RTL4 (retrotransposon Gag like 4) - Rat Genome Database

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Gene: RTL4 (retrotransposon Gag like 4) Sus scrofa
Analyze
Symbol: RTL4
Name: retrotransposon Gag like 4
RGD ID: 14074788
Description: ENCODES a protein that exhibits nucleic acid binding (inferred); zinc ion binding (inferred); INVOLVED IN cognition (ortholog); norepinephrine metabolic process (ortholog); ASSOCIATED WITH autistic disorder (ortholog); genetic disease (ortholog); schizophrenia (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: ZCCHC16; zinc finger CCHC domain-containing protein 16; zinc finger CCHC-type containing 16
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX92,223,747 - 92,335,430 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X91,920,451 - 92,333,326 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X106,588,456 - 106,697,981 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
RTL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX92,223,747 - 92,335,430 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X91,920,451 - 92,333,326 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X106,588,456 - 106,697,981 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RTL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X112,083,013 - 112,457,514 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX112,083,016 - 112,457,514 (+)EnsemblGRCh38hg38GRCh38
GRCh37X111,326,241 - 111,700,742 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X111,212,909 - 111,587,129 (+)NCBINCBI36Build 36hg18NCBI36
CeleraX111,805,763 - 112,184,591 (+)NCBICelera
Cytogenetic MapXq23NCBI
HuRefX100,946,374 - 101,322,365 (+)NCBIHuRef
CHM1_1X111,237,477 - 111,611,887 (+)NCBICHM1_1
T2T-CHM13v2.0X110,531,358 - 110,907,626 (+)NCBIT2T-CHM13v2.0
Rtl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X143,471,147 - 143,905,410 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX143,471,903 - 143,905,407 (+)EnsemblGRCm39 Ensembl
GRCm38X144,688,209 - 145,122,414 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX144,688,907 - 145,122,411 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X141,123,450 - 141,556,953 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X140,365,456 - 140,368,776 (+)NCBIMGSCv36mm8
CeleraX128,644,641 - 129,073,163 (+)NCBICelera
Cytogenetic MapXF2NCBI
cM MapX65.85NCBI
Rtl4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X113,027,697 - 113,438,382 (+)NCBIGRCr8
mRatBN7.2X108,231,052 - 108,641,768 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX108,633,651 - 108,640,050 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X115,908,999 - 116,402,406 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX116,399,611 - 116,400,516 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X116,465,029 - 116,543,231 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X33,404,885 - 33,405,790 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX107,618,493 - 108,025,880 (+)NCBICelera
Cytogenetic MapXq34NCBI
Rtl4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554903,403,958 - 3,497,789 (-)NCBIChiLan1.0ChiLan1.0
RTL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X111,916,075 - 111,946,035 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X111,919,823 - 111,949,643 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X101,191,619 - 101,570,815 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X112,024,468 - 112,027,070 (+)NCBIpanpan1.1PanPan1.1panPan2
RTL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X85,117,015 - 85,609,928 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX85,512,467 - 85,513,375 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX71,610,796 - 71,623,667 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X87,193,067 - 87,205,938 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX87,202,198 - 87,203,106 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X84,656,673 - 84,669,544 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X86,331,789 - 86,344,656 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X86,168,927 - 86,181,831 (+)NCBIUU_Cfam_GSD_1.0
Rtl4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X84,383,324 - 84,757,393 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364992,901,534 - 2,904,565 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTL4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X99,857,087 - 100,206,786 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX100,203,031 - 100,203,963 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606525,548,015 - 25,552,986 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtl4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248033,016,865 - 3,494,115 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RTL4
6646 total Variants

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

alimentary part of gastrointestinal system endocrine system nervous system renal system reproductive system
High
Medium
Low 5 3 1
Below cutoff 5 1 9 1 1

Sequence


RefSeq Acc Id: ENSSSCT00000033985   ⟹   ENSSSCP00000050771
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 EnsemblX92,223,747 - 92,335,430 (+)Ensembl
RefSeq Acc Id: XM_005673835   ⟹   XP_005673892
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X92,222,662 - 92,333,326 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021080439   ⟹   XP_020936098
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X91,920,451 - 92,333,326 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021080440   ⟹   XP_020936099
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X91,920,451 - 92,333,326 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021080441   ⟹   XP_020936100
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1X91,988,490 - 92,333,326 (+)NCBI
Sequence:
RefSeq Acc Id: XP_020936098   ⟸   XM_021080439
- UniProtKB: A0A4X1W4Q4 (UniProtKB/TrEMBL),   A0A287B3U8 (UniProtKB/TrEMBL),   A0A8D1BRL6 (UniProtKB/TrEMBL),   A0A8D1X9B9 (UniProtKB/TrEMBL),   A0A8D0HZF4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020936099   ⟸   XM_021080440
- UniProtKB: A0A4X1W4Q4 (UniProtKB/TrEMBL),   A0A287B3U8 (UniProtKB/TrEMBL),   A0A8D1BRL6 (UniProtKB/TrEMBL),   A0A8D1X9B9 (UniProtKB/TrEMBL),   A0A8D0HZF4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020936100   ⟸   XM_021080441
- UniProtKB: A0A4X1W4Q4 (UniProtKB/TrEMBL),   A0A287B3U8 (UniProtKB/TrEMBL),   A0A8D1BRL6 (UniProtKB/TrEMBL),   A0A8D1X9B9 (UniProtKB/TrEMBL),   A0A8D0HZF4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005673892   ⟸   XM_005673835
- UniProtKB: A0A287B3U8 (UniProtKB/TrEMBL),   A0A4X1W4Q4 (UniProtKB/TrEMBL),   A0A8D1BRL6 (UniProtKB/TrEMBL),   A0A8D1X9B9 (UniProtKB/TrEMBL),   A0A8D0HZF4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000050771   ⟸   ENSSSCT00000033985
Protein Domains
CCHC-type


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000012589 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005002732 UniProtKB/TrEMBL
  ENSSSCG00015054339 UniProtKB/TrEMBL
  ENSSSCG00025004205 UniProtKB/TrEMBL
  ENSSSCG00035008005 UniProtKB/TrEMBL
  ENSSSCG00040002660 UniProtKB/TrEMBL
  ENSSSCG00045019050 UniProtKB/TrEMBL
  ENSSSCG00050036917 UniProtKB/TrEMBL
  ENSSSCG00060016924 UniProtKB/TrEMBL
  ENSSSCG00065003957 UniProtKB/TrEMBL
  ENSSSCG00070028993 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000033985 ENTREZGENE
  ENSSSCT00000033985.3 UniProtKB/TrEMBL
  ENSSSCT00005004146.1 UniProtKB/TrEMBL
  ENSSSCT00015072322.1 UniProtKB/TrEMBL
  ENSSSCT00025005568.1 UniProtKB/TrEMBL
  ENSSSCT00035009976.1 UniProtKB/TrEMBL
  ENSSSCT00040003257.1 UniProtKB/TrEMBL
  ENSSSCT00045032397.1 UniProtKB/TrEMBL
  ENSSSCT00050049656.1 UniProtKB/TrEMBL
  ENSSSCT00060022597.1 UniProtKB/TrEMBL
  ENSSSCT00065005429.1 UniProtKB/TrEMBL
  ENSSSCT00070058153.1 UniProtKB/TrEMBL
InterPro LDOC1-rel UniProtKB/TrEMBL
  Znf_CCHC UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/TrEMBL
KEGG Report ssc:100524357 UniProtKB/TrEMBL
NCBI Gene RTL4 ENTREZGENE
PANTHER PTHR15503 UniProtKB/TrEMBL
  RETROTRANSPOSON GAG-LIKE PROTEIN 4 UniProtKB/TrEMBL
PROSITE ZF_CCHC UniProtKB/TrEMBL
Superfamily-SCOP SSF57756 UniProtKB/TrEMBL
UniProt A0A287B3U8 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1W4Q4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0HZF4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1BRL6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1X9B9 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:92497 ENTREZGENE