Rroxscaffold_1G00028950

Integrase core domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0000154
Physical Location & Seq
Forward (+)
37359831 .. 37365023
5193 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00028950.1

Sequence Viewer

Length: 456 bp
ATGATGTTAGAGTTTAAGGAGTCCATGATGAAGGTTTTTGATATGATCGATCCGGGAAAAATGAGATTTTTCTTTGGAATAGAAGTGTTACAAATAGAAGATGGGATATATATGGGACAGAGAAAGTATGCTTTGGAAGTGTTGAAGCGCTTCGGAATGGAAGAGAGCAATGCGTTGTTGAACCCGATTGTGCACGGAGTCAAAGTTGGGAAGGACAAGGCAGGAGTGAAGATTGATGAGACCTACTTCAAACAAATAGTAGGTAGTCTTATGTACATCACGGCTACTAGGCCTGATTTGATGTTTGTTGTGAGCCTAATCGGTAGATACATGGCAAGACCAACGCAACCGCATCCGCAAATTGCAAAAAGAGCCTTGAGATATTTGAAGGGGACAAGTAGACTATGGCATCTGCTACAAGAAAGAAGGCAACAAGAAACTAGTTGGTTTCATTGA
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
RVT_2 gag_pre-integrs rve

Protein Analysis

151

Amino Acids

17.72

Weight (kDa)

9.69

Isoelectric Point (pI)

49.06

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_2 PF07727 2 - 64 1.3e-09 Reverse transcriptase (RNA-dependent DNA polymerase)
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: OG0000154)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g02351 FvH4_1g18383 FvH4_1g18442 FvH4_1g19622 FvH4_2g08148 FvH4_2g16312 FvH4_3g06912 FvH4_3g10761 FvH4_3g12332 FvH4_3g12332 FvH4_3g14182 FvH4_3g21021 FvH4_3g35231 FvH4_3g45132 FvH4_4g08663 FvH4_4g30271 FvH4_4g30272 FvH4_4g30901 FvH4_4g30902 FvH4_5g12471 FvH4_5g22951 FvH4_6g07331 FvH4_6g07332 FvH4_6g41872 FvH4_6g43841 FvH4_6g43842 FvH4_6g48811 FvH4_7g03911 FvH4_7g13272 FvH4_7g21181 FvH4_7g29024 FvH4_7g33702
malus_domestica MD00G1037700.v1.1 MD01G1037300.v1.1 MD01G1096700.v1.1 MD01G1101100.v1.1 MD01G1129400.v1.1 MD02G1295200.v1.1 MD03G1131300.v1.1 MD04G1072100.v1.1 MD05G1104800.v1.1 MD07G1028600.v1.1 MD07G1274600.v1.1 MD08G1027200.v1.1 MD09G1044400.v1.1 MD09G1044700.v1.1 MD09G1129500.v1.1 MD09G1238700.v1.1 MD10G1011700.v1.1 MD10G1071400.v1.1 MD10G1108600.v1.1 MD10G1162100.v1.1 MD10G1162300.v1.1 MD11G1016700.v1.1 MD11G1074500.v1.1 MD15G1058600.v1.1 MD15G1383000.v1.1 MD16G1192200.v1.1 MD17G1077400.v1.1 MD17G1077500.v1.1
pyrus_communis pycom01g03520 pycom02g00350 pycom03g09910 pycom03g13960 pycom03g13970 pycom03g19180 pycom04g08410 pycom04g10140 pycom06g03750 pycom07g09240 pycom07g09260 pycom08g20130 pycom09g11020 pycom10g12690 pycom14g04140 pycom14g05710 pycom16g06380 pycom17g05500 pycom808g00140
rosa_chinensis RchiOBHm_Chr1g0316211 RchiOBHm_Chr1g0319901 RchiOBHm_Chr1g0321811 RchiOBHm_Chr1g0329831 RchiOBHm_Chr1g0330721 RchiOBHm_Chr1g0330731 RchiOBHm_Chr1g0368461 RchiOBHm_Chr1g0381111 RchiOBHm_Chr2g0154461 RchiOBHm_Chr2g0164521 RchiOBHm_Chr2g0175301 RchiOBHm_Chr3g0451301 RchiOBHm_Chr3g0453691 RchiOBHm_Chr3g0470191 RchiOBHm_Chr3g0486561 RchiOBHm_Chr4g0409141 RchiOBHm_Chr4g0409151 RchiOBHm_Chr4g0421231 RchiOBHm_Chr4g0440701 RchiOBHm_Chr5g0018211 RchiOBHm_Chr5g0023611 RchiOBHm_Chr5g0045971 RchiOBHm_Chr5g0056061 RchiOBHm_Chr5g0063381 RchiOBHm_Chr5g0064011 RchiOBHm_Chr5g0064021 RchiOBHm_Chr5g0064041 RchiOBHm_Chr6g0259681 RchiOBHm_Chr6g0259691 RchiOBHm_Chr6g0296531 RchiOBHm_Chr7g0186421 RchiOBHm_Chr7g0192321 RchiOBHm_Chr7g0198271 RchiOBHm_Chr7g0198951 RchiOBHm_Chr7g0237911
rosa_laevigata RLG00000026946
rosa_roxburghii Rroxscaffold_1G00014460 Rroxscaffold_1G00014610 Rroxscaffold_1G00028950 Rroxscaffold_1G00052630 Rroxscaffold_2G00104760 Rroxscaffold_2G00138900 Rroxscaffold_2G00145210 Rroxscaffold_3G00220110 Rroxscaffold_4G00297860 Rroxscaffold_4G00321570 Rroxscaffold_5G00332990 Rroxscaffold_5G00360870
rosa_samantha Rh1AG319600 Rh1CG299100 Rh4DG385900 Rh5BG032200
rosa_wichuraiana Rw0G002380 Rw0G003050 Rw0G003940 Rw1G002730 Rw1G003260 Rw1G005490 Rw1G016140 Rw1G016150 Rw1G017930 Rw1G017940 Rw1G022540 Rw1G022630 Rw1G031080 Rw1G039680 Rw2G003340 Rw2G003720 Rw2G006640 Rw2G020790 Rw2G025650 Rw2G028430 Rw2G029550 Rw2G034920 Rw2G040820 Rw2G048420 Rw2G048570 Rw3G010040 Rw3G022790 Rw3G023350 Rw3G025140 Rw3G028810 Rw4G000680 Rw4G003350 Rw4G004640 Rw4G026650 Rw4G034500 Rw5G008490 Rw5G020650 Rw5G023000 Rw5G033610 Rw5G037280 Rw5G046620 Rw5G050250 Rw6G001410 Rw6G005690 Rw6G005820 Rw6G010920 Rw6G022790 Rw6G023940 Rw6G026290 Rw6G028610 Rw6G031260 Rw6G036550 Rw6G036560 Rw7G015300 Rw7G017250 Rw7G018150 Rw7G031960 Rw7G036490

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 400
AciI CCGC 2 cut(s) 350, 356
AclWI GGATC 1 cut(s) 44
AfaI GTAC 1 cut(s) 275
AfeI AGCGCT 1 cut(s) 149
AgsI TTSAA 4 cut(s) 145, 181, 250, 388
AhlI ACTAGT 1 cut(s) 440
Alw21I GWGCWC 1 cut(s) 195
Alw26I GTCTC 1 cut(s) 233
Alw44I GTGCAC 1 cut(s) 191
AlwI GGATC 1 cut(s) 44
Aor51HI AGCGCT 1 cut(s) 149
AoxI GGCC 1 cut(s) 290
ApaLI GTGCAC 1 cut(s) 191
Asp700I GAANNNNTTC 1 cut(s) 149
AspLEI GCGC 1 cut(s) 150
AsuC2I CCSGG 1 cut(s) 54
BaeGI GKGCMC 1 cut(s) 195
Bbv12I GWGCWC 1 cut(s) 195
BccI CCATC 1 cut(s) 95
BceAI ACGGC 1 cut(s) 297
BcnI CCSGG 1 cut(s) 54
BcoDI GTCTC 1 cut(s) 233
BcuI ACTAGT 1 cut(s) 440
BfaI CTAG 2 cut(s) 288, 441
BfoI RGCGCY 1 cut(s) 151
Bme1390I CCNGG 1 cut(s) 54
BmrFI CCNGG 1 cut(s) 54
BmsI GCATC 2 cut(s) 361, 418
BpuEI CTTGAG 1 cut(s) 397
BpuMI CCSGG 1 cut(s) 54
Bsa29I ATCGAT 1 cut(s) 48
BsaI GGTCTC 1 cut(s) 233
BsaXI ACNNNNNCTCC 2 cut(s) 189, 219
Bse3DI GCAATG 1 cut(s) 175
BseCI ATCGAT 1 cut(s) 48
BseGI GGATG 1 cut(s) 352
BseMI GCAATG 1 cut(s) 175
BseSI GKGCMC 1 cut(s) 195
BshFI GGCC 1 cut(s) 292
BshVI ATCGAT 1 cut(s) 48
BsiHKAI GWGCWC 1 cut(s) 195
BsiSI CCGG 1 cut(s) 53
BslFI GGGAC 2 cut(s) 129, 406
BsmAI GTCTC 1 cut(s) 233
BsmFI GGGAC 2 cut(s) 129, 406
BsnI GGCC 1 cut(s) 292
Bso31I GGTCTC 1 cut(s) 233
Bsp1286I GDGCHC 1 cut(s) 195
Bsp1407I TGTACA 1 cut(s) 273
Bsp143I GATC 2 cut(s) 45, 49
BspACI CCGC 2 cut(s) 350, 356
BspANI GGCC 1 cut(s) 292
BspDI ATCGAT 1 cut(s) 48
BspPI GGATC 1 cut(s) 44
BspTNI GGTCTC 1 cut(s) 233
BsrDI GCAATG 1 cut(s) 175
BsrGI TGTACA 1 cut(s) 273
BssMI GATC 2 cut(s) 45, 49
Bst6I CTCTTC 1 cut(s) 156
BstAUI TGTACA 1 cut(s) 273
BstF5I GGATG 1 cut(s) 352
BstH2I RGCGCY 1 cut(s) 151
BstHHI GCGC 1 cut(s) 150
BstKTI GATC 2 cut(s) 48, 52
BstMAI GTCTC 1 cut(s) 233
BstMBI GATC 2 cut(s) 45, 49
BstMWI GCNNNNNNNGC 1 cut(s) 371
BstSCI CCNGG 1 cut(s) 52
BstSLI GKGCMC 1 cut(s) 195
Bsu15I ATCGAT 1 cut(s) 48
BsuRI GGCC 1 cut(s) 292
BsuTUI ATCGAT 1 cut(s) 48
BtsCI GGATG 1 cut(s) 352
CfoI GCGC 1 cut(s) 150
ClaI ATCGAT 1 cut(s) 48
Csp6I GTAC 1 cut(s) 274
CviAII CATG 2 cut(s) 25, 331
CviJI RGCY 4 cut(s) 284, 292, 315, 374
CviKI_1 RGCY 4 cut(s) 284, 292, 315, 374
CviQI GTAC 1 cut(s) 274
DpnI GATC 2 cut(s) 47, 51
DpnII GATC 2 cut(s) 45, 49
Eam1104I CTCTTC 1 cut(s) 156
EarI CTCTTC 1 cut(s) 156
Eco147I AGGCCT 1 cut(s) 292
Eco31I GGTCTC 1 cut(s) 233
Eco47III AGCGCT 1 cut(s) 149
FaeI CATG 2 cut(s) 28, 334
FaiI YATR 9 cut(s) 26, 44, 109, 111, 113, 129, 272, 332, 406
FaqI GGGAC 2 cut(s) 129, 406
FatI CATG 2 cut(s) 24, 330
FblI GTMKAC 1 cut(s) 400
FokI GGATG 1 cut(s) 339
FspBI CTAG 2 cut(s) 288, 441
GlaI GCGC 1 cut(s) 149
HaeII RGCGCY 1 cut(s) 151
HaeIII GGCC 1 cut(s) 292
HapII CCGG 1 cut(s) 53
HhaI GCGC 1 cut(s) 150
Hin1II CATG 2 cut(s) 28, 334
Hin6I GCGC 1 cut(s) 148
HinP1I GCGC 1 cut(s) 148
HinfI GANTC 2 cut(s) 20, 198
HpaII CCGG 1 cut(s) 53
Hpy166II GTNNAC 2 cut(s) 193, 401
Hpy188I TCNGA 1 cut(s) 155
Hpy8I GTNNAC 2 cut(s) 193, 401
HpyAV CCTTC 4 cut(s) 25, 205, 382, 420
HpyCH4V TGCA 2 cut(s) 193, 365
HpyF10VI GCNNNNNNNGC 1 cut(s) 371
Hsp92II CATG 2 cut(s) 28, 334
HspAI GCGC 1 cut(s) 148
Kzo9I GATC 2 cut(s) 45, 49
LpnPI CCDG 3 cut(s) 66, 207, 306
LweI GCATC 2 cut(s) 361, 418
MaeI CTAG 2 cut(s) 288, 441
MaeIII GTNAC 1 cut(s) 87
MalI GATC 2 cut(s) 47, 51
MboI GATC 2 cut(s) 45, 49
MboII GAAGA 3 cut(s) 110, 173, 241
MhlI GDGCHC 1 cut(s) 195
MluCI AATT 1 cut(s) 360
MlyI GAGTC 2 cut(s) 29, 207
MroXI GAANNNNTTC 1 cut(s) 149
MseI TTAA 1 cut(s) 15
MspI CCGG 1 cut(s) 53
MspR9I CCNGG 1 cut(s) 54
MwoI GCNNNNNNNGC 1 cut(s) 371
NciI CCSGG 1 cut(s) 54
NdeII GATC 2 cut(s) 45, 49
NlaIII CATG 2 cut(s) 28, 334
PceI AGGCCT 1 cut(s) 292
PdmI GAANNNNTTC 1 cut(s) 149
PfoI TCCNGGA 1 cut(s) 52
PleI GAGTC 2 cut(s) 28, 206
PpsI GAGTC 2 cut(s) 28, 206
RsaI GTAC 1 cut(s) 275
RsaNI GTAC 1 cut(s) 274
SaqAI TTAA 1 cut(s) 15
Sau3AI GATC 2 cut(s) 45, 49
SchI GAGTC 2 cut(s) 29, 207
ScrFI CCNGG 1 cut(s) 54
SduI GDGCHC 1 cut(s) 195
SetI ASST 3 cut(s) 36, 245, 265
SfaNI GCATC 2 cut(s) 361, 418
SmlI CTYRAG 1 cut(s) 376
SmoI CTYRAG 1 cut(s) 376
SpeI ACTAGT 1 cut(s) 440
Sse9I AATT 1 cut(s) 360
SseBI AGGCCT 1 cut(s) 292
SsiI CCGC 2 cut(s) 350, 356
SspMI CTAG 2 cut(s) 288, 441
StuI AGGCCT 1 cut(s) 292
StyD4I CCNGG 1 cut(s) 52
TaqI TCGA 1 cut(s) 48
TasI AATT 1 cut(s) 360
TatI WGTACW 1 cut(s) 273
Tru1I TTAA 1 cut(s) 15
Tru9I TTAA 1 cut(s) 15
TspDTI ATGAA 2 cut(s) 44, 440
TspGWI ACGGA 1 cut(s) 210
VneI GTGCAC 1 cut(s) 191
XmiI GTMKAC 1 cut(s) 400
XmnI GAANNNNTTC 1 cut(s) 149
XspI CTAG 2 cut(s) 288, 441
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.