RchiOBHm_Chr2g0106171

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
2
OG0000291
Physical Location & Seq
Forward (+)
17566357 .. 17568198
1842 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ48027

Sequence Viewer

Length: 1842 bp
ATGGTTGAATTGCCATATGAAAAAGACTTTGACGAAAGAAAAATCCCTACAAAGGCAAGACCAATTCAAATGAACAATGAATTATTAGAATATTGCAAAAAAGAAATTCAAGATCTTCTAGACAAAAGGTTGATAAGACCTAGCAAATCTCCATGGAGTTGTTCAGCTTTTTATGTTCAGAAGGCTTCTGAACTAGAAAGAGGAGCTCCAAGACTTGTAATTAATTACAAACCTTTAAACAAAGTCCTTCAGTGGATAAGATACCCCATTCCAAACAAAAGAGATTTACTCAAAAGACTAGTTCAAGCAAATGTTTTCTCAAAATTTGATATGAAATCTGGTTTTTGGCAAATCCAAATCGCAGAAAAAGACAAGTACAAAACAGCATTTAATGTTCCCTTCGGACACTACGAATGGAATGTTATGCCCTTTGGACTCAAAAATGCCCCTTCAGAATTTCAAAATATGATGAATGATATTTTTAATCCTTATTCAAATTTTTCAATTGTTTACATAGATGATGTTTTAATCTTTTCAGAAAATATTGATCAACACTGGAAACATCTCTACAAATTCTTTCAAATCATTAAAACCAATGGATTAGTGTTGTCAGCACCAAAAATCAAATTATTTCAAACAGAAATTAGATTCTTAGGACACAATATCAAACAAGGTACTATAGTCCCAATCTCTAGAGCAATTGAGTTTGCTAACAAATTTCCTGATGAAATTAAGGATAAAACTCAATTACAAAGATTTTTAGGATGTCTCAATTATATCTCTGACTTTTATGAGAAACTAACAGTTGTGTGCAAACCTCTTTATCAAAGACTAAAGAAAACCCCTCCAGCATGGACGGATGCTCATACTCAAATAGTTAGAGAAGTCAAAGCTTATGTCAAAACCCTACCATGTCTAGGACTACCAGACCCAGAGTCCTATAAAATTGTCGAGACAGATGCGTCCGACATCGGATATGGTGGAATCTTAAAACAAAGATTAGCAAACGACCAACCTGAACAATTGGTTAGATTTACCTCAGGTTTATGGAACCAAGCTCAGCAAAATTATAGCATTATCAAAAAAGAAATTTTAGCTATAGTGCTATGTATCACAAAGTTTCAAGATGATCTTTTGAACAAAAGGTTTTTACTTCGCATTGATTGTAAAGCAGCAAAATCAGTTTTAGAAAAGGATGTTCAAAACCTTGCCTCTAAACAGATTTTTGCAAGATGGCAAGCAATACTTTCAGTATTTGATTTTGACATTGCATTCATCAAAGGAGAGAGATACAAATTACCAAAAGTTCATGTATGTGTAGATAATATCTGCATCCAAACATTTCTCACAGTTGTCACCAACTTAGACACTAAACTGATTCTAGGAACCCCTTTTATCAGTTTAATCCATCCATTTTTGACAACTGATGAAGGTCTAGAAACAACAATTTTAGGTCAAACAATTCGTTTTCCTTTTATTGAAAAGGCAAAAACTAGAAACTTGAACCTAATTCGAAATGCTGCAATCACCAAAAGGGTCAATTTAATTCAAAACAAAGAAAATCACATAAACTACCTCAAAGAAGATCTACAAATTAAAAGAATTGAACATCAACTTCAACAGCCTTATTTACAAAATAGAATTAAAGAATTTAAAGAAAAATTAGAAAAGGAAGTAAGCTCAAACATCCCAAATGCTTTTTGGAATAGAAAAACCCACATGGTTGAAATCAAAACAGACAGAAGGGAGGACAACAGGGTATTTGGCTTCTACAAATTACTTTTCGAAGTTGAAATTGATATTCAGCAATATCTAATTTTAATTGCAAATATAAAGACATGA
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
RVP RVT_1 zf-CCHC

Protein Analysis

613

Amino Acids

71.98

Weight (kDa)

9.34

Isoelectric Point (pI)

40.72

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_1 PF00078 61 - 222 1.4e-38 Reverse transcriptase (RNA-dependent DNA polymerase)
RT_RNaseH_2 PF17919 285 - 384 6.4e-24 RNase H-like domain found in reverse transcriptase
RT_RNaseH PF17917 310 - 418 3.7e-22 RNase H-like domain found in reverse transcriptase
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: OG0000291)

Species Orthologous Gene IDs
arabidopsis_thaliana ATMG00860
fragaria_vesca FvH4_1g23712 FvH4_1g29809 FvH4_1g29810 FvH4_2g02661 FvH4_2g13451 FvH4_2g17921 FvH4_2g17922 FvH4_2g19251 FvH4_2g19252 FvH4_2g28221 FvH4_2g35961 FvH4_3g10372 FvH4_3g12461 FvH4_3g12461 FvH4_3g27861 FvH4_3g34591 FvH4_3g40201 FvH4_3g44612 FvH4_4g08352 FvH4_4g12251 FvH4_4g12742 FvH4_4g13904 FvH4_4g14287 FvH4_4g15243 FvH4_4g24071 FvH4_4g33448 FvH4_5g21912 FvH4_5g39371 FvH4_6g14992 FvH4_6g15221 FvH4_6g20603 FvH4_6g31093 FvH4_6g32372 FvH4_6g33012
malus_domestica MD11G1009100.v1.1 MD13G1145000.v1.1 MD16G1138700.v1.1
prunus_persica Prupe.5G246300_v2.0.a1 Prupe.7G034800_v2.0.a1 Prupe.8G084500_v2.0.a1
pyrus_communis pycom01g18240 pycom04g00330 pycom05g09010 pycom06g01670 pycom06g01690 pycom06g07180 pycom06g11620 pycom10g05720 pycom1134g00040 pycom1134g00060 pycom12486g00010 pycom12555g00230 pycom13g21670 pycom13g23130 pycom13g23140 pycom14g10580
rosa_chinensis RchiOBHm_Chr1g0330691 RchiOBHm_Chr2g0106171 RchiOBHm_Chr2g0134731 RchiOBHm_Chr2g0142791 RchiOBHm_Chr2g0149861 RchiOBHm_Chr3g0452401 RchiOBHm_Chr3g0461881 RchiOBHm_Chr4g0401341 RchiOBHm_Chr5g0075641 RchiOBHm_Chr6g0265961 RchiOBHm_Chr7g0200201 RchiOBHm_Chr7g0237811
rosa_laevigata RLG00000002773
rosa_multiflora Rmu_co8037806.1_g000001 Rmu_co8445989.1_g000001 Rmu_sc0000745.1_g000039 Rmu_sc0004448.1_g000029 Rmu_sc0004488.1_g000002 Rmu_sc0004591.1_g000018 Rmu_sc0005065.1_g000030 Rmu_sc0005150.1_g000005 Rmu_sc0005654.1_g000011 Rmu_sc0006986.1_g000016
rosa_roxburghii Rroxscaffold_164G00436490 Rroxscaffold_175G00432490 Rroxscaffold_1G00059440 Rroxscaffold_1G00064410 Rroxscaffold_2G00100310 Rroxscaffold_2G00128170 Rroxscaffold_3G00239420 Rroxscaffold_3G00264970 Rroxscaffold_3G00271550 Rroxscaffold_4G00300240 Rroxscaffold_5G00385050 Rroxscaffold_6G00399720
rosa_rugosa Rorug02G0252200
rosa_samantha Rh2DG251900 Rh7CG329900
rosa_wichuraiana Rw0G004800 Rw1G000850 Rw1G022350 Rw2G027030 Rw2G027760 Rw2G028410 Rw2G029130 Rw2G029390 Rw2G032490 Rw2G039460 Rw2G047800 Rw2G050340 Rw3G026430 Rw4G018370 Rw4G030750 Rw4G033140 Rw5G011950 Rw5G012010 Rw5G029280 Rw5G040190 Rw5G044570 Rw5G048240 Rw6G000340 Rw6G010140 Rw6G026480 Rw7G033750 Rw7G037250 Rw7G042080

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 961
AcsI RAATTY 8 cut(s) 105, 323, 455, 496, 572, 716, 1089, 1649
AcuI CTGAAG 2 cut(s) 233, 435
AfaI GTAC 2 cut(s) 377, 676
AfiI CCNNNNNNNGG 2 cut(s) 52, 917
AhdI GACNNNNNGTC 1 cut(s) 934
AhlI ACTAGT 1 cut(s) 298
AluBI AGCT 6 cut(s) 167, 206, 893, 1058, 1097, 1680
AluI AGCT 6 cut(s) 167, 206, 893, 1058, 1097, 1680
Alw21I GWGCWC 1 cut(s) 208
Alw26I GTCTC 2 cut(s) 773, 947
ApeKI GCWGC 2 cut(s) 1172, 1520
ApoI RAATTY 8 cut(s) 105, 323, 455, 496, 572, 716, 1089, 1649
ArsI GACNNNNNNTTYG 2 cut(s) 882, 914
AseI ATTAAT 1 cut(s) 222
AsuHPI GGTGA 2 cut(s) 1348, 1519
AsuII TTCGAA 2 cut(s) 1513, 1785
AxyI CCTNAGG 1 cut(s) 1039
BaeI ACNNNNGTAYC 2 cut(s) 666, 699
BanII GRGCYC 1 cut(s) 208
Bbv12I GWGCWC 1 cut(s) 208
BbvI GCAGC 2 cut(s) 1184, 1507
BccI CCATC 2 cut(s) 1227, 1416
BcgI CGANNNNNNTGC 2 cut(s) 941, 975
BclI TGATCA 1 cut(s) 547
BcoDI GTCTC 2 cut(s) 773, 947
BcuI ACTAGT 1 cut(s) 298
BfaI CTAG 9 cut(s) 119, 141, 194, 299, 693, 917, 1382, 1436, 1494
BfmI CTRYAG 2 cut(s) 678, 1098
BglII AGATCT 2 cut(s) 112, 1585
BisI GCNGC 2 cut(s) 1173, 1521
BlpI GCTNAGC 1 cut(s) 1059
BlsI GCNGC 2 cut(s) 1174, 1522
BmeRI GACNNNNNGTC 1 cut(s) 934
BmiI GGNNCC 2 cut(s) 1052, 1387
BmsI GCATC 3 cut(s) 850, 949, 1341
BplI GAGNNNNNCTC 2 cut(s) 273, 305
BpmI CTGGAG 1 cut(s) 831
Bpu1102I GCTNAGC 1 cut(s) 1059
Bpu14I TTCGAA 2 cut(s) 1513, 1785
BsaJI CCNNGG 1 cut(s) 152
Bsc4I CCNNNNNNNGG 2 cut(s) 52, 917
Bse1I ACTGG 1 cut(s) 560
Bse21I CCTNAGG 1 cut(s) 1039
Bse3DI GCAATG 1 cut(s) 1266
BseDI CCNNGG 1 cut(s) 152
BseGI GGATG 6 cut(s) 770, 865, 1201, 1332, 1408, 1686
BseLI CCNNNNNNNGG 2 cut(s) 52, 917
BseMI GCAATG 1 cut(s) 1266
BseMII CTCAG 2 cut(s) 1053, 1073
BseNI ACTGG 1 cut(s) 560
BseRI GAGGAG 1 cut(s) 216
BseXI GCAGC 2 cut(s) 1184, 1507
BsiHKAI GWGCWC 1 cut(s) 208
BslFI GGGAC 1 cut(s) 668
BslI CCNNNNNNNGG 2 cut(s) 52, 917
BsmAI GTCTC 2 cut(s) 773, 947
BsmFI GGGAC 1 cut(s) 668
BsmI GAATGC 1 cut(s) 1271
Bsp119I TTCGAA 2 cut(s) 1513, 1785
Bsp1286I GDGCHC 1 cut(s) 208
Bsp143I GATC 4 cut(s) 112, 547, 1129, 1585
Bsp1720I GCTNAGC 1 cut(s) 1059
Bsp19I CCATGG 1 cut(s) 152
BspCNI CTCAG 2 cut(s) 1052, 1072
BspLI GGNNCC 2 cut(s) 1052, 1387
BspT104I TTCGAA 2 cut(s) 1513, 1785
BsrDI GCAATG 1 cut(s) 1266
BsrI ACTGG 1 cut(s) 560
BssECI CCNNGG 1 cut(s) 152
BssMI GATC 4 cut(s) 112, 547, 1129, 1585
BssT1I CCWWGG 1 cut(s) 152
Bst4CI ACNGT 2 cut(s) 805, 1351
BstBI TTCGAA 2 cut(s) 1513, 1785
BstC8I GCNNGC 1 cut(s) 1239
BstDEI CTNAG 4 cut(s) 652, 1039, 1059, 1363
BstDSI CCRYGG 1 cut(s) 152
BstF5I GGATG 6 cut(s) 770, 865, 1201, 1332, 1408, 1686
BstKTI GATC 4 cut(s) 115, 550, 1132, 1588
BstMAI GTCTC 2 cut(s) 773, 947
BstMBI GATC 4 cut(s) 112, 547, 1129, 1585
BstSFI CTRYAG 2 cut(s) 678, 1098
BstV1I GCAGC 2 cut(s) 1184, 1507
BstX2I RGATCY 2 cut(s) 112, 1585
BstYI RGATCY 2 cut(s) 112, 1585
Bsu36I CCTNAGG 1 cut(s) 1039
BtgI CCRYGG 1 cut(s) 152
BtsCI GGATG 6 cut(s) 770, 865, 1201, 1332, 1408, 1686
BtsIMutI CAGTG 2 cut(s) 257, 553
Cac8I GCNNGC 1 cut(s) 1239
CseI GACGC 1 cut(s) 951
Csp6I GTAC 2 cut(s) 376, 675
CviAII CATG 6 cut(s) 153, 852, 912, 1310, 1720, 1839
CviJI RGCY 9 cut(s) 167, 185, 206, 893, 1058, 1097, 1624, 1680, 1767
CviKI_1 RGCY 9 cut(s) 167, 185, 206, 893, 1058, 1097, 1624, 1680, 1767
CviQI GTAC 2 cut(s) 376, 675
DdeI CTNAG 4 cut(s) 652, 1039, 1059, 1363
DpnI GATC 4 cut(s) 114, 549, 1131, 1587
DpnII GATC 4 cut(s) 112, 547, 1129, 1585
DraI TTTAAA 2 cut(s) 237, 1654
DrdI GACNNNNNNGTC 1 cut(s) 961
DriI GACNNNNNGTC 1 cut(s) 934
DseDI GACNNNNNNGTC 1 cut(s) 961
Eam1105I GACNNNNNGTC 1 cut(s) 934
Ecl136II GAGCTC 1 cut(s) 206
Eco130I CCWWGG 1 cut(s) 152
Eco24I GRGCYC 1 cut(s) 208
Eco53kI GAGCTC 1 cut(s) 206
Eco57I CTGAAG 2 cut(s) 233, 435
Eco81I CCTNAGG 1 cut(s) 1039
EcoICRI GAGCTC 1 cut(s) 206
EcoT14I CCWWGG 1 cut(s) 152
EcoT38I GRGCYC 1 cut(s) 208
ErhI CCWWGG 1 cut(s) 152
FaeI CATG 6 cut(s) 156, 855, 915, 1313, 1723, 1842
FalI AAGNNNNNCTT 4 cut(s) 1116, 1148, 1230, 1262
FaqI GGGAC 1 cut(s) 668
FatI CATG 6 cut(s) 152, 851, 911, 1309, 1719, 1838
FauNDI CATATG 1 cut(s) 16
FbaI TGATCA 1 cut(s) 547
Fnu4HI GCNGC 2 cut(s) 1173, 1521
FokI GGATG 6 cut(s) 777, 872, 1208, 1319, 1395, 1673
FriOI GRGCYC 1 cut(s) 208
Fsp4HI GCNGC 2 cut(s) 1173, 1521
FspBI CTAG 9 cut(s) 119, 141, 194, 299, 693, 917, 1382, 1436, 1494
GluI GCNGC 2 cut(s) 1173, 1521
GsuI CTGGAG 1 cut(s) 831
HgaI GACGC 1 cut(s) 951
Hin1II CATG 6 cut(s) 156, 855, 915, 1313, 1723, 1842
HindIII AAGCTT 1 cut(s) 891
HinfI GANTC 5 cut(s) 435, 648, 935, 984, 1378
HphI GGTGA 2 cut(s) 1348, 1519
Hpy166II GTNNAC 1 cut(s) 511
Hpy188I TCNGA 8 cut(s) 180, 190, 404, 454, 538, 784, 967, 974
Hpy188III TCNNGA 7 cut(s) 110, 119, 693, 722, 952, 1124, 1436
Hpy8I GTNNAC 1 cut(s) 511
HpyAV CCTTC 6 cut(s) 175, 257, 409, 459, 1424, 1737
HpyCH4III ACNGT 2 cut(s) 805, 1351
HpyCH4V TGCA 7 cut(s) 96, 813, 1229, 1271, 1332, 1523, 1826
HpyF3I CTNAG 4 cut(s) 652, 1039, 1059, 1363
Hsp92II CATG 6 cut(s) 156, 855, 915, 1313, 1723, 1842
Ksp22I TGATCA 1 cut(s) 547
Kzo9I GATC 4 cut(s) 112, 547, 1129, 1585
LmnI GCTCC 2 cut(s) 203, 211
LpnPI CCDG 9 cut(s) 324, 541, 735, 861, 939, 945, 1026, 1029, 1741
Lsp1109I GCAGC 2 cut(s) 1184, 1507
LweI GCATC 3 cut(s) 850, 949, 1341
MaeI CTAG 9 cut(s) 119, 141, 194, 299, 693, 917, 1382, 1436, 1494
MaeIII GTNAC 1 cut(s) 1354
MalI GATC 4 cut(s) 114, 549, 1131, 1587
MboI GATC 4 cut(s) 112, 547, 1129, 1585
MboII GAAGA 2 cut(s) 107, 1595
MfeI CAATTG 3 cut(s) 504, 699, 1022
MflI RGATCY 2 cut(s) 112, 1585
MhlI GDGCHC 1 cut(s) 208
MlyI GAGTC 2 cut(s) 429, 944
MmeI TCCRAC 1 cut(s) 990
MnlI CCTC 7 cut(s) 194, 828, 855, 1048, 1222, 1586, 1741
MslI CAYNNNNRTG 1 cut(s) 1314
MunI CAATTG 3 cut(s) 504, 699, 1022
Mva1269I GAATGC 1 cut(s) 1271
NcoI CCATGG 1 cut(s) 152
NdeI CATATG 1 cut(s) 16
NdeII GATC 4 cut(s) 112, 547, 1129, 1585
NlaIII CATG 6 cut(s) 156, 855, 915, 1313, 1723, 1842
NlaIV GGNNCC 2 cut(s) 1052, 1387
NmuCI GTSAC 1 cut(s) 1354
NspV TTCGAA 2 cut(s) 1513, 1785
PcsI WCGNNNNNNNCGW 1 cut(s) 408
PctI GAATGC 1 cut(s) 1271
PfeI GAWTC 3 cut(s) 648, 984, 1378
PkrI GCNGC 2 cut(s) 1174, 1522
PleI GAGTC 2 cut(s) 429, 943
PpsI GAGTC 2 cut(s) 429, 943
PshBI ATTAAT 1 cut(s) 222
Psp124BI GAGCTC 1 cut(s) 208
PspN4I GGNNCC 2 cut(s) 1052, 1387
PsuI RGATCY 2 cut(s) 112, 1585
RsaI GTAC 2 cut(s) 377, 676
RsaNI GTAC 2 cut(s) 376, 675
RseI CAYNNNNRTG 1 cut(s) 1314
SacI GAGCTC 1 cut(s) 208
SatI GCNGC 2 cut(s) 1173, 1521
Sau3AI GATC 4 cut(s) 112, 547, 1129, 1585
SchI GAGTC 2 cut(s) 429, 944
SduI GDGCHC 1 cut(s) 208
SfaNI GCATC 3 cut(s) 850, 949, 1341
SfcI CTRYAG 2 cut(s) 678, 1098
SfuI TTCGAA 2 cut(s) 1513, 1785
SmiMI CAYNNNNRTG 1 cut(s) 1314
SpeI ACTAGT 1 cut(s) 298
SspI AATATT 2 cut(s) 92, 544
SspMI CTAG 9 cut(s) 119, 141, 194, 299, 693, 917, 1382, 1436, 1494
SstI GAGCTC 1 cut(s) 208
StyI CCWWGG 1 cut(s) 152
TaaI ACNGT 2 cut(s) 805, 1351
TaqI TCGA 3 cut(s) 951, 1513, 1785
TatI WGTACW 1 cut(s) 375
TfiI GAWTC 3 cut(s) 648, 984, 1378
TscAI CASTG 2 cut(s) 257, 560
TseFI GTSAC 1 cut(s) 1354
TseI GCWGC 2 cut(s) 1172, 1520
Tsp45I GTSAC 1 cut(s) 1354
TspDTI ATGAA 9 cut(s) 33, 86, 93, 347, 485, 741, 1264, 1298, 1443
TspGWI ACGGA 1 cut(s) 872
TspRI CASTG 2 cut(s) 257, 560
VspI ATTAAT 1 cut(s) 222
XapI RAATTY 8 cut(s) 105, 323, 455, 496, 572, 716, 1089, 1649
XbaI TCTAGA 3 cut(s) 118, 692, 1435
XcmI CCANNNNNNNNNTGG 1 cut(s) 1698
XspI CTAG 9 cut(s) 119, 141, 194, 299, 693, 917, 1382, 1436, 1494
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.