Rh7CG225200

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr7C
OG0000278
Physical Location & Seq
Forward (+)
20857880 .. 20858723
844 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh7CG225200.1

Sequence Viewer

Length: 663 bp
ATGGCGACGAAGTACGAAATAAAGAAGTTCAACGGGAACAATTTCTCTTTGTGGAAAATGAGGATAAAAGCAGTTTTGAGAAAAGATAACTTTTTGGCCGCAATTGGAGATTGGCCTGAGGAGATCACTGACGATGGCAAGTGGAATGAGATGGATGGCAATGCGATTGCTAATCTGCACCTAGCACTAGCCGATGAAGTATTGTCAAGTGTGGAGGAGAAGAAGACGGCAAAAGAGATATGGGATACACTCACAAAATTGTATGTGGCCAAATCACTACACAACAAAATCTTCTTGAAGAGAAAGCTTTACAACCTTCGGATGATGGAGTCGACGACAATGACCGACCACATCAACACACTCAACACCTTGTTCTCACAGCTCACAGCAATGGGGCATAATATAGAGACGGGTGAACGTGCTGAAATTCTACTTCGAAGTCTACATGATTCGTATGATCAACTCATCATCAACTTAACCAACAATCTAGAAATACTAGTCTTCGATGATATTGCAGCTGCGGTTCTTGAAGAAGAAAGTCGGCGCAAGAGCAAAGAAGATAGATTGGGAGGCTCACAACAGGCTGAAGCTTTGATGATAACGAGAGGGAGATCAACGAAACGTGGCCCTAGTGGGAGTCGAAATCAGACGAGGCAACAATAG
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

220

Amino Acids

25.17

Weight (kDa)

7.91

Isoelectric Point (pI)

50.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 43 - 186 1.5e-32 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)
AccI GTMKAC 2 cut(s) 332, 442
AciI CCGC 2 cut(s) 99, 521
AcoI YGGCCR 2 cut(s) 96, 267
AcsI RAATTY 1 cut(s) 426
AcuI CTGAAG 1 cut(s) 606
AfaI GTAC 1 cut(s) 14
AgsI TTSAA 3 cut(s) 31, 298, 530
AhlI ACTAGT 1 cut(s) 496
AluBI AGCT 4 cut(s) 307, 382, 518, 590
AluI AGCT 4 cut(s) 307, 382, 518, 590
Alw26I GTCTC 1 cut(s) 401
AoxI GGCC 4 cut(s) 96, 113, 267, 625
ApeKI GCWGC 2 cut(s) 515, 518
ApoI RAATTY 1 cut(s) 426
Asp700I GAANNNNTTC 1 cut(s) 41
AspLEI GCGC 1 cut(s) 546
AspS9I GGNCC 1 cut(s) 626
AsuHPI GGTGA 1 cut(s) 425
AsuII TTCGAA 1 cut(s) 436
AxyI CCTNAGG 1 cut(s) 117
BalI TGGCCA 1 cut(s) 269
BbsI GAAGAC 2 cut(s) 230, 493
BbvI GCAGC 2 cut(s) 505, 527
BccI CCATC 4 cut(s) 128, 145, 149, 319
BceAI ACGGC 1 cut(s) 243
BcgI CGANNNNNNTGC 2 cut(s) 494, 528
BciVI GTATCC 1 cut(s) 238
BclI TGATCA 1 cut(s) 457
BcoDI GTCTC 1 cut(s) 401
BcuI ACTAGT 1 cut(s) 496
BfaI CTAG 5 cut(s) 182, 188, 488, 497, 630
BfuI GTATCC 1 cut(s) 238
BisI GCNGC 3 cut(s) 99, 516, 519
BlsI GCNGC 3 cut(s) 100, 517, 520
BmgT120I GGNCC 1 cut(s) 626
BpiI GAAGAC 2 cut(s) 230, 493
Bpu14I TTCGAA 1 cut(s) 436
Bse21I CCTNAGG 1 cut(s) 117
Bse3DI GCAATG 2 cut(s) 166, 396
BseGI GGATG 2 cut(s) 160, 327
BseMI GCAATG 2 cut(s) 166, 396
BseMII CTCAG 1 cut(s) 108
BseRI GAGGAG 2 cut(s) 134, 230
BseXI GCAGC 2 cut(s) 505, 527
BsgI GTGCAG 1 cut(s) 161
BshFI GGCC 4 cut(s) 98, 115, 269, 627
BsmAI GTCTC 1 cut(s) 401
BsmBI CGTCTC 1 cut(s) 401
BsnI GGCC 4 cut(s) 98, 115, 269, 627
Bsp119I TTCGAA 1 cut(s) 436
Bsp143I GATC 3 cut(s) 123, 457, 611
BspACI CCGC 2 cut(s) 99, 521
BspANI GGCC 4 cut(s) 98, 115, 269, 627
BspCNI CTCAG 1 cut(s) 109
BspT104I TTCGAA 1 cut(s) 436
BsrDI GCAATG 2 cut(s) 166, 396
BssMI GATC 3 cut(s) 123, 457, 611
Bst6I CTCTTC 1 cut(s) 293
BstBI TTCGAA 1 cut(s) 436
BstDEI CTNAG 1 cut(s) 117
BstF5I GGATG 2 cut(s) 160, 327
BstHHI GCGC 1 cut(s) 546
BstKTI GATC 3 cut(s) 126, 460, 614
BstMAI GTCTC 1 cut(s) 401
BstMBI GATC 3 cut(s) 123, 457, 611
BstV1I GCAGC 2 cut(s) 505, 527
BstV2I GAAGAC 2 cut(s) 230, 493
Bsu36I CCTNAGG 1 cut(s) 117
BsuI GTATCC 1 cut(s) 238
BsuRI GGCC 4 cut(s) 98, 115, 269, 627
BtsCI GGATG 2 cut(s) 160, 327
BtsIMutI CAGTG 1 cut(s) 126
CfoI GCGC 1 cut(s) 546
Cfr13I GGNCC 1 cut(s) 626
Csp6I GTAC 1 cut(s) 13
CviAII CATG 1 cut(s) 446
CviQI GTAC 1 cut(s) 13
DdeI CTNAG 1 cut(s) 117
DpnI GATC 3 cut(s) 125, 459, 613
DpnII GATC 3 cut(s) 123, 457, 611
EaeI YGGCCR 2 cut(s) 96, 267
Eam1104I CTCTTC 1 cut(s) 293
EarI CTCTTC 1 cut(s) 293
Eco57I CTGAAG 1 cut(s) 606
Eco81I CCTNAGG 1 cut(s) 117
Esp3I CGTCTC 1 cut(s) 401
FaeI CATG 1 cut(s) 449
FaiI YATR 6 cut(s) 241, 264, 399, 404, 447, 456
FatI CATG 1 cut(s) 445
FbaI TGATCA 1 cut(s) 457
FblI GTMKAC 2 cut(s) 332, 442
Fnu4HI GCNGC 3 cut(s) 99, 516, 519
FokI GGATG 2 cut(s) 167, 334
Fsp4HI GCNGC 3 cut(s) 99, 516, 519
FspBI CTAG 5 cut(s) 182, 188, 488, 497, 630
GlaI GCGC 1 cut(s) 545
GluI GCNGC 3 cut(s) 99, 516, 519
HaeIII GGCC 4 cut(s) 98, 115, 269, 627
HhaI GCGC 1 cut(s) 546
Hin1II CATG 1 cut(s) 449
Hin6I GCGC 1 cut(s) 544
HinP1I GCGC 1 cut(s) 544
HincII GTYRAC 1 cut(s) 333
HindII GTYRAC 1 cut(s) 333
HindIII AAGCTT 2 cut(s) 305, 588
HinfI GANTC 3 cut(s) 329, 449, 637
HphI GGTGA 1 cut(s) 425
Hpy166II GTNNAC 3 cut(s) 333, 416, 443
Hpy188I TCNGA 2 cut(s) 321, 648
Hpy188III TCNNGA 3 cut(s) 295, 488, 527
Hpy8I GTNNAC 3 cut(s) 333, 416, 443
Hpy99I CGWCG 2 cut(s) 10, 337
HpyAV CCTTC 1 cut(s) 326
HpyCH4IV ACGT 2 cut(s) 418, 622
HpyCH4V TGCA 2 cut(s) 178, 515
HpyF3I CTNAG 1 cut(s) 117
HpySE526I ACGT 2 cut(s) 418, 622
Hsp92II CATG 1 cut(s) 449
HspAI GCGC 1 cut(s) 544
Ksp22I TGATCA 1 cut(s) 457
Kzo9I GATC 3 cut(s) 123, 457, 611
LpnPI CCDG 2 cut(s) 129, 566
Lsp1109I GCAGC 2 cut(s) 505, 527
MaeI CTAG 5 cut(s) 182, 188, 488, 497, 630
MaeII ACGT 2 cut(s) 418, 622
MalI GATC 3 cut(s) 125, 459, 613
MboI GATC 3 cut(s) 123, 457, 611
MboII GAAGA 8 cut(s) 232, 235, 283, 310, 493, 542, 545, 569
MfeI CAATTG 1 cut(s) 102
MlsI TGGCCA 1 cut(s) 269
MluCI AATT 4 cut(s) 40, 102, 257, 426
MluNI TGGCCA 1 cut(s) 269
MlyI GAGTC 2 cut(s) 338, 646
MnlI CCTC 6 cut(s) 54, 112, 208, 563, 599, 645
Mox20I TGGCCA 1 cut(s) 269
MroXI GAANNNNTTC 1 cut(s) 41
MscI TGGCCA 1 cut(s) 269
MseI TTAA 1 cut(s) 476
MslI CAYNNNNRTG 1 cut(s) 389
Msp20I TGGCCA 1 cut(s) 269
MspA1I CMGCKG 1 cut(s) 518
MunI CAATTG 1 cut(s) 102
NdeII GATC 3 cut(s) 123, 457, 611
NlaIII CATG 1 cut(s) 449
NspV TTCGAA 1 cut(s) 436
PdmI GAANNNNTTC 1 cut(s) 41
PfeI GAWTC 1 cut(s) 449
PkrI GCNGC 3 cut(s) 100, 517, 520
PleI GAGTC 2 cut(s) 337, 645
PpsI GAGTC 2 cut(s) 337, 645
PspPI GGNCC 1 cut(s) 626
PvuII CAGCTG 1 cut(s) 518
RsaI GTAC 1 cut(s) 14
RsaNI GTAC 1 cut(s) 13
RseI CAYNNNNRTG 1 cut(s) 389
SalI GTCGAC 1 cut(s) 331
SaqAI TTAA 1 cut(s) 476
SatI GCNGC 3 cut(s) 99, 516, 519
Sau3AI GATC 3 cut(s) 123, 457, 611
Sau96I GGNCC 1 cut(s) 626
SchI GAGTC 2 cut(s) 338, 646
SetI ASST 9 cut(s) 183, 309, 318, 371, 384, 421, 520, 592, 625
SfuI TTCGAA 1 cut(s) 436
SmiMI CAYNNNNRTG 1 cut(s) 389
SpeI ACTAGT 1 cut(s) 496
Sse9I AATT 4 cut(s) 40, 102, 257, 426
SsiI CCGC 2 cut(s) 99, 521
SspMI CTAG 5 cut(s) 182, 188, 488, 497, 630
TaiI ACGT 2 cut(s) 421, 625
TaqI TCGA 4 cut(s) 332, 436, 504, 640
TaqII GACCGA 1 cut(s) 359
TasI AATT 4 cut(s) 40, 102, 257, 426
TauI GCSGC 1 cut(s) 101
TfiI GAWTC 1 cut(s) 449
Tru1I TTAA 1 cut(s) 476
Tru9I TTAA 1 cut(s) 476
TscAI CASTG 1 cut(s) 133
TseI GCWGC 2 cut(s) 515, 518
TspDTI ATGAA 1 cut(s) 210
TspRI CASTG 1 cut(s) 133
XapI RAATTY 1 cut(s) 426
XbaI TCTAGA 1 cut(s) 487
XmiI GTMKAC 2 cut(s) 332, 442
XmnI GAANNNNTTC 1 cut(s) 41
XspI CTAG 5 cut(s) 182, 188, 488, 497, 630
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.