PGBD2 (piggyBac transposable element derived 2)

Gene: PGBD2 (piggyBac transposable element derived 2) Chlorocebus sabaeus

Analyze

Symbol:

PGBD2

Name:

piggyBac transposable element derived 2

RGD ID:

18701715

Description:

ENCODES a protein that exhibits sequence-specific DNA binding (inferred); ASSOCIATED WITH developmental and epileptic encephalopathy 54 (ortholog); genetic disease (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

piggyBac transposable element-derived protein 2

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	25	85,759,173 - 85,764,661 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	25	85,746,168 - 85,767,885 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666055	88,342,765 - 88,393,630 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

developmental and epileptic encephalopathy 54 (ISO)

genetic disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Molecular Function

sequence-specific DNA binding (IEA)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

PGBD2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	25	85,759,173 - 85,764,661 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	25	85,746,168 - 85,767,885 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666055	88,342,765 - 88,393,630 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

PGBD2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	248,872,851 - 248,930,191 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	248,906,196 - 248,919,946 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	249,200,434 - 249,213,345 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	247,167,065 - 247,179,968 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	245,410,193 - 245,423,099	NCBI
Celera	1	222,361,518 - 222,374,710 (+)	NCBI		Celera
Cytogenetic Map	1	q44	NCBI
HuRef	1	219,441,450 - 219,454,481 (+)	NCBI		HuRef
CHM1_1	1	250,472,741 - 250,485,645 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	248,311,348 - 248,368,818 (+)	NCBI		T2T-CHM13v2.0

Pgbd2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955418	29,951,644 - 29,985,188 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955418	29,951,478 - 29,985,800 (+)	NCBI	ChiLan1.0	ChiLan1.0

PGBD2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	1	120,162 - 139,482 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	390,179 - 409,517 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	224,517,353 - 224,567,161 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3

PGBD2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	16	13,800,934 - 13,839,690 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	16	13,811,208 - 13,822,017 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	16	11,386,859 - 11,408,080 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	16	13,778,661 - 13,800,077 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	16	13,778,740 - 13,804,334 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	16	10,918,813 - 10,940,213 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	16	13,312,667 - 13,439,760 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	16	13,489,124 - 13,574,951 (+)	NCBI		UU_Cfam_GSD_1.0

LOC101959387
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024407213	121,087,037 - 121,095,447 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936739	2,003,015 - 2,011,504 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PGBD2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	52,170,931 - 52,211,098 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	52,169,715 - 52,211,373 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

Pgbd2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624743	806,296 - 813,107 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624743	806,595 - 811,721 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	endocrine system	hemolymphoid system	nervous system
High
Medium		4	10
Low	36	16	50
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_007990148	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_007990149	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_037986142	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_037986143	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000006964 ⟹ ENSCSAP00000005160

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	25	85,746,168 - 85,767,885 (+)	Ensembl

RefSeq Acc Id:

XM_007990148 ⟹ XP_007988339

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	25	85,759,173 - 85,764,661 (+)	NCBI
Vero_WHO_p1.0	NW_023666055	88,374,172 - 88,393,630 (+)	NCBI

Sequence:

show sequence

GTTCTTAGACTCTGTGAGTAAAGACAGCTTCGTCTTCCCAGTTCATCATGGCTTCAACATCCAG
AGATGTCATTGCTGGGAGAGGTACCCACTCAAAGGTGAAGTCTGCAAAGCTGCTCGAGGTTCTG
AATGCTATGGAGGAGGAAGAGTCCAACAGCAACAGGGAAGAGATTTTCATTGCACCTCCCGACA
ATGCTGCGGGGGAATTCACTGATGAGGACTCAGGTGATGAAGACAGCCAGCGAGGTGCTCACCT
GCCTGGCAGTGTGCTGCATGCTTCAGTCCTGTGTGAGGACTCTGGCACCGGCGAGGATAACGAT
GACCTGGAGCTGCAACCAGCCAAGAAGAGGCAGAAAGCAGTTGTGAAACCTCAGCGCATTTGGA
CAAAAAGAGATATTCGTCCAGACTTTGGCAGTTGGACGGCATCAGATCCTCATATTGAGGATCT
GAAAAGCCAAGAGCTGAGTCCTGTGGGCCTTTTTGAGTTGTTTTTCGATGAAGGAACAATTAAT
TTCATTGTTAATGAAACCAATCGTTATGCTTGGCAGAAAAATGTCAATCTGAGTCTTACGGCTC
AGGAATTGAAGTGTGTTTTGGGCATTTTGATTTTAAGTGGGTACATCTCTTACCCAAGGAGAAG
GATGTTCTGGGAAACCTCTCCTGATTCACATCATCATCTTGTGGCCGATGCAATTAGAAGGGAC
AGATTCGAACTAATCTTCTCATACTTACATTTTGCAGATAACAACGAACTTGATGCAGGTGATA
GGTTTGCCAAGGTCAGACCTCTCATCATCCGGATGAACTGCAATTTCCAGAAGCACGCACCCCT
GGAAGAGTTCTACAGCTTTGGCGAGTCTATGTGTGAGTACTTTGGGCACCGGGGCTCCAAGCAG
CTGCACAGGGGGAAGCCTGTGCGACTTGGCTACAAGATTTGGTGTGGGACAACCAGCAGAGGCT
ACTTGGTGTGGTTCGAGCCCTCACAGGGCACACTTTTTACCAAGCCAGACAGGAGCCTGGATCT
AGGAGGCAGTATGGTAATAAAATTTGTGGATGCGCTTCAGGAGCGTGGTTTTCTGCCATATCAC
ATATTTTTTGACAAGGTTTTTACAAGTGTTAAACTGATGTCCATTTTGAGGAAAAAGGGGGTGA
AGGCCACAGGAACTGTTCGTGAGTACAGGACTGAGCGATGTCCCCTAAAAGACCCCAAAGAACT
GAAAAAAATGAAGAGGGGTTCATTTGATTACAAAGTCGATGAGAGTGAGGAGATCATCGTGTGC
CGCTGGCACGATAGCAGCGTGGTCAACATCTGCTCCAATGCCGTGGGCATAGAGCCAGTGAGGC
TGACCAGTCGTCACTCTGGAGCAACTAAAACGCGGACTCAGGTCCACCAGCCATCACTGGTGAA
GCTGTATCAGGAGAAGGTGGGCGGTGTTGGTAGGATGGACCAGAATATTGCCAAGTACAAGGTG
AAGATCCGAGGCATGAAGTGGTACTCAAGCTTTATTGGCTATGTCATTGATGCTGCCCTCAACA
ATGCATGGCAGCTGCACAGGATCTGCTGCCAAGATGCCCAGGTGGACCTCCTTGCCTTCCGGAG
ATACGTCGCCTGTGTGTACCTGGAGAGCAATGCTGACACGACCTCTCAAGGGAGGCGAAGCAGG
CGGTTGGAGACTGAGAGCCGCTTTGATATGGTTGGACACTGGATTATCCACCAGGACAAGAGGA
CCCGATGTGCCCTCTGCCACTCGCAGACCAACACCCGGTGCGAGAAGTGCCAGAAGGGTGTCCA
TGCCAAGTGCTTCAGGGAGTACCATATCCGGTGACATCAGGAGACATGCTTGTTTGGTTTATAA
TGAGATGTTCACAGTTAAATAACAGATAGCAGTTGATCACTTCTGTTTTGTGTTGGAAAAAAGA
CCTGAATTTCTGATGACTTGGTTTTCTCTTTTCTCCCTACCCACAATTGTTATCTTTTTTATTG
TGTTCTATTATGCCTACATGTGATATCAATTAATATTTATATTCATTTATATTTATATTTTTGA
ACTTATTTATTTAAAGTTGTGGGACCACTTTTTATTCAGATAAAAGTTGTGCTTTGGGGTATAT
TTGAATCCTAGGAAGAAGAATCAGAGGAAAACTTGCAAGAACAGTAAGAAGACTTGACCATTGC
ATGCCATGGTTTATAATCTAACATAGGCAATAGTGTATAAATATCATGTAAATGTGATGGATTT
CTTAATCCTATTTATTTCATATTAATCTAAGTTTATCAAACTTTCCAAGGATAGATAATCTGCC
TTGTATTTAGTCAGAGGGCTAGAGTTTCAGAGTTCATATTTTCTTGATAAAAATATTTTCCTAA
TACACATATATCAATGTGGGATTCATTTTATAAAAAATTATTTTTTTAA

hide sequence

RefSeq Acc Id:

XM_007990149 ⟹ XP_007988340

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	25	85,759,236 - 85,764,661 (+)	NCBI
Vero_WHO_p1.0	NW_023666055	88,374,172 - 88,393,630 (+)	NCBI

Sequence:

show sequence

GTTTCTGTTATCTGGAGTGATGACAGCAGCATCTGGATTCATCACTAAAGGGGATCCTCTGTTT
TAGAACACGTCATTTAAGAAGGAAAGGAGAGATGTCATTGCTGGGAGAGGTACCCACTCAAAGG
TGAAGTCTGCAAAGCTGCTCGAGGTTCTGAATGCTATGGAGGAGGAAGAGTCCAACAGCAACAG
GGAAGAGATTTTCATTGCACCTCCCGACAATGCTGCGGGGGAATTCACTGATGAGGACTCAGGT
GATGAAGACAGCCAGCGAGGTGCTCACCTGCCTGGCAGTGTGCTGCATGCTTCAGTCCTGTGTG
AGGACTCTGGCACCGGCGAGGATAACGATGACCTGGAGCTGCAACCAGCCAAGAAGAGGCAGAA
AGCAGTTGTGAAACCTCAGCGCATTTGGACAAAAAGAGATATTCGTCCAGACTTTGGCAGTTGG
ACGGCATCAGATCCTCATATTGAGGATCTGAAAAGCCAAGAGCTGAGTCCTGTGGGCCTTTTTG
AGTTGTTTTTCGATGAAGGAACAATTAATTTCATTGTTAATGAAACCAATCGTTATGCTTGGCA
GAAAAATGTCAATCTGAGTCTTACGGCTCAGGAATTGAAGTGTGTTTTGGGCATTTTGATTTTA
AGTGGGTACATCTCTTACCCAAGGAGAAGGATGTTCTGGGAAACCTCTCCTGATTCACATCATC
ATCTTGTGGCCGATGCAATTAGAAGGGACAGATTCGAACTAATCTTCTCATACTTACATTTTGC
AGATAACAACGAACTTGATGCAGGTGATAGGTTTGCCAAGGTCAGACCTCTCATCATCCGGATG
AACTGCAATTTCCAGAAGCACGCACCCCTGGAAGAGTTCTACAGCTTTGGCGAGTCTATGTGTG
AGTACTTTGGGCACCGGGGCTCCAAGCAGCTGCACAGGGGGAAGCCTGTGCGACTTGGCTACAA
GATTTGGTGTGGGACAACCAGCAGAGGCTACTTGGTGTGGTTCGAGCCCTCACAGGGCACACTT
TTTACCAAGCCAGACAGGAGCCTGGATCTAGGAGGCAGTATGGTAATAAAATTTGTGGATGCGC
TTCAGGAGCGTGGTTTTCTGCCATATCACATATTTTTTGACAAGGTTTTTACAAGTGTTAAACT
GATGTCCATTTTGAGGAAAAAGGGGGTGAAGGCCACAGGAACTGTTCGTGAGTACAGGACTGAG
CGATGTCCCCTAAAAGACCCCAAAGAACTGAAAAAAATGAAGAGGGGTTCATTTGATTACAAAG
TCGATGAGAGTGAGGAGATCATCGTGTGCCGCTGGCACGATAGCAGCGTGGTCAACATCTGCTC
CAATGCCGTGGGCATAGAGCCAGTGAGGCTGACCAGTCGTCACTCTGGAGCAACTAAAACGCGG
ACTCAGGTCCACCAGCCATCACTGGTGAAGCTGTATCAGGAGAAGGTGGGCGGTGTTGGTAGGA
TGGACCAGAATATTGCCAAGTACAAGGTGAAGATCCGAGGCATGAAGTGGTACTCAAGCTTTAT
TGGCTATGTCATTGATGCTGCCCTCAACAATGCATGGCAGCTGCACAGGATCTGCTGCCAAGAT
GCCCAGGTGGACCTCCTTGCCTTCCGGAGATACGTCGCCTGTGTGTACCTGGAGAGCAATGCTG
ACACGACCTCTCAAGGGAGGCGAAGCAGGCGGTTGGAGACTGAGAGCCGCTTTGATATGGTTGG
ACACTGGATTATCCACCAGGACAAGAGGACCCGATGTGCCCTCTGCCACTCGCAGACCAACACC
CGGTGCGAGAAGTGCCAGAAGGGTGTCCATGCCAAGTGCTTCAGGGAGTACCATATCCGGTGAC
ATCAGGAGACATGCTTGTTTGGTTTATAATGAGATGTTCACAGTTAAATAACAGATAGCAGTTG
ATCACTTCTGTTTTGTGTTGGAAAAAAGACCTGAATTTCTGATGACTTGGTTTTCTCTTTTCTC
CCTACCCACAATTGTTATCTTTTTTATTGTGTTCTATTATGCCTACATGTGATATCAATTAATA
TTTATATTCATTTATATTTATATTTTTGAACTTATTTATTTAAAGTTGTGGGACCACTTTTTAT
TCAGATAAAAGTTGTGCTTTGGGGTATATTTGAATCCTAGGAAGAAGAATCAGAGGAAAACTTG
CAAGAACAGTAAGAAGACTTGACCATTGCATGCCATGGTTTATAATCTAACATAGGCAATAGTG
TATAAATATCATGTAAATGTGATGGATTTCTTAATCCTATTTATTTCATATTAATCTAAGTTTA
TCAAACTTTCCAAGGATAGATAATCTGCCTTGTATTTAGTCAGAGGGCTAGAGTTTCAGAGTTC
ATATTTTCTTGATAAAAATATTTTCCTAATACACATATATCAATGTGGGATTCATTTTATAAAA
AATTATTTTTTTAA

hide sequence

RefSeq Acc Id:

XM_037986142 ⟹ XP_037842070

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
Vero_WHO_p1.0	NW_023666055	88,342,765 - 88,393,630 (+)	NCBI

RefSeq Acc Id:

XM_037986143 ⟹ XP_037842071

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
Vero_WHO_p1.0	NW_023666055	88,374,172 - 88,393,630 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_007988339	(Get FASTA)	NCBI Sequence Viewer
	XP_007988340	(Get FASTA)	NCBI Sequence Viewer
	XP_037842070	(Get FASTA)	NCBI Sequence Viewer
	XP_037842071	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000005160
	ENSCSAP00000005160.1

RefSeq Acc Id:	XP_007988339 ⟸ XM_007990148
- Peptide Label:	isoform X1
- UniProtKB:	A0A0D9R971 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_007988340 ⟸ XM_007990149
- Peptide Label:	isoform X2

RefSeq Acc Id:

ENSCSAP00000005160 ⟸ ENSCSAT00000006964

RefSeq Acc Id:	XP_037842070 ⟸ XM_037986142
- Peptide Label:	isoform X1
- UniProtKB:	A0A0D9R971 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_037842071 ⟸ XM_037986143
- Peptide Label:	isoform X3

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000008894	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000006964.1	UniProtKB/TrEMBL
InterPro	PGBD	UniProtKB/TrEMBL
KEGG Report	csab:103230991	UniProtKB/TrEMBL
NCBI Gene	PGBD2	ENTREZGENE
PANTHER	DDE_TNP_1_7 DOMAIN-CONTAINING PROTEIN	UniProtKB/TrEMBL
	PIGGYBAC TRANSPOSABLE ELEMENT-DERIVED PROTEIN 2-RELATED	UniProtKB/TrEMBL
Pfam	DDE_Tnp_1_7	UniProtKB/TrEMBL
UniProt	A0A0D9R971	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar