RchiOBHm_Chr5g0013181

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0000562
Physical Location & Seq
Forward (+)
8925305 .. 8925713
409 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ29372

Sequence Viewer

Length: 225 bp
ATGACTGGGGGTTCATCTATTGTTGATACTGAGACTGTCTCAGTAACCTCTTCTCCAACCTCTGAGGTTGAGGGGAATCCTAACCAAAGGTTGTGTTCAGTTGTGTTGAACGAATTCAACTATTTGCCATGGTCTCGTGCTGTTACTTTGGCTCTAGGGGGAAGGTCAAAGCTGAGCTTCATAAATGGAAGCTTGGAAGCTCCTGATATCACCTCACCTATGTAA
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 Retrotran_gag_2 Retrotran_gag_3 Retrotrans_gag gag_pre-integrs rve

Protein Analysis

74

Amino Acids

7.82

Weight (kDa)

4.49

Isoelectric Point (pI)

32.03

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 26 - 69 3.7e-15 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)
AcsI RAATTY 1 cut(s) 113
AgsI TTSAA 2 cut(s) 109, 118
AluBI AGCT 4 cut(s) 172, 177, 192, 200
AluI AGCT 4 cut(s) 172, 177, 192, 200
Alw26I GTCTC 3 cut(s) 26, 43, 138
ApoI RAATTY 1 cut(s) 113
Asp700I GAANNNNTTC 1 cut(s) 113
AsuHPI GGTGA 2 cut(s) 202, 207
BauI CACGAG 1 cut(s) 135
BcoDI GTCTC 3 cut(s) 26, 43, 138
BfaI CTAG 1 cut(s) 155
BlpI GCTNAGC 1 cut(s) 173
BmrI ACTGGG 1 cut(s) 15
BmuI ACTGGG 1 cut(s) 15
BplI GAGNNNNNCTC 2 cut(s) 23, 55
Bpu1102I GCTNAGC 1 cut(s) 173
BsaI GGTCTC 1 cut(s) 138
BsaJI CCNNGG 1 cut(s) 128
BsaXI ACNNNNNCTCC 2 cut(s) 37, 67
Bse1I ACTGG 1 cut(s) 10
BseDI CCNNGG 1 cut(s) 128
BseMII CTCAG 4 cut(s) 21, 54, 54, 164
BseNI ACTGG 1 cut(s) 10
BsmAI GTCTC 3 cut(s) 26, 43, 138
Bso31I GGTCTC 1 cut(s) 138
Bsp1720I GCTNAGC 1 cut(s) 173
Bsp19I CCATGG 1 cut(s) 128
BspCNI CTCAG 4 cut(s) 22, 53, 55, 165
BspTNI GGTCTC 1 cut(s) 138
BsrI ACTGG 1 cut(s) 10
BssECI CCNNGG 1 cut(s) 128
BssSI CACGAG 1 cut(s) 135
BssT1I CCWWGG 1 cut(s) 128
Bst2BI CACGAG 1 cut(s) 135
Bst4CI ACNGT 1 cut(s) 37
Bst6I CTCTTC 1 cut(s) 55
BstDEI CTNAG 4 cut(s) 30, 40, 63, 173
BstDSI CCRYGG 1 cut(s) 128
BstMAI GTCTC 3 cut(s) 26, 43, 138
BtgI CCRYGG 1 cut(s) 128
CviAII CATG 1 cut(s) 129
CviJI RGCY 5 cut(s) 152, 172, 177, 192, 200
CviKI_1 RGCY 5 cut(s) 152, 172, 177, 192, 200
DdeI CTNAG 4 cut(s) 30, 40, 63, 173
Eam1104I CTCTTC 1 cut(s) 55
EarI CTCTTC 1 cut(s) 55
Eco130I CCWWGG 1 cut(s) 128
Eco31I GGTCTC 1 cut(s) 138
Eco32I GATATC 1 cut(s) 208
EcoRI GAATTC 1 cut(s) 113
EcoRV GATATC 1 cut(s) 208
EcoT14I CCWWGG 1 cut(s) 128
ErhI CCWWGG 1 cut(s) 128
FaeI CATG 1 cut(s) 132
FaiI YATR 3 cut(s) 130, 182, 221
FalI AAGNNNNNCTT 2 cut(s) 161, 193
FatI CATG 1 cut(s) 128
FspBI CTAG 1 cut(s) 155
Hin1II CATG 1 cut(s) 132
HindIII AAGCTT 1 cut(s) 190
HinfI GANTC 1 cut(s) 76
HphI GGTGA 2 cut(s) 202, 207
Hpy188I TCNGA 1 cut(s) 64
Hpy188III TCNNGA 1 cut(s) 203
HpyAV CCTTC 1 cut(s) 156
HpyCH4III ACNGT 1 cut(s) 37
HpyF3I CTNAG 4 cut(s) 30, 40, 63, 173
Hsp92II CATG 1 cut(s) 132
LmnI GCTCC 1 cut(s) 205
LpnPI CCDG 1 cut(s) 216
MaeI CTAG 1 cut(s) 155
MaeIII GTNAC 2 cut(s) 43, 142
MboII GAAGA 1 cut(s) 42
MluCI AATT 1 cut(s) 113
MmeI TCCRAC 1 cut(s) 80
MnlI CCTC 5 cut(s) 58, 58, 64, 70, 223
MroXI GAANNNNTTC 1 cut(s) 113
NcoI CCATGG 1 cut(s) 128
NlaIII CATG 1 cut(s) 132
PdmI GAANNNNTTC 1 cut(s) 113
PfeI GAWTC 1 cut(s) 76
SgeI CNNG 7 cut(s) 18, 141, 147, 149, 167, 205, 215
Sse9I AATT 1 cut(s) 113
SspMI CTAG 1 cut(s) 155
StyI CCWWGG 1 cut(s) 128
TaaI ACNGT 1 cut(s) 37
TasI AATT 1 cut(s) 113
TfiI GAWTC 1 cut(s) 76
TspDTI ATGAA 1 cut(s) 169
XapI RAATTY 1 cut(s) 113
XmnI GAANNNNTTC 1 cut(s) 113
XspI CTAG 1 cut(s) 155
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.