SNX27 (sorting nexin 27) - Rat Genome Database

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Gene: SNX27 (sorting nexin 27) Chlorocebus sabaeus
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Symbol: SNX27
Name: sorting nexin 27
RGD ID: 18531789
Description: ENCODES a protein that exhibits calcium-dependent protein binding (ortholog); ionotropic glutamate receptor binding (ortholog); INVOLVED IN cellular response to nerve growth factor stimulus (ortholog); endocytic recycling (ortholog); endosomal transport (ortholog); PARTICIPATES IN retromer-mediated pathway; ASSOCIATED WITH Disease Progression (ortholog); Dravet syndrome (ortholog); Experimental Liver Neoplasms (ortholog); FOUND IN cytosol (ortholog); endosome (ortholog); glutamatergic synapse (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: sorting nexin family member 27; sorting nexin-27
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12011,997,768 - 12,083,929 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2011,998,527 - 12,083,528 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603811,566,349 - 11,655,415 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SNX27
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12011,997,768 - 12,083,929 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2011,998,527 - 12,083,528 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603811,566,349 - 11,655,415 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
SNX27
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381151,612,050 - 151,699,080 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1151,612,006 - 151,699,091 (+)EnsemblGRCh38hg38GRCh38
GRCh371151,584,526 - 151,671,556 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361149,851,286 - 149,938,183 (+)NCBINCBI36Build 36hg18NCBI36
Build 341148,397,734 - 148,484,628NCBI
Celera1124,699,311 - 124,786,191 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1122,961,620 - 123,048,521 (+)NCBIHuRef
CHM1_11152,979,810 - 153,066,720 (+)NCBICHM1_1
T2T-CHM13v2.01150,734,456 - 150,822,464 (+)NCBIT2T-CHM13v2.0
Snx27
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39394,404,849 - 94,490,023 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl394,404,851 - 94,490,023 (-)EnsemblGRCm39 Ensembl
GRCm38394,497,542 - 94,582,736 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl394,497,544 - 94,582,716 (-)EnsemblGRCm38mm10GRCm38
MGSCv37394,301,466 - 94,386,624 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36394,582,946 - 94,668,131 (-)NCBIMGSCv36mm8
Celera395,943,750 - 96,021,485 (-)NCBICelera
Cytogenetic Map3F2.1NCBI
cM Map340.74NCBI
Snx27
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82184,824,930 - 184,907,931 (-)NCBIGRCr8
mRatBN7.22182,135,904 - 182,218,906 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2182,135,905 - 182,218,906 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2189,798,908 - 189,875,569 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02187,603,298 - 187,679,782 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02182,431,376 - 182,508,034 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02195,738,613 - 195,821,608 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2195,738,619 - 195,821,608 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02215,217,238 - 215,300,226 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42189,471,254 - 189,554,249 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12189,421,366 - 189,507,587 (-)NCBI
Celera2174,686,309 - 174,766,065 (-)NCBICelera
Cytogenetic Map2q34NCBI
Snx27
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955589719,898 - 799,366 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955589719,892 - 799,367 (-)NCBIChiLan1.0ChiLan1.0
SNX27
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2198,125,664 - 98,216,807 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1197,876,822 - 97,965,572 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01126,968,370 - 127,052,942 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11130,612,702 - 130,696,020 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1130,612,787 - 130,695,863 (+)Ensemblpanpan1.1panPan2
SNX27
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11760,653,719 - 60,727,928 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1760,653,732 - 60,724,253 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1760,096,255 - 60,169,627 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01761,670,181 - 61,744,403 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1761,670,153 - 61,744,393 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11760,497,733 - 60,571,614 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01760,583,470 - 60,657,201 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01761,312,756 - 61,386,709 (+)NCBIUU_Cfam_GSD_1.0
Snx27
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505822,785,222 - 22,862,694 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365801,815,651 - 1,893,753 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365801,815,582 - 1,893,076 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNX27
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl497,525,181 - 97,620,788 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1497,533,643 - 97,620,816 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24106,665,218 - 106,752,321 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Snx27
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477219,305,359 - 19,385,292 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477219,305,355 - 19,385,298 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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 32 57
Low 4 20 3
Below cutoff

Sequence


RefSeq Acc Id: ENSCSAT00000016719   ⟹   ENSCSAP00000016220
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl2011,998,527 - 12,083,528 (-)Ensembl
RefSeq Acc Id: XM_007977186   ⟹   XP_007975377
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12011,997,768 - 12,083,929 (-)NCBI
Vero_WHO_p1.0NW_02366603811,566,349 - 11,655,414 (-)NCBI
Sequence:
RefSeq Acc Id: XM_007977187   ⟹   XP_007975378
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12011,997,863 - 12,083,929 (-)NCBI
Vero_WHO_p1.0NW_02366603811,566,349 - 11,655,415 (-)NCBI
Sequence:
RefSeq Acc Id: XM_007977188   ⟹   XP_007975379
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12011,997,768 - 12,082,981 (-)NCBI
Vero_WHO_p1.0NW_02366603811,566,349 - 11,655,093 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_007975377 (Get FASTA)   NCBI Sequence Viewer  
  XP_007975378 (Get FASTA)   NCBI Sequence Viewer  
  XP_007975379 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000016220
  ENSCSAP00000016220.1
RefSeq Acc Id: XP_007975377   ⟸   XM_007977186
- Peptide Label: isoform X1
RefSeq Acc Id: XP_007975379   ⟸   XM_007977188
- Peptide Label: isoform X3
RefSeq Acc Id: XP_007975378   ⟸   XM_007977187
- Peptide Label: isoform X2
- UniProtKB: A0A0D9S5T1 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000016220   ⟸   ENSCSAT00000016719


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000001810 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000016719.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.80.60 UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/TrEMBL
  3.30.1520.10 UniProtKB/TrEMBL
InterPro PDZ UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  Phox UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/TrEMBL
  RA_dom UniProtKB/TrEMBL
  SNX17/27/31 UniProtKB/TrEMBL
  SNX27_FERM-like_dom UniProtKB/TrEMBL
  SNX27_PX UniProtKB/TrEMBL
  SNX27_RA UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/TrEMBL
NCBI Gene SNX27 ENTREZGENE
PANTHER PTHR12431 UniProtKB/TrEMBL
  SORTING NEXIN-27 UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
  PF00787 UniProtKB/TrEMBL
  PF00788 UniProtKB/TrEMBL
PROSITE PDZ UniProtKB/TrEMBL
  PS50195 UniProtKB/TrEMBL
  PS50200 UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
  SM00312 UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/TrEMBL
  SSF54236 UniProtKB/TrEMBL
  SSF64268 UniProtKB/TrEMBL
UniProt A0A0D9S5T1 ENTREZGENE, UniProtKB/TrEMBL