SYNE4 (spectrin repeat containing nuclear envelope family member 4) - Rat Genome Database

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Gene: SYNE4 (spectrin repeat containing nuclear envelope family member 4) Chlorocebus sabaeus
Analyze
Symbol: SYNE4
Name: spectrin repeat containing nuclear envelope family member 4
RGD ID: 18592054
Description: INVOLVED IN establishment of epithelial cell apical/basal polarity (inferred); ASSOCIATED WITH autosomal recessive nonsyndromic deafness 76 (ortholog); Brugada syndrome 5 (ortholog); hereditary spastic paraplegia 75 (ortholog); FOUND IN nuclear outer membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: nesprin-4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1630,914,081 - 30,920,154 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl630,914,119 - 30,919,752 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660738,709,024 - 8,715,061 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
SYNE4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1630,914,081 - 30,920,154 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl630,914,119 - 30,919,752 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660738,709,024 - 8,715,061 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
SYNE4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381936,003,307 - 36,008,813 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1936,003,307 - 36,008,813 (-)EnsemblGRCh38hg38GRCh38
GRCh371936,494,209 - 36,499,715 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361941,185,842 - 41,191,512 (-)NCBINCBI36Build 36hg18NCBI36
Celera1933,208,182 - 33,213,852 (-)NCBICelera
Cytogenetic Map19q13.12NCBI
HuRef1932,999,551 - 33,005,221 (-)NCBIHuRef
CHM1_11936,495,363 - 36,501,021 (-)NCBICHM1_1
T2T-CHM13v2.01938,549,106 - 38,554,612 (-)NCBIT2T-CHM13v2.0
Syne4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39730,014,268 - 30,018,471 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl730,014,232 - 30,018,471 (+)EnsemblGRCm39 Ensembl
GRCm38730,314,816 - 30,319,045 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl730,314,807 - 30,319,046 (+)EnsemblGRCm38mm10GRCm38
MGSCv37731,099,835 - 31,104,064 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36730,023,589 - 30,027,802 (+)NCBIMGSCv36mm8
Celera724,910,949 - 24,915,178 (+)NCBICelera
Cytogenetic Map7B1NCBI
cM Map717.39NCBI
Syne4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8194,696,866 - 94,701,230 (+)NCBIGRCr8
mRatBN7.2185,569,409 - 85,573,775 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl185,569,545 - 85,573,760 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx190,985,692 - 90,989,914 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0199,453,869 - 99,458,094 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0192,743,953 - 92,748,175 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0188,772,729 - 88,777,044 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl190,951,771 - 90,957,082 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl188,772,904 - 88,776,999 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0192,089,513 - 92,094,265 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4185,261,148 - 85,265,361 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera179,943,400 - 79,947,613 (+)NCBICelera
Cytogenetic Map1q21NCBI
Syne4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554682,580,743 - 2,584,967 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554682,580,743 - 2,584,967 (+)NCBIChiLan1.0ChiLan1.0
SYNE4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22042,004,219 - 42,009,995 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11943,980,063 - 43,993,549 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01932,921,175 - 32,927,266 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11941,671,236 - 41,675,697 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1941,671,236 - 41,675,697 (-)Ensemblpanpan1.1panPan2
SYNE4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11116,676,365 - 116,686,911 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1116,670,841 - 116,680,515 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1116,082,051 - 116,086,286 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01117,279,504 - 117,283,709 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1117,279,808 - 117,283,665 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11116,843,545 - 116,847,745 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01116,467,111 - 116,471,289 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01117,522,317 - 117,526,499 (+)NCBIUU_Cfam_GSD_1.0
Syne4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934911,270,511 - 11,274,218 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493692240,684 - 44,312 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493692240,640 - 44,414 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNE4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl645,380,218 - 45,384,671 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1645,377,914 - 45,384,869 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2640,782,889 - 40,787,555 (-)NCBISscrofa10.2Sscrofa10.2susScr3


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 16 16
Low 6 16 38
Below cutoff 14 4 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000002314   ⟹   ENSCSAP00000000634
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl630,914,119 - 30,919,752 (-)Ensembl
RefSeq Acc Id: XM_007996459   ⟹   XP_007994650
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1630,914,089 - 30,920,142 (-)NCBI
Vero_WHO_p1.0NW_0236660738,709,024 - 8,715,061 (-)NCBI
Sequence:
RefSeq Acc Id: XM_007996462   ⟹   XP_007994653
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1630,914,089 - 30,920,154 (-)NCBI
Vero_WHO_p1.0NW_0236660738,709,024 - 8,715,061 (-)NCBI
Sequence:
RefSeq Acc Id: XM_037991576   ⟹   XP_037847504
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_0236660738,709,024 - 8,715,061 (-)NCBI
Protein Sequences
Protein RefSeqs XP_007994650 (Get FASTA)   NCBI Sequence Viewer  
  XP_007994653 (Get FASTA)   NCBI Sequence Viewer  
  XP_037847504 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000000634.1
Reference Protein Sequences
RefSeq Acc Id: XP_007994653   ⟸   XM_007996462
- Peptide Label: isoform X3
- UniProtKB: A0A0D9QW95 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007994650   ⟸   XM_007996459
- Peptide Label: isoform X1
- UniProtKB: A0A0D9QW95 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000000634   ⟸   ENSCSAT00000002314
RefSeq Acc Id: XP_037847504   ⟸   XM_037991576
- Peptide Label: isoform X2
- UniProtKB: A0A0D9QW95 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000004284 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000002314.1 UniProtKB/TrEMBL
InterPro KASH UniProtKB/TrEMBL
  SYNE4 UniProtKB/TrEMBL
KEGG Report csab:103234553 UniProtKB/TrEMBL
NCBI Gene SYNE4 ENTREZGENE
PANTHER NESPRIN-4 UniProtKB/TrEMBL
  PTHR21640 UniProtKB/TrEMBL
Pfam KASH UniProtKB/TrEMBL
PROSITE KASH UniProtKB/TrEMBL
SMART KASH UniProtKB/TrEMBL
Superfamily-SCOP Spectrin repeat UniProtKB/TrEMBL
UniProt A0A0D9QW95 ENTREZGENE, UniProtKB/TrEMBL