RchiOBHm_Chr4g0436251

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0015778
Physical Location & Seq
Forward (+)
59585329 .. 59586009
681 bp
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UTR
Exon/CDS
Intron
PRQ40459

Sequence Viewer

Length: 480 bp
ATGTTGCTCCATATACAGCTTCTGATACAGTTCAAGTTGGTAATGGACAAGGTGCTGGGAAGAATCCTATATCAGGGATTGAGTAAACAAGGGATGTACCCCATACCATTTGATCTGCCACTCAAGTTTGGTTCTACATCAACTTCTACTATTCCTAGTTCTTTTTCCAAGACTGCATATGTTGGGAAAACTATAAAAAATTTACTTTGGCATCAAAGACTTGGTCACCCTACTAATGAGGTAGTCAAAAGTATGTTGAAAAAGTGCAAAATTTTTGGTGACCCTACTGTTGATTCGACATCTTGTGAAGCATGCTTGCTTGGTAAATTTCACAAGCTTCCTTTCCCAGTTTCTCAAACAAGAAGTGAAGTACCTTTTGATATAGTGCATTCTGATGTTTGGGGACTTGCTCTTCATTTGTCTTTAGATGGATTTAAGTACTTTGTAATTTTCATAGATGATTGTACTTGGTATACTTAG
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
Retrotran_gag_2 gag_pre-integrs

Protein Analysis

159

Amino Acids

18.04

Weight (kDa)

9.05

Isoelectric Point (pI)

36.75

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
gag_pre-integrs PF13976 63 - 109 3.1e-12 GAG-pre-integrase domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 473
AcsI RAATTY 3 cut(s) 199, 270, 326
AfaI GTAC 4 cut(s) 98, 372, 440, 466
AfiI CCNNNNNNNGG 1 cut(s) 73
AgsI TTSAA 2 cut(s) 34, 259
AluBI AGCT 2 cut(s) 19, 337
AluI AGCT 2 cut(s) 19, 337
AlwNI CAGNNNCTG 1 cut(s) 22
ApoI RAATTY 3 cut(s) 199, 270, 326
ArsI GACNNNNNNTTYG 2 cut(s) 208, 240
AsuHPI GGTGA 2 cut(s) 218, 290
BccI CCATC 1 cut(s) 422
BfaI CTAG 1 cut(s) 156
BmcAI AGTACT 1 cut(s) 440
BmrI ACTGGG 1 cut(s) 341
BmsI GCATC 1 cut(s) 220
BmuI ACTGGG 1 cut(s) 341
BpuEI CTTGAG 1 cut(s) 107
Bsc4I CCNNNNNNNGG 1 cut(s) 73
Bse1I ACTGG 1 cut(s) 347
BseGI GGATG 1 cut(s) 99
BseLI CCNNNNNNNGG 1 cut(s) 73
BseNI ACTGG 1 cut(s) 347
BseYI CCCAGC 1 cut(s) 55
BslFI GGGAC 1 cut(s) 417
BslI CCNNNNNNNGG 1 cut(s) 73
BsmFI GGGAC 1 cut(s) 417
BsmI GAATGC 1 cut(s) 388
Bsp143I GATC 1 cut(s) 112
BspQI GCTCTTC 1 cut(s) 417
BsrI ACTGG 1 cut(s) 347
BssMI GATC 1 cut(s) 112
BssNAI GTATAC 1 cut(s) 474
Bst1107I GTATAC 1 cut(s) 474
Bst4CI ACNGT 2 cut(s) 30, 289
Bst6I CTCTTC 1 cut(s) 417
BstC8I GCNNGC 2 cut(s) 313, 317
BstDEI CTNAG 1 cut(s) 477
BstEII GGTNACC 2 cut(s) 224, 278
BstENI CCTNNNNNAGG 1 cut(s) 71
BstF5I GGATG 1 cut(s) 99
BstKTI GATC 1 cut(s) 115
BstMBI GATC 1 cut(s) 112
BstNSI RCATGY 1 cut(s) 315
BstPI GGTNACC 2 cut(s) 224, 278
BstZ17I GTATAC 1 cut(s) 474
BtsCI GGATG 1 cut(s) 99
Cac8I GCNNGC 2 cut(s) 313, 317
CaiI CAGNNNCTG 1 cut(s) 22
Csp6I GTAC 4 cut(s) 97, 371, 439, 465
CviAII CATG 1 cut(s) 312
CviJI RGCY 2 cut(s) 19, 337
CviKI_1 RGCY 2 cut(s) 19, 337
CviQI GTAC 4 cut(s) 97, 371, 439, 465
DdeI CTNAG 1 cut(s) 477
DpnI GATC 1 cut(s) 114
DpnII GATC 1 cut(s) 112
Eam1104I CTCTTC 1 cut(s) 417
EarI CTCTTC 1 cut(s) 417
Eco91I GGTNACC 2 cut(s) 224, 278
EcoNI CCTNNNNNAGG 1 cut(s) 71
EcoO65I GGTNACC 2 cut(s) 224, 278
FaeI CATG 1 cut(s) 315
FaqI GGGAC 1 cut(s) 417
FatI CATG 1 cut(s) 311
FauNDI CATATG 1 cut(s) 178
FblI GTMKAC 1 cut(s) 473
FokI GGATG 1 cut(s) 106
FspBI CTAG 1 cut(s) 156
GsaI CCCAGC 1 cut(s) 59
Hin1II CATG 1 cut(s) 315
HindIII AAGCTT 1 cut(s) 335
HinfI GANTC 2 cut(s) 63, 293
HphI GGTGA 2 cut(s) 218, 290
Hpy166II GTNNAC 2 cut(s) 86, 474
Hpy188I TCNGA 2 cut(s) 24, 394
Hpy8I GTNNAC 2 cut(s) 86, 474
HpyCH4III ACNGT 2 cut(s) 30, 289
HpyCH4V TGCA 3 cut(s) 176, 267, 388
HpyF3I CTNAG 1 cut(s) 477
Hsp92II CATG 1 cut(s) 315
Kzo9I GATC 1 cut(s) 112
LguI GCTCTTC 1 cut(s) 417
LmnI GCTCC 1 cut(s) 12
LpnPI CCDG 3 cut(s) 41, 59, 360
LweI GCATC 1 cut(s) 220
MaeI CTAG 1 cut(s) 156
MaeIII GTNAC 2 cut(s) 224, 278
MalI GATC 1 cut(s) 114
MboI GATC 1 cut(s) 112
MboII GAAGA 2 cut(s) 72, 404
MluCI AATT 4 cut(s) 199, 270, 326, 447
MnlI CCTC 1 cut(s) 232
MseI TTAA 1 cut(s) 435
MslI CAYNNNNRTG 1 cut(s) 393
Mva1269I GAATGC 1 cut(s) 388
NdeI CATATG 1 cut(s) 178
NdeII GATC 1 cut(s) 112
NlaIII CATG 1 cut(s) 315
NmuCI GTSAC 2 cut(s) 224, 278
NspI RCATGY 1 cut(s) 315
PaeI GCATGC 1 cut(s) 315
PciSI GCTCTTC 1 cut(s) 417
PctI GAATGC 1 cut(s) 388
PfeI GAWTC 2 cut(s) 63, 293
PflFI GACNNNGTC 1 cut(s) 222
PspEI GGTNACC 2 cut(s) 224, 278
PspFI CCCAGC 1 cut(s) 55
PstNI CAGNNNCTG 1 cut(s) 22
PsyI GACNNNGTC 1 cut(s) 222
RsaI GTAC 4 cut(s) 98, 372, 440, 466
RsaNI GTAC 4 cut(s) 97, 371, 439, 465
RseI CAYNNNNRTG 1 cut(s) 393
SapI GCTCTTC 1 cut(s) 417
SaqAI TTAA 1 cut(s) 435
Sau3AI GATC 1 cut(s) 112
ScaI AGTACT 1 cut(s) 440
SetI ASST 5 cut(s) 21, 54, 243, 339, 376
SfaNI GCATC 1 cut(s) 220
SmiMI CAYNNNNRTG 1 cut(s) 393
SmlI CTYRAG 1 cut(s) 122
SmoI CTYRAG 1 cut(s) 122
SphI GCATGC 1 cut(s) 315
Sse9I AATT 4 cut(s) 199, 270, 326, 447
SspMI CTAG 1 cut(s) 156
TaaI ACNGT 2 cut(s) 30, 289
TaqI TCGA 1 cut(s) 296
TasI AATT 4 cut(s) 199, 270, 326, 447
TatI WGTACW 2 cut(s) 438, 464
TfiI GAWTC 2 cut(s) 63, 293
Tru1I TTAA 1 cut(s) 435
Tru9I TTAA 1 cut(s) 435
TseFI GTSAC 2 cut(s) 224, 278
Tsp45I GTSAC 2 cut(s) 224, 278
TspDTI ATGAA 2 cut(s) 404, 442
Tth111I GACNNNGTC 1 cut(s) 222
XagI CCTNNNNNAGG 1 cut(s) 71
XapI RAATTY 3 cut(s) 199, 270, 326
XceI RCATGY 1 cut(s) 315
XmiI GTMKAC 1 cut(s) 473
XspI CTAG 1 cut(s) 156
ZrmI AGTACT 1 cut(s) 440
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.