AG060300 Rh3AG213000 Rh3BG246600 Rh3CG240400 Rh3DG239700 Rh5AG324400 Rh5AG462100 Rh5BG335500 Rh5BG480200 Rh5BG480300 Rh5CG360200 Rh5CG504500 Rh5CG504600 Rh5DG347800 Rh5DG492200 Rh5DG492300
rosa_wichuraiana Rw3G019270 Rw3G026910 Rw5G030650 Rw5G032610 Rw5G043040

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 3 cut(s) 44, 98, 250
AatII GACGTC 1 cut(s) 144
AccB1I GGYRCC 1 cut(s) 186
AccI GTMKAC 2 cut(s) 6, 90
AccIII TCCGGA 1 cut(s) 424
AciI CCGC 4 cut(s) 273, 304, 319, 641
AclWI GGATC 2 cut(s) 157, 170
AcoI YGGCCR 3 cut(s) 148, 342, 652
AcvI CACGTG 1 cut(s) 217
AcyI GRCGYC 2 cut(s) 45, 141
AdeI CACNNNGTG 1 cut(s) 556
AfaI GTAC 2 cut(s) 221, 311
AfiI CCNNNNNNNGG 5 cut(s) 196, 409, 495, 542, 633
AflIII ACRYGT 1 cut(s) 216
AgsI TTSAA 3 cut(s) 418, 502, 649
AluBI AGCT 2 cut(s) 228, 316
AluI AGCT 2 cut(s) 228, 316
Alw26I GTCTC 3 cut(s) 58, 227, 236
AlwI GGATC 2 cut(s) 157, 170
Aor13HI TCCGGA 1 cut(s) 424
AoxI GGCC 5 cut(s) 148, 342, 624, 638, 652
ApeKI GCWGC 1 cut(s) 561
AsuC2I CCSGG 2 cut(s) 131, 184
AsuHPI GGTGA 6 cut(s) 106, 262, 505, 542, 568, 677
BaeGI GKGCMC 1 cut(s) 336
BalI TGGCCA 2 cut(s) 150, 654
BamHI GGATCC 1 cut(s) 162
BanI GGYRCC 1 cut(s) 186
BarI GAAGNNNNNNTAC 2 cut(s) 293, 325
BauI CACGAG 1 cut(s) 239
BbrPI CACGTG 1 cut(s) 217
BbvI GCAGC 1 cut(s) 573
BccI CCATC 4 cut(s) 334, 365, 382, 710
BcnI CCSGG 2 cut(s) 131, 184
BcoDI GTCTC 3 cut(s) 58, 227, 236
BisI GCNGC 2 cut(s) 562, 641
BlsI GCNGC 2 cut(s) 563, 642
Bme1390I CCNGG 2 cut(s) 131, 184
BmiI GGNNCC 3 cut(s) 164, 188, 202
BmrFI CCNGG 2 cut(s) 131, 184
BmsI GCATC 2 cut(s) 435, 691
BplI GAGNNNNNCTC 2 cut(s) 368, 400
BpmI CTGGAG 1 cut(s) 82
Bpu10I CCTNAGC 1 cut(s) 569
BpuMI CCSGG 2 cut(s) 131, 184
BsaAI YACGTR 2 cut(s) 217, 328
BsaHI GRCGYC 2 cut(s) 45, 141
BsaJI CCNNGG 3 cut(s) 129, 345, 489
BsaWI WCCGGW 1 cut(s) 424
Bsc4I CCNNNNNNNGG 5 cut(s) 196, 409, 495, 542, 633
Bse3DI GCAATG 1 cut(s) 655
BseAI TCCGGA 1 cut(s) 424
BseDI CCNNGG 3 cut(s) 129, 345, 489
BseGI GGATG 2 cut(s) 312, 357
BseLI CCNNNNNNNGG 5 cut(s) 196, 409, 495, 542, 633
BseMI GCAATG 1 cut(s) 655
BseMII CTCAG 1 cut(s) 583
BseRI GAGGAG 5 cut(s) 626, 629, 632, 635, 649
BseSI GKGCMC 1 cut(s) 336
BseXI GCAGC 1 cut(s) 573
BsgI GTGCAG 1 cut(s) 682
BshFI GGCC 5 cut(s) 150, 344, 626, 640, 654
BshNI GGYRCC 1 cut(s) 186
BsiSI CCGG 4 cut(s) 131, 184, 425, 464
BslFI GGGAC 2 cut(s) 238, 488
BslI CCNNNNNNNGG 5 cut(s) 196, 409, 495, 542, 633
BsmAI GTCTC 3 cut(s) 58, 227, 236
BsmFI GGGAC 2 cut(s) 238, 488
BsnI GGCC 5 cut(s) 150, 344, 626, 640, 654
Bsp1286I GDGCHC 1 cut(s) 336
Bsp13I TCCGGA 1 cut(s) 424
Bsp1407I TGTACA 2 cut(s) 219, 309
Bsp143I GATC 3 cut(s) 162, 397, 576
BspACI CCGC 4 cut(s) 273, 304, 319, 641
BspANI GGCC 5 cut(s) 150, 344, 626, 640, 654
BspCNI CTCAG 1 cut(s) 582
BspEI TCCGGA 1 cut(s) 424
BspLI GGNNCC 3 cut(s) 164, 188, 202
BspPI GGATC 2 cut(s) 157, 170
BspT107I GGYRCC 1 cut(s) 186
BsrDI GCAATG 1 cut(s) 655
BsrGI TGTACA 2 cut(s) 219, 309
BssECI CCNNGG 3 cut(s) 129, 345, 489
BssMI GATC 3 cut(s) 162, 397, 576
BssNAI GTATAC 1 cut(s) 7
BssNI GRCGYC 2 cut(s) 45, 141
BssSI CACGAG 1 cut(s) 239
Bst1107I GTATAC 1 cut(s) 7
Bst2BI CACGAG 1 cut(s) 239
Bst4CI ACNGT 2 cut(s) 490, 689
BstACI GRCGYC 2 cut(s) 45, 141
BstAUI TGTACA 2 cut(s) 219, 309
BstBAI YACGTR 2 cut(s) 217, 328
BstC8I GCNNGC 3 cut(s) 148, 461, 566
BstDEI CTNAG 2 cut(s) 522, 569
BstDSI CCRYGG 1 cut(s) 489
BstF5I GGATG 2 cut(s) 312, 357
BstKTI GATC 3 cut(s) 165, 400, 579
BstMAI GTCTC 3 cut(s) 58, 227, 236
BstMBI GATC 3 cut(s) 162, 397, 576
BstMWI GCNNNNNNNGC 2 cut(s) 272, 637
BstSCI CCNGG 2 cut(s) 129, 182
BstSLI GKGCMC 1 cut(s) 336
BstV1I GCAGC 1 cut(s) 573
BstX2I RGATCY 1 cut(s) 162
BstXI CCANNNNNNTGG 1 cut(s) 668
BstYI RGATCY 1 cut(s) 162
BstZ17I GTATAC 1 cut(s) 7
BsuRI GGCC 5 cut(s) 150, 344, 626, 640, 654
BtgI CCRYGG 1 cut(s) 489
BtgZI GCGATG 2 cut(s) 163, 688
BtsCI GGATG 2 cut(s) 312, 357
BtsI GCAGTG 1 cut(s) 694
BtsIMutI CAGTG 1 cut(s) 694
Cac8I GCNNGC 3 cut(s) 148, 461, 566
CseI GACGC 2 cut(s) 34, 272
Csp6I GTAC 2 cut(s) 220, 310
CviAII CATG 6 cut(s) 196, 223, 259, 362, 505, 709
CviQI GTAC 2 cut(s) 220, 310
DdeI CTNAG 2 cut(s) 522, 569
DpnI GATC 3 cut(s) 164, 399, 578
DpnII GATC 3 cut(s) 162, 397, 576
DraIII CACNNNGTG 1 cut(s) 556
DrdI GACNNNNNNGTC 3 cut(s) 44, 98, 250
DseDI GACNNNNNNGTC 3 cut(s) 44, 98, 250
EaeI YGGCCR 3 cut(s) 148, 342, 652
Eco72I CACGTG 1 cut(s) 217
FaeI CATG 6 cut(s) 199, 226, 262, 365, 508, 712
FaqI GGGAC 2 cut(s) 238, 488
FatI CATG 6 cut(s) 195, 222, 258, 361, 504, 708
FblI GTMKAC 2 cut(s) 6, 90
Fnu4HI GCNGC 2 cut(s) 562, 641
FokI GGATG 2 cut(s) 319, 344
Fsp4HI GCNGC 2 cut(s) 562, 641
GluI GCNGC 2 cut(s) 562, 641
GsuI CTGGAG 1 cut(s) 82
HaeIII GGCC 5 cut(s) 150, 344, 626, 640, 654
HapII CCGG 4 cut(s) 131, 184, 425, 464
HgaI GACGC 2 cut(s) 34, 272
Hin1I GRCGYC 2 cut(s) 45, 141
Hin1II CATG 6 cut(s) 199, 226, 262, 365, 508, 712
HincII GTYRAC 3 cut(s) 49, 91, 103
HindII GTYRAC 3 cut(s) 49, 91, 103
HinfI GANTC 2 cut(s) 33, 421
HpaII CCGG 4 cut(s) 131, 184, 425, 464
HphI GGTGA 6 cut(s) 106, 262, 505, 542, 568, 677
Hpy166II GTNNAC 5 cut(s) 7, 49, 91, 103, 220
Hpy188I TCNGA 1 cut(s) 603
Hpy188III TCNNGA 3 cut(s) 19, 61, 425
Hpy8I GTNNAC 5 cut(s) 7, 49, 91, 103, 220
Hpy99I CGWCG 3 cut(s) 92, 146, 173
HpyCH4III ACNGT 2 cut(s) 490, 689
HpyCH4IV ACGT 4 cut(s) 108, 141, 216, 327
HpyCH4V TGCA 2 cut(s) 550, 699
HpyF10VI GCNNNNNNNGC 2 cut(s) 272, 637
HpyF3I CTNAG 2 cut(s) 522, 569
HpySE526I ACGT 4 cut(s) 108, 141, 216, 327
Hsp92I GRCGYC 2 cut(s) 45, 141
Hsp92II CATG 6 cut(s) 199, 226, 262, 365, 508, 712
Kpn2I TCCGGA 1 cut(s) 424
Kzo9I GATC 3 cut(s) 162, 397, 576
LmnI GCTCC 1 cut(s) 321
Lsp1109I GCAGC 1 cut(s) 573
LweI GCATC 2 cut(s) 435, 691
MaeII ACGT 4 cut(s) 108, 141, 216, 327
MalI GATC 3 cut(s) 164, 399, 578
MboI GATC 3 cut(s) 162, 397, 576
MboII GAAGA 1 cut(s) 430
MflI RGATCY 1 cut(s) 162
MhlI GDGCHC 1 cut(s) 336
MlsI TGGCCA 2 cut(s) 150, 654
MluNI TGGCCA 2 cut(s) 150, 654
MlyI GAGTC 1 cut(s) 27
Mox20I TGGCCA 2 cut(s) 150, 654
MroI TCCGGA 1 cut(s) 424
MscI TGGCCA 2 cut(s) 150, 654
MslI CAYNNNNRTG 3 cut(s) 648, 666, 707
Msp20I TGGCCA 2 cut(s) 150, 654
MspI CCGG 4 cut(s) 131, 184, 425, 464
MspR9I CCNGG 2 cut(s) 131, 184
MwoI GCNNNNNNNGC 2 cut(s) 272, 637
NciI CCSGG 2 cut(s) 131, 184
NdeII GATC 3 cut(s) 162, 397, 576
NlaIII CATG 6 cut(s) 199, 226, 262, 365, 508, 712
NlaIV GGNNCC 3 cut(s) 164, 188, 202
NmeAIII GCCGAG 1 cut(s) 370
PcsI WCGNNNNNNNCGW 4 cut(s) 42, 87, 114, 237
PfeI GAWTC 1 cut(s) 421
PkrI GCNGC 2 cut(s) 563, 642
PleI GAGTC 1 cut(s) 27
PmaCI CACGTG 1 cut(s) 217
PmlI CACGTG 1 cut(s) 217
PpsI GAGTC 1 cut(s) 27
Ppu21I YACGTR 2 cut(s) 217, 328
PspCI CACGTG 1 cut(s) 217
PspN4I GGNNCC 3 cut(s) 164, 188, 202
PsuI RGATCY 1 cut(s) 162
RsaI GTAC 2 cut(s) 221, 311
RsaNI GTAC 2 cut(s) 220, 310
RseI CAYNNNNRTG 3 cut(s) 648, 666, 707
SalI GTCGAC 1 cut(s) 89
SatI GCNGC 2 cut(s) 562, 641
Sau3AI GATC 3 cut(s) 162, 397, 576
SchI GAGTC 1 cut(s) 27
ScrFI CCNGG 2 cut(s) 131, 184
SduI GDGCHC 1 cut(s) 336
SfaNI GCATC 2 cut(s) 435, 691
SmiMI CAYNNNNRTG 3 cut(s) 648, 666, 707
SmlI CTYRAG 1 cut(s) 17
SmoI CTYRAG 1 cut(s) 17
SsiI CCGC 4 cut(s) 273, 304, 319, 641
StyD4I CCNGG 2 cut(s) 129, 182
TaaI ACNGT 2 cut(s) 490, 689
TaiI ACGT 4 cut(s) 111, 144, 219, 330
TaqI TCGA 5 cut(s) 36, 90, 293, 386, 513
TatI WGTACW 2 cut(s) 219, 309
TauI GCSGC 1 cut(s) 643
TfiI GAWTC 1 cut(s) 421
TscAI CASTG 1 cut(s) 701
TseI GCWGC 1 cut(s) 561
TspDTI ATGAA 3 cut(s) 44, 166, 467
TspRI CASTG 1 cut(s) 701
XcmI CCANNNNNNNNNTGG 1 cut(s) 256
XmiI GTMKAC 2 cut(s) 6, 90
ZraI GACGTC 1 cut(s) 142
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.