LSM8 (LSM8 homolog, U6 small nuclear RNA associated) - Rat Genome Database

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Gene: LSM8 (LSM8 homolog, U6 small nuclear RNA associated) Sus scrofa
Analyze
Symbol: LSM8
Name: LSM8 homolog, U6 small nuclear RNA associated
RGD ID: 13889061
Description: ENCODES a protein that exhibits RNA binding (inferred); INVOLVED IN mRNA processing (inferred); mRNA splicing, via spliceosome (inferred); RNA splicing (inferred); PARTICIPATES IN spliceosome pathway; ASSOCIATED WITH pleomorphic xanthoastrocytoma (ortholog); FOUND IN U4/U6 x U5 tri-snRNP complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1828,108,308 - 28,130,330 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11828,124,116 - 28,130,375 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21829,761,550 - 29,767,808 (-)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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14681463   PMID:15679890   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
LSM8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1828,108,308 - 28,130,330 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11828,124,116 - 28,130,375 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21829,761,550 - 29,767,808 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSM8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387118,184,164 - 118,204,035 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7118,184,144 - 118,204,035 (+)EnsemblGRCh38hg38GRCh38
GRCh377117,824,218 - 117,844,089 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367117,611,322 - 117,620,116 (+)NCBINCBI36Build 36hg18NCBI36
Build 347117,418,169 - 117,426,827NCBI
Celera7112,633,566 - 112,653,561 (+)NCBICelera
Cytogenetic Map7q31.31NCBI
HuRef7112,190,045 - 112,210,037 (+)NCBIHuRef
CHM1_17117,757,651 - 117,777,658 (+)NCBICHM1_1
T2T-CHM13v2.07119,499,900 - 119,519,771 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27117,219,509 - 117,239,504 (+)NCBI
Lsm8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39618,848,634 - 18,854,051 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl618,848,578 - 18,855,750 (+)EnsemblGRCm39 Ensembl
GRCm38618,848,635 - 18,854,052 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl618,848,579 - 18,855,751 (+)EnsemblGRCm38mm10GRCm38
MGSCv37618,798,635 - 18,804,052 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36618,798,636 - 18,804,053 (+)NCBIMGSCv36mm8
Celera618,915,775 - 18,921,192 (+)NCBICelera
Cytogenetic Map6A2NCBI
cM Map68.16NCBI
Lsm8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8448,272,128 - 48,277,994 (+)NCBIGRCr8
mRatBN7.2447,306,259 - 47,312,125 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl447,306,295 - 47,314,293 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx452,288,762 - 52,294,635 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0448,209,920 - 48,215,793 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0446,638,575 - 46,644,463 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0445,555,077 - 45,560,943 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl445,555,077 - 45,560,943 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0443,016,688 - 43,022,554 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4444,717,003 - 44,722,869 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1444,947,578 - 44,953,397 (-)NCBI
Celera442,561,436 - 42,567,302 (+)NCBICelera
Cytogenetic Map4q22NCBI
Lsm8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543223,818,227 - 23,823,382 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543223,818,036 - 23,823,550 (+)NCBIChiLan1.0ChiLan1.0
LSM8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26155,010,418 - 155,019,137 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan177,020,642 - 7,029,394 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07110,150,584 - 110,160,864 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17122,844,848 - 122,856,577 (+)NCBIpanpan1.1PanPan1.1panPan2
LSM8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11456,908,344 - 56,916,512 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1456,303,593 - 56,310,860 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01456,949,516 - 56,956,795 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11456,985,386 - 56,992,649 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01456,667,268 - 56,675,163 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01457,039,159 - 57,046,455 (+)NCBIUU_Cfam_GSD_1.0
Lsm8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511845,576,455 - 45,584,161 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365891,105,341 - 1,113,452 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365891,107,534 - 1,113,439 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSM8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12186,838,350 - 86,846,675 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2186,838,375 - 86,846,517 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604216,871,635 - 16,880,717 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsm8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248271,192,380 - 1,201,994 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in LSM8
58 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 circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 2 3 5 2 19 2 3 3
Low 2 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000018096   ⟹   ENSSSCP00000017606
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1828,108,308 - 28,130,302 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000087769   ⟹   ENSSSCP00000068189
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1828,124,925 - 28,130,330 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000091733   ⟹   ENSSSCP00000075215
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1828,108,308 - 28,126,960 (-)Ensembl
RefSeq Acc Id: XM_003134753   ⟹   XP_003134801
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11828,124,116 - 28,130,375 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_003134801   ⟸   XM_003134753
- UniProtKB: F2Z5P9 (UniProtKB/TrEMBL),   A0A4X1W3A0 (UniProtKB/TrEMBL),   A0A8D0Z7I4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000068189   ⟸   ENSSSCT00000087769
RefSeq Acc Id: ENSSSCP00000017606   ⟸   ENSSSCT00000018096
RefSeq Acc Id: ENSSSCP00000075215   ⟸   ENSSSCT00000091733
Protein Domains
Sm


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000021652 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005010303 UniProtKB/TrEMBL
  ENSSSCG00015067703 UniProtKB/TrEMBL
  ENSSSCG00025063881 UniProtKB/TrEMBL
  ENSSSCG00030071132 UniProtKB/TrEMBL
  ENSSSCG00035026295 UniProtKB/TrEMBL
  ENSSSCG00040022698 UniProtKB/TrEMBL
  ENSSSCG00045014114 UniProtKB/TrEMBL
  ENSSSCG00050050283 UniProtKB/TrEMBL
  ENSSSCG00055026815 UniProtKB/TrEMBL
  ENSSSCG00060064974 UniProtKB/TrEMBL
  ENSSSCG00065058073 UniProtKB/TrEMBL
  ENSSSCG00070028520 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000018096 ENTREZGENE
  ENSSSCT00000018096.5 UniProtKB/TrEMBL
  ENSSSCT00000087769.2 UniProtKB/TrEMBL
  ENSSSCT00000091733.1 UniProtKB/TrEMBL
  ENSSSCT00005015855.1 UniProtKB/TrEMBL
  ENSSSCT00005015941.1 UniProtKB/TrEMBL
  ENSSSCT00015090738.1 UniProtKB/TrEMBL
  ENSSSCT00015090868.1 UniProtKB/TrEMBL
  ENSSSCT00025087518.1 UniProtKB/TrEMBL
  ENSSSCT00025087641.1 UniProtKB/TrEMBL
  ENSSSCT00030099502.1 UniProtKB/TrEMBL
  ENSSSCT00030099524.1 UniProtKB/TrEMBL
  ENSSSCT00035034680.1 UniProtKB/TrEMBL
  ENSSSCT00035034683.1 UniProtKB/TrEMBL
  ENSSSCT00040030442.1 UniProtKB/TrEMBL
  ENSSSCT00040030489.1 UniProtKB/TrEMBL
  ENSSSCT00045024049.1 UniProtKB/TrEMBL
  ENSSSCT00045024076.1 UniProtKB/TrEMBL
  ENSSSCT00050068408.1 UniProtKB/TrEMBL
  ENSSSCT00050068413.1 UniProtKB/TrEMBL
  ENSSSCT00055053040.1 UniProtKB/TrEMBL
  ENSSSCT00055053100.1 UniProtKB/TrEMBL
  ENSSSCT00060088702.1 UniProtKB/TrEMBL
  ENSSSCT00060088717.1 UniProtKB/TrEMBL
  ENSSSCT00065079462.1 UniProtKB/TrEMBL
  ENSSSCT00065079470.1 UniProtKB/TrEMBL
  ENSSSCT00070057199.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  Lsm8 UniProtKB/TrEMBL
  LSM_dom_euk/arc UniProtKB/TrEMBL
  LSM_dom_sf UniProtKB/TrEMBL
  PTHR15588 UniProtKB/TrEMBL
KEGG Report ssc:100739296 UniProtKB/TrEMBL
NCBI Gene LSM8 ENTREZGENE
PANTHER PTHR15588 UniProtKB/TrEMBL
  U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM8 UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PROSITE PS52002 UniProtKB/TrEMBL
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP SSF50182 UniProtKB/TrEMBL
UniProt A0A4X1W3A0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0SXC9_PIG UniProtKB/TrEMBL
  A0A8D0Y3G8_PIG UniProtKB/TrEMBL
  A0A8D0Z7I4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8W4F8R8_PIG UniProtKB/TrEMBL
  F2Z5P9 ENTREZGENE
UniProt Secondary A0A5G2RC45 UniProtKB/TrEMBL
  F2Z5P9 UniProtKB/TrEMBL
VGNC ID VGNC:89877 ENTREZGENE