Rw7G011010

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr7
OG0000562
Physical Location & Seq
Forward (+)
10241995 .. 10243445
1451 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw7G011010.1

Sequence Viewer

Length: 1044 bp
ATGACAGAAAGAGAAGGTTCTCTCTATGCAAAGACAGAAAGCCCAGATGGGAATCCGAATCAGCGTCTATGCTCAGTGCTTCTAAATGAGTTCAACTATCTTGCTTGGTCAAGAGCCATCACTCTAGCCCTTGGTGGAAGATCAAAGCTCAGCTTCATCAATGACAAAAACAACATCCCAGATGCCTCATCATCTGAATATGAAAGTTGGTTATCCAAAGACCAACTTGTTATGTCATGGCTTATTAATTCAATGGAGCCAAAGCTTGCTGAAATCTTCAGCTATTCGGAGTCATCTCGACATCTCTGGGATGCTGTTAAAGACATGTATGGCAACCTAGACAATGCAGCAAGAGTGTTCCAAGTCAAAAAGGATCTTGCAGGGATTCAACAAGGTAATCTCTCATTTGTTCAACATCTTGGCAACTTAAAAGCCAAGTGGAATGAACTTGATATGTATAGACCTCACACCACTGATACCACCATATTGTTGAAAAGAGCTGAAGAAGATAAAGTTCATCTTTTGATGAGCCCTGAGTTTCCTTCGTTCACAACAGTATGCAACTCCATTCAACGTGAAGAAATGTGCAAAAAGGTAATGAATATGGACAACAGAGCTGGAGGATCAGAAGCTAGAGCATTTGCTGCAAACAAAAGTGTCACAAGCGACAGAACGTACAAGGGCAAGATGCCAGATCTGAAGTGCACTCATTGTGAACACATTGGACGAACTGGTATAGGCCACACAAGAGAGAGATGTTGGATATTACATCCAGAACTGAAACCTAAGTTCAATAAGGACCAGAAGAATCAAAGAGGCACCATTCAGAGAAGCTCTTACATCTCTAATCCAAATGCAAACTTCAGCAACACTTCTGAAGATGTGATGAAGTTCACGTCCAATCCAATAACTATCATAAATGAGTTTGCTACATATCTTCAAAAGAACACAACTGCTATGCTTGGAAAGTTTGCAGGTTTTCTAGCAAAATCAAATATGGCTTCTTCCCAGGTATTATTTGCTGTCCAAGAAGAAGATTGGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00940 ko01110 map00940 map01110
Pfam Domains
Protein Families
Retrotran_gag_2

Protein Analysis

347

Amino Acids

39.41

Weight (kDa)

8.4

Isoelectric Point (pI)

41.3

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 18 - 54 1.8e-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: OG0000562)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g17331 FvH4_3g36541
malus_domestica MD07G1078600.v1.1 MD10G1237700.v1.1 MD10G1333400.v1.1 MD11G1102200.v1.1 MD13G1138400.v1.1 MD14G1033400.v1.1 MD15G1053300.v1.1
prunus_persica Prupe.1G465400_v2.0.a1 Prupe.3G136000_v2.0.a1 Prupe.7G119900_v2.0.a1
pyrus_communis pycom01g04630 pycom03g13050 pycom04g21190 pycom05g04910 pycom05g05510 pycom08g15850 pycom09g15040 pycom1094g00010 pycom11g02000 pycom12g06150 pycom13g24110 pycom13g24910 pycom14g00050 pycom15g21970 pycom15g35170 pycom15g35180 pycom16g14620 pycom16g14630 pycom808g00110
rosa_chinensis RchiOBHm_Chr1g0322851 RchiOBHm_Chr1g0365941 RchiOBHm_Chr3g0453341 RchiOBHm_Chr4g0388371 RchiOBHm_Chr4g0394021 RchiOBHm_Chr5g0013181 RchiOBHm_Chr6g0261721 RchiOBHm_Chr6g0261731 RchiOBHm_Chr7g0188861 RchiOBHm_Chr7g0192331 RchiOBHm_Chr7g0231721
rosa_multiflora Rmu_sc0002521.1_g000006 Rmu_sc0003255.1_g000026 Rmu_sc0004191.1_g000036 Rmu_sc0004414.1_g000014 Rmu_sc0005670.1_g000006 Rmu_sc0006081.1_g000001 Rmu_sc0007215.1_g000004 Rmu_sc0010088.1_g000010 Rmu_sc0020285.1_g000003 Rmu_sc0026896.1_g000002 Rmu_ssc0000019.1_g000029
rosa_roxburghii Rroxscaffold_3G00224890 Rroxscaffold_6G00400640 Rroxscaffold_7G00176590 Rroxscaffold_7G00189230
rosa_samantha Rh4BG046700
rosa_wichuraiana Rw1G012690 Rw1G031370 Rw2G042180 Rw2G043670 Rw2G046240 Rw2G049890 Rw2G050760 Rw2G051280 Rw2G053590 Rw3G007590 Rw3G026850 Rw4G001540 Rw4G009760 Rw4G019270 Rw5G000720 Rw5G005620 Rw5G041560 Rw6G007370 Rw6G009830 Rw6G015360 Rw6G031160 Rw7G004930 Rw7G011010 Rw7G024230 Rw7G028240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 965
AccB1I GGYRCC 1 cut(s) 818
AclWI GGATC 2 cut(s) 381, 631
AcuI CTGAAG 5 cut(s) 262, 522, 719, 847, 897
AfaI GTAC 1 cut(s) 677
AflIII ACRYGT 1 cut(s) 324
AgsI TTSAA 8 cut(s) 94, 252, 389, 413, 493, 572, 793, 941
AjiI CACGTC 1 cut(s) 897
AjnI CCWGG 1 cut(s) 1008
AluBI AGCT 8 cut(s) 148, 153, 265, 282, 500, 617, 632, 834
AluI AGCT 8 cut(s) 148, 153, 265, 282, 500, 617, 632, 834
Alw21I GWGCWC 1 cut(s) 707
Alw44I GTGCAC 1 cut(s) 703
AlwI GGATC 2 cut(s) 381, 631
AoxI GGCC 1 cut(s) 739
ApaLI GTGCAC 1 cut(s) 703
ApeKI GCWGC 2 cut(s) 347, 644
AseI ATTAAT 1 cut(s) 246
AspS9I GGNCC 1 cut(s) 799
AvaII GGWCC 1 cut(s) 799
BaeGI GKGCMC 1 cut(s) 707
BanI GGYRCC 1 cut(s) 818
BanII GRGCYC 1 cut(s) 533
Bbv12I GWGCWC 1 cut(s) 707
BbvI GCAGC 2 cut(s) 359, 631
BccI CCATC 2 cut(s) 41, 125
BciT130I CCWGG 1 cut(s) 1010
BfaI CTAG 4 cut(s) 125, 338, 633, 983
BfuAI ACCTGC 1 cut(s) 965
BglII AGATCT 1 cut(s) 694
BisI GCNGC 2 cut(s) 348, 645
BlpI GCTNAGC 1 cut(s) 149
BlsI GCNGC 2 cut(s) 349, 646
Bme1390I CCNGG 1 cut(s) 1010
Bme18I GGWCC 1 cut(s) 799
BmgBI CACGTC 1 cut(s) 897
BmgT120I GGNCC 1 cut(s) 799
BmiI GGNNCC 2 cut(s) 258, 820
BmrFI CCNGG 1 cut(s) 1010
BmsI GCATC 3 cut(s) 172, 301, 678
BpmI CTGGAG 1 cut(s) 639
Bpu1102I GCTNAGC 1 cut(s) 149
BsaBI GATNNNNATC 1 cut(s) 51
BsaJI CCNNGG 2 cut(s) 130, 1008
Bse1I ACTGG 1 cut(s) 736
Bse8I GATNNNNATC 1 cut(s) 51
BseBI CCWGG 1 cut(s) 1010
BseDI CCNNGG 2 cut(s) 130, 1008
BseGI GGATG 3 cut(s) 174, 316, 769
BseJI GATNNNNATC 1 cut(s) 51
BseMII CTCAG 3 cut(s) 87, 163, 525
BseNI ACTGG 1 cut(s) 736
BseSI GKGCMC 1 cut(s) 707
BseXI GCAGC 2 cut(s) 359, 631
BshFI GGCC 1 cut(s) 741
BshNI GGYRCC 1 cut(s) 818
BsiHKAI GWGCWC 1 cut(s) 707
BsnI GGCC 1 cut(s) 741
Bsp1286I GDGCHC 2 cut(s) 533, 707
Bsp143I GATC 4 cut(s) 140, 373, 623, 694
Bsp1720I GCTNAGC 1 cut(s) 149
BspANI GGCC 1 cut(s) 741
BspCNI CTCAG 3 cut(s) 86, 162, 526
BspLI GGNNCC 2 cut(s) 258, 820
BspMI ACCTGC 1 cut(s) 965
BspPI GGATC 2 cut(s) 381, 631
BspT107I GGYRCC 1 cut(s) 818
BsrI ACTGG 1 cut(s) 736
BssECI CCNNGG 2 cut(s) 130, 1008
BssMI GATC 4 cut(s) 140, 373, 623, 694
BssT1I CCWWGG 1 cut(s) 130
Bst2UI CCWGG 1 cut(s) 1010
Bst4CI ACNGT 1 cut(s) 556
BstAPI GCANNNNNTGC 1 cut(s) 644
BstC8I GCNNGC 1 cut(s) 267
BstDEI CTNAG 4 cut(s) 73, 149, 534, 786
BstF5I GGATG 3 cut(s) 174, 316, 769
BstKTI GATC 4 cut(s) 143, 376, 626, 697
BstMBI GATC 4 cut(s) 140, 373, 623, 694
BstMWI GCNNNNNNNGC 1 cut(s) 644
BstNI CCWGG 1 cut(s) 1010
BstNSI RCATGY 1 cut(s) 328
BstSCI CCNGG 1 cut(s) 1008
BstSLI GKGCMC 1 cut(s) 707
BstV1I GCAGC 2 cut(s) 359, 631
BstX2I RGATCY 2 cut(s) 373, 694
BstYI RGATCY 2 cut(s) 373, 694
BsuRI GGCC 1 cut(s) 741
BtrI CACGTC 1 cut(s) 897
BtsCI GGATG 3 cut(s) 174, 316, 769
BtsIMutI CAGTG 2 cut(s) 81, 471
BveI ACCTGC 1 cut(s) 965
Cac8I GCNNGC 1 cut(s) 267
Cfr13I GGNCC 1 cut(s) 799
CseI GACGC 1 cut(s) 53
Csp6I GTAC 1 cut(s) 676
CviAII CATG 2 cut(s) 237, 325
CviQI GTAC 1 cut(s) 676
DdeI CTNAG 4 cut(s) 73, 149, 534, 786
DpnI GATC 4 cut(s) 142, 375, 625, 696
DpnII GATC 4 cut(s) 140, 373, 623, 694
Eco130I CCWWGG 1 cut(s) 130
Eco24I GRGCYC 1 cut(s) 533
Eco47I GGWCC 1 cut(s) 799
Eco57I CTGAAG 5 cut(s) 262, 522, 719, 847, 897
EcoRII CCWGG 1 cut(s) 1008
EcoT14I CCWWGG 1 cut(s) 130
EcoT38I GRGCYC 1 cut(s) 533
ErhI CCWWGG 1 cut(s) 130
FaeI CATG 2 cut(s) 240, 328
FalI AAGNNNNNCTT 6 cut(s) 137, 169, 210, 242, 504, 536
FatI CATG 2 cut(s) 236, 324
Fnu4HI GCNGC 2 cut(s) 348, 645
FokI GGATG 3 cut(s) 161, 323, 756
FriOI GRGCYC 1 cut(s) 533
Fsp4HI GCNGC 2 cut(s) 348, 645
FspBI CTAG 4 cut(s) 125, 338, 633, 983
GluI GCNGC 2 cut(s) 348, 645
GsuI CTGGAG 1 cut(s) 639
HaeIII GGCC 1 cut(s) 741
HgaI GACGC 1 cut(s) 53
Hin1II CATG 2 cut(s) 240, 328
HindIII AAGCTT 1 cut(s) 263
HinfI GANTC 5 cut(s) 52, 58, 290, 385, 808
Hpy166II GTNNAC 4 cut(s) 549, 705, 716, 894
Hpy188I TCNGA 7 cut(s) 57, 196, 289, 628, 699, 828, 877
Hpy188III TCNNGA 3 cut(s) 111, 297, 773
Hpy8I GTNNAC 4 cut(s) 549, 705, 716, 894
HpyAV CCTTC 2 cut(s) 8, 552
HpyCH4III ACNGT 1 cut(s) 556
HpyCH4IV ACGT 3 cut(s) 574, 674, 896
HpyCH4V TGCA 9 cut(s) 29, 347, 380, 561, 588, 647, 705, 857, 974
HpyF10VI GCNNNNNNNGC 1 cut(s) 644
HpyF3I CTNAG 4 cut(s) 73, 149, 534, 786
HpySE526I ACGT 3 cut(s) 574, 674, 896
Hsp92II CATG 2 cut(s) 240, 328
Kzo9I GATC 4 cut(s) 140, 373, 623, 694
LmnI GCTCC 1 cut(s) 256
Lsp1109I GCAGC 2 cut(s) 359, 631
LweI GCATC 3 cut(s) 172, 301, 678
MaeI CTAG 4 cut(s) 125, 338, 633, 983
MaeII ACGT 3 cut(s) 574, 674, 896
MaeIII GTNAC 1 cut(s) 658
MalI GATC 4 cut(s) 142, 375, 625, 696
MboI GATC 4 cut(s) 140, 373, 623, 694
MflI RGATCY 2 cut(s) 373, 694
MhlI GDGCHC 2 cut(s) 533, 707
MluCI AATT 1 cut(s) 247
MlyI GAGTC 1 cut(s) 299
MmeI TCCRAC 1 cut(s) 740
MnlI CCTC 4 cut(s) 196, 474, 614, 809
MseI TTAA 3 cut(s) 246, 318, 428
MspR9I CCNGG 1 cut(s) 1010
MvaI CCWGG 1 cut(s) 1010
MwoI GCNNNNNNNGC 1 cut(s) 644
NdeII GATC 4 cut(s) 140, 373, 623, 694
NlaIII CATG 2 cut(s) 240, 328
NlaIV GGNNCC 2 cut(s) 258, 820
NmuCI GTSAC 1 cut(s) 658
NspI RCATGY 1 cut(s) 328
PciI ACATGT 1 cut(s) 324
PfeI GAWTC 4 cut(s) 52, 58, 385, 808
PkrI GCNGC 2 cut(s) 349, 646
PleI GAGTC 1 cut(s) 298
PpsI GAGTC 1 cut(s) 298
PscI ACATGT 1 cut(s) 324
PshBI ATTAAT 1 cut(s) 246
Psp6I CCWGG 1 cut(s) 1008
PspGI CCWGG 1 cut(s) 1008
PspN4I GGNNCC 2 cut(s) 258, 820
PspPI GGNCC 1 cut(s) 799
PsuI RGATCY 2 cut(s) 373, 694
RsaI GTAC 1 cut(s) 677
RsaNI GTAC 1 cut(s) 676
SaqAI TTAA 3 cut(s) 246, 318, 428
SatI GCNGC 2 cut(s) 348, 645
Sau3AI GATC 4 cut(s) 140, 373, 623, 694
Sau96I GGNCC 1 cut(s) 799
SchI GAGTC 1 cut(s) 299
ScrFI CCNGG 1 cut(s) 1010
SduI GDGCHC 2 cut(s) 533, 707
SfaNI GCATC 3 cut(s) 172, 301, 678
SinI GGWCC 1 cut(s) 799
Sse9I AATT 1 cut(s) 247
SspMI CTAG 4 cut(s) 125, 338, 633, 983
StyD4I CCNGG 1 cut(s) 1008
StyI CCWWGG 1 cut(s) 130
TaaI ACNGT 1 cut(s) 556
TaiI ACGT 3 cut(s) 577, 677, 899
TaqI TCGA 1 cut(s) 298
TasI AATT 1 cut(s) 247
TfiI GAWTC 4 cut(s) 52, 58, 385, 808
Tru1I TTAA 3 cut(s) 246, 318, 428
Tru9I TTAA 3 cut(s) 246, 318, 428
TscAI CASTG 2 cut(s) 81, 478
TseFI GTSAC 1 cut(s) 658
TseI GCWGC 2 cut(s) 347, 644
Tsp45I GTSAC 1 cut(s) 658
TspDTI ATGAA 6 cut(s) 145, 216, 459, 506, 614, 902
TspRI CASTG 2 cut(s) 81, 478
VneI GTGCAC 1 cut(s) 703
VpaK11BI GGWCC 1 cut(s) 799
VspI ATTAAT 1 cut(s) 246
XceI RCATGY 1 cut(s) 328
XspI CTAG 4 cut(s) 125, 338, 633, 983
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.