RTL3 (retrotransposon Gag like 3)

Gene: RTL3 (retrotransposon Gag like 3) Sus scrofa

Analyze

Symbol:

RTL3

Name:

retrotransposon Gag like 3

RGD ID:

14150389

Description:

ASSOCIATED WITH autistic disorder (ortholog); genetic disease (ortholog); syndromic X-linked intellectual disability Lubs type (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

ZCCHC5; zinc finger CCHC domain-containing protein 5; zinc finger CCHC-type containing 5

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	X	62,725,700 - 62,727,236 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	71,813,713 - 71,815,249 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

genetic disease (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

References

Genomics

Comparative Map Data

RTL3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	X	62,725,700 - 62,727,236 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	71,813,713 - 71,815,249 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RTL3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	X	78,656,068 - 78,659,328 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	X	78,656,068 - 78,659,328 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	X	77,911,565 - 77,914,825 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	77,798,222 - 77,801,481 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	X	77,717,710 - 77,720,970	NCBI
Celera	X	78,152,142 - 78,155,399 (-)	NCBI		Celera
Cytogenetic Map	X	q21.1	NCBI
HuRef	X	71,491,595 - 71,494,852 (-)	NCBI		HuRef
CHM1_1	X	77,804,581 - 77,807,838 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	X	77,092,886 - 77,096,144 (-)	NCBI		T2T-CHM13v2.0

Rtl3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	105,880,688 - 105,884,145 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	105,880,688 - 105,884,250 (-)	Ensembl		GRCm39 Ensembl
GRCm38	X	106,837,082 - 106,840,539 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	106,837,082 - 106,840,644 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	104,032,421 - 104,035,982 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	X	103,039,801 - 103,043,362 (-)	NCBI		MGSCv36	mm8
Celera	X	93,683,649 - 93,687,210 (-)	NCBI		Celera
Cytogenetic Map	X	D	NCBI
cM Map	X	47.37	NCBI

Rtl3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	76,020,183 - 76,023,848 (-)	NCBI		GRCr8
mRatBN7.2	X	71,947,343 - 71,951,008 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	71,948,253 - 71,950,121 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	X	73,451,623 - 73,455,278 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	76,963,512 - 76,967,177 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	74,531,782 - 74,535,437 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	77,953,574 - 77,957,261 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	77,954,484 - 77,956,352 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	78,149,884 - 78,153,576 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	95,091,549 - 95,093,417 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	X	73,247,794 - 73,251,481 (-)	NCBI		Celera
Cytogenetic Map	X	q22	NCBI

RTL3
(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	X	78,196,617 - 78,198,044 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	X	78,200,228 - 78,201,655 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	X	67,797,133 - 67,798,613 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	X	77,906,629 - 77,909,100 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

RTL3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	60,668,592 - 60,670,164 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	51,680,593 - 51,682,165 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	X	61,921,600 - 61,923,172 (-)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	X	59,612,513 - 59,614,085 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	X	61,222,822 - 61,224,394 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	X	60,810,866 - 60,812,438 (-)	NCBI		UU_Cfam_GSD_1.0

Rtl3
(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	X	54,409,680 - 54,413,340 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936547	731,006 - 732,745 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936547	730,937 - 732,945 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RTL3
(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	X	67,686,831 - 67,690,932 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666067	13,759,308 - 13,760,756 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in RTL3
31 total Variants

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003135208	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000117	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU407122	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_003135208 ⟹ XP_003135256

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	X	62,725,700 - 62,727,236 (-)	NCBI

Sequence:

show sequence

ATGGTAGAGAACTTAGCAGCCTCCTATATTGCTCTGAAATTGGAGAATGAAATTCTGCAGGCTC
AAGTGCAGTGGCTGATGGAGGAAAATGCTGCCTTGCAGTCTCAGATTCCAGAGCTCCAGAAGCC
CTAAGAAGCCAAAGAGGATGAACCACTCCAGAAGCCCTCAAAGGCCCAGGAGCCCCAGAGACCC
CCAGAGCCCCTGGACTTGCCAGAAACCTTGGGGTCCCAAGAACCCCCAGAGGTCGAGACACAGA
AGCCCAGAGAATCTCAGGACTTCCCATTCTGGGAGCCCCTAACAGCCCAGGAGCCCAAGAAGTC
CTTGGAGCCCCCAGCAGCTCTGGAACCCCTGAAGCCCCCAGCTACTGAAGATCCCCAGGAACCT
TTAATGGTCCACAAACTCTCAGGAGCATGGGAGTCCCAAAAATGCCCAGGATGCCAGGATTCCA
CAGTGGCACAGGAGCCTGAGATTTCAGAGCCCCAGTATCCCCCAAATGTCCAGGAGCCTCAGGA
GATACCAGAATCCCAGGAGACCTCAATACATCTGGAGTTCCTTGAACTTNACAGCCCCCAGGAG
CTCCTGGATCTTTCAGATGCCCAGGAGTTCCTAGGGCTCTTAGCACCCCAAGAGTACCTTAACA
GCCTAACAGCTGCTGAGACAGCAGCTTCAGAGTTTCCGCAGTCCTCCAGTTGGCTAGAGCCTGA
AGCCTTCCCCCTAGAATACCCCTTAGTCTTCAATGGGGATGCCCAGAAGCTTCCTGAGTTTCTG
GTTCAATTGAATAGTTACATGAGAGTCAGAGGGCACATGTATCCCACCAAAGCAGGCCTGGTAA
GCTTTGTTGGCAACTGCTTCTCAGGTGAAGCAGGAAAGTGGTTCCATCCCATAGTAAATACTCA
AAGCCCCCTGCTGGAGCAATTTGAAAGTTTTATACAAGTGTTCCAAGATACTTTTGACAATCCA
GAAAACATGGAAGATTCCAACCACCATATCCGTCAACTCTGCCAAGGGGGGGACCACATCCACC
AGTATGCCATTCACTTCCACTTCATTGCTCAAGAGATAAAATGGAATGAAAGCACTCTTTGCAT
TCAATTTCAGGAAGGGCATGCCAGGTCTATCCAAGAACTGTCTCACACAAGCCCAGCCACCAAC
CTATCTGATCTGATCACCCAATGTATCACCCTAGAAGAGAAGCTAAATGATAAGCCTGATCTAA
GTCCACAAGAGGCAAGTCCCTCTGAGGAGAAATTAGATCTTGATAGTCCACCAGCTGAAAACCA
GCCAGTGAAGGCTTCAAGCAATCACCCACACCTCAGTGAAGCTGAACAAGCCCATCGTCTTGAA
AGACACTTGCGCCTCTACTGCGGTAATCCTGGTCATCTTGCCAGAGGTTGCCCTGTCAAGCCCC
ATCACGCCCAGCAGGTGGGAAACATCGTGGCCTGGCAGTAA

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Protein Sequences


Protein RefSeqs	XP_003135256	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_003135256 ⟸ XM_003135208

- Sequence:

show sequence

MVENLAASYIALKLENEILQAQVQWLMEENAALQSQIPELQKPXEAKEDEPLQKPSKAQEPQRP
PEPLDLPETLGSQEPPEVETQKPRESQDFPFWEPLTAQEPKKSLEPPAALEPLKPPATEDPQEP
LMVHKLSGAWESQKCPGCQDSTVAQEPEISEPQYPPNVQEPQEIPESQETSIHLEFLELXSPQE
LLDLSDAQEFLGLLAPQEYLNSLTAAETAASEFPQSSSWLEPEAFPLEYPLVFNGDAQKLPEFL
VQLNSYMRVRGHMYPTKAGLVSFVGNCFSGEAGKWFHPIVNTQSPLLEQFESFIQVFQDTFDNP
ENMEDSNHHIRQLCQGGDHIHQYAIHFHFIAQEIKWNESTLCIQFQEGHARSIQELSHTSPATN
LSDLITQCITLEEKLNDKPDLSPQEASPSEEKLDLDSPPAENQPVKASSNHPHLSEAEQAHRLE
RHLRLYCGNPGHLARGCPVKPHHAQQVGNIVAWQ

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Additional Information

External Database Links

Database	Acc Id	Source(s)
NCBI Gene	RTL3	ENTREZGENE

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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