RchiOBHm_Chr4g0421211

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000703
Physical Location & Seq
Forward (+)
46862000 .. 46864108
2109 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ39087

Sequence Viewer

Length: 525 bp
ATGTCAATGGGGACTGACCAGTCAATAGATGATTTTCATGCTAGACTTATCAATGTGACAAGTCAATGTTATAGCCTTGGTGATCCGTTTGAAGAACATCGTATTGTTAAGAAATTCCTTAGGTCTCTTCCACCTAGTTTTCAGTCCAAGCAAACAGCCATAGAGGAAGCCCAAGACATTGACACTTATTCCTTAGATGAACTTGTGGGGAATCTCAAAACTTTTGAGATGAGGGTTAATCCTGCAAAAAAGGTGAAAAGTGTTGCCTTTAATTCTGTCAAAAAGGAAGAAGAAACTGAGGTTAGCACAGAAGACTTGGCCTATTTGACTAAACAGTTCAAAAAATTCTTCAAGTTTAGAAACTCTAGTGGTCAAGGCTCAAAAATTATTTTGACTCTAGTTCAAAACGCAGCTTGCCTTCTGAAAATTCTTTTGAAAGAAACTCCAAATCAAACAAAATTTTCCAAAAGAAAAACTTCAGTGAAAAACCTAAATGTTTTGAGTGTGGTGGGATTGGGCATCTAG
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 gag_pre-integrs rve zf-CCHC

Protein Analysis

174

Amino Acids

19.64

Weight (kDa)

9.28

Isoelectric Point (pI)

42.84

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 3 - 80 7e-08 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 19
AclWI GGATC 1 cut(s) 77
AcsI RAATTY 4 cut(s) 113, 344, 426, 458
AcuI CTGAAG 1 cut(s) 462
AgsI TTSAA 5 cut(s) 92, 340, 352, 404, 436
AluBI AGCT 1 cut(s) 413
AluI AGCT 1 cut(s) 413
Alw26I GTCTC 1 cut(s) 129
AlwI GGATC 1 cut(s) 77
AoxI GGCC 1 cut(s) 318
ApeKI GCWGC 1 cut(s) 410
ApoI RAATTY 4 cut(s) 113, 344, 426, 458
Asp700I GAANNNNTTC 1 cut(s) 475
AsuHPI GGTGA 2 cut(s) 92, 265
AxyI CCTNAGG 1 cut(s) 119
BbsI GAAGAC 1 cut(s) 318
BbvI GCAGC 1 cut(s) 422
BcoDI GTCTC 1 cut(s) 129
BfaI CTAG 5 cut(s) 42, 135, 366, 398, 523
BisI GCNGC 1 cut(s) 411
BlsI GCNGC 1 cut(s) 412
BpiI GAAGAC 1 cut(s) 318
BsaI GGTCTC 1 cut(s) 129
BsaJI CCNNGG 1 cut(s) 76
Bse1I ACTGG 1 cut(s) 19
Bse21I CCTNAGG 1 cut(s) 119
BseDI CCNNGG 1 cut(s) 76
BseMII CTCAG 1 cut(s) 288
BseNI ACTGG 1 cut(s) 19
BseXI GCAGC 1 cut(s) 422
BshFI GGCC 1 cut(s) 320
BslFI GGGAC 1 cut(s) 25
BsmAI GTCTC 1 cut(s) 129
BsmFI GGGAC 1 cut(s) 25
BsnI GGCC 1 cut(s) 320
Bso31I GGTCTC 1 cut(s) 129
Bsp143I GATC 1 cut(s) 82
BspANI GGCC 1 cut(s) 320
BspCNI CTCAG 1 cut(s) 289
BspPI GGATC 1 cut(s) 77
BspTNI GGTCTC 1 cut(s) 129
BsrI ACTGG 1 cut(s) 19
BssECI CCNNGG 1 cut(s) 76
BssMI GATC 1 cut(s) 82
BssT1I CCWWGG 1 cut(s) 76
Bst4CI ACNGT 1 cut(s) 336
Bst6I CTCTTC 1 cut(s) 132
BstC8I GCNNGC 1 cut(s) 415
BstDEI CTNAG 3 cut(s) 119, 193, 297
BstKTI GATC 1 cut(s) 85
BstMAI GTCTC 1 cut(s) 129
BstMBI GATC 1 cut(s) 82
BstV1I GCAGC 1 cut(s) 422
BstV2I GAAGAC 1 cut(s) 318
Bsu36I CCTNAGG 1 cut(s) 119
BsuRI GGCC 1 cut(s) 320
BtsIMutI CAGTG 1 cut(s) 486
Cac8I GCNNGC 1 cut(s) 415
CviAII CATG 1 cut(s) 38
CviJI RGCY 6 cut(s) 75, 158, 170, 320, 378, 413
CviKI_1 RGCY 6 cut(s) 75, 158, 170, 320, 378, 413
DdeI CTNAG 3 cut(s) 119, 193, 297
DpnI GATC 1 cut(s) 84
DpnII GATC 1 cut(s) 82
DrdI GACNNNNNNGTC 1 cut(s) 19
DseDI GACNNNNNNGTC 1 cut(s) 19
Eam1104I CTCTTC 1 cut(s) 132
EarI CTCTTC 1 cut(s) 132
Eco130I CCWWGG 1 cut(s) 76
Eco31I GGTCTC 1 cut(s) 129
Eco57I CTGAAG 1 cut(s) 462
Eco81I CCTNAGG 1 cut(s) 119
EcoT14I CCWWGG 1 cut(s) 76
ErhI CCWWGG 1 cut(s) 76
FaeI CATG 1 cut(s) 41
FaiI YATR 3 cut(s) 39, 72, 161
FalI AAGNNNNNCTT 2 cut(s) 460, 492
FaqI GGGAC 1 cut(s) 25
FatI CATG 1 cut(s) 37
Fnu4HI GCNGC 1 cut(s) 411
Fsp4HI GCNGC 1 cut(s) 411
FspBI CTAG 5 cut(s) 42, 135, 366, 398, 523
GluI GCNGC 1 cut(s) 411
HaeIII GGCC 1 cut(s) 320
Hin1II CATG 1 cut(s) 41
HinfI GANTC 2 cut(s) 211, 394
HphI GGTGA 2 cut(s) 92, 265
Hpy188I TCNGA 1 cut(s) 423
HpyAV CCTTC 1 cut(s) 428
HpyCH4III ACNGT 1 cut(s) 336
HpyCH4V TGCA 1 cut(s) 245
HpyF3I CTNAG 3 cut(s) 119, 193, 297
Hsp92II CATG 1 cut(s) 41
Kzo9I GATC 1 cut(s) 82
LpnPI CCDG 2 cut(s) 32, 255
Lsp1109I GCAGC 1 cut(s) 422
MaeI CTAG 5 cut(s) 42, 135, 366, 398, 523
MaeIII GTNAC 1 cut(s) 55
MalI GATC 1 cut(s) 84
MboI GATC 1 cut(s) 82
MboII GAAGA 6 cut(s) 104, 119, 299, 302, 323, 340
MluCI AATT 6 cut(s) 113, 271, 344, 384, 426, 458
MlyI GAGTC 1 cut(s) 388
MnlI CCTC 3 cut(s) 157, 225, 292
MroXI GAANNNNTTC 1 cut(s) 475
MseI TTAA 3 cut(s) 108, 237, 270
NdeII GATC 1 cut(s) 82
NlaIII CATG 1 cut(s) 41
NmuCI GTSAC 1 cut(s) 55
PdmI GAANNNNTTC 1 cut(s) 475
PfeI GAWTC 1 cut(s) 211
PkrI GCNGC 1 cut(s) 412
PleI GAGTC 1 cut(s) 388
PpsI GAGTC 1 cut(s) 388
SaqAI TTAA 3 cut(s) 108, 237, 270
SatI GCNGC 1 cut(s) 411
Sau3AI GATC 1 cut(s) 82
SchI GAGTC 1 cut(s) 388
SetI ASST 6 cut(s) 125, 136, 255, 303, 415, 492
Sse9I AATT 6 cut(s) 113, 271, 344, 384, 426, 458
SspMI CTAG 5 cut(s) 42, 135, 366, 398, 523
StyI CCWWGG 1 cut(s) 76
TaaI ACNGT 1 cut(s) 336
TasI AATT 6 cut(s) 113, 271, 344, 384, 426, 458
TfiI GAWTC 1 cut(s) 211
Tru1I TTAA 3 cut(s) 108, 237, 270
Tru9I TTAA 3 cut(s) 108, 237, 270
TscAI CASTG 1 cut(s) 486
TseFI GTSAC 1 cut(s) 55
TseI GCWGC 1 cut(s) 410
Tsp45I GTSAC 1 cut(s) 55
TspDTI ATGAA 2 cut(s) 26, 213
TspGWI ACGGA 1 cut(s) 75
TspRI CASTG 1 cut(s) 486
XapI RAATTY 4 cut(s) 113, 344, 426, 458
XmnI GAANNNNTTC 1 cut(s) 475
XspI CTAG 5 cut(s) 42, 135, 366, 398, 523
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.