SSB (small RNA binding exonuclease protection factor La) - Rat Genome Database

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Gene: SSB (small RNA binding exonuclease protection factor La) Canis lupus familiaris
Analyze
Symbol: SSB
Name: small RNA binding exonuclease protection factor La
RGD ID: 12056569
Description: ENCODES a protein that exhibits poly(U) RNA binding (inferred); RNA binding (inferred); sequence-specific mRNA binding (inferred); INVOLVED IN tRNA processing (ortholog); PARTICIPATES IN tRNA maturation pathway; ASSOCIATED WITH COVID-19 (ortholog); FOUND IN cytoplasm (inferred); nucleus (inferred); ribonucleoprotein complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Sjogren syndrome antigen B
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13614,465,088 - 14,476,786 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3614,465,129 - 14,476,609 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3614,477,215 - 14,488,515 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03614,584,035 - 14,595,782 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3614,584,083 - 14,597,032 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13614,667,144 - 14,678,600 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03614,659,402 - 14,670,867 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03614,770,849 - 14,782,579 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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


Genomics

Comparative Map Data
SSB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13614,465,088 - 14,476,786 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3614,465,129 - 14,476,609 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3614,477,215 - 14,488,515 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03614,584,035 - 14,595,782 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3614,584,083 - 14,597,032 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13614,667,144 - 14,678,600 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03614,659,402 - 14,670,867 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03614,770,849 - 14,782,579 (+)NCBIUU_Cfam_GSD_1.0
SSB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382169,798,871 - 169,812,064 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2169,791,933 - 169,812,064 (+)EnsemblGRCh38hg38GRCh38
GRCh372170,655,381 - 170,668,574 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362170,363,635 - 170,376,821 (+)NCBINCBI36Build 36hg18NCBI36
Build 342170,480,895 - 170,494,082NCBI
Celera2164,271,755 - 164,284,947 (+)NCBICelera
Cytogenetic Map2q31.1NCBI
HuRef2162,543,375 - 162,556,636 (+)NCBIHuRef
CHM1_12170,659,176 - 170,674,430 (+)NCBICHM1_1
T2T-CHM13v2.02170,276,405 - 170,289,608 (+)NCBIT2T-CHM13v2.0
Ssb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39269,691,963 - 69,702,185 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl269,691,906 - 69,702,190 (+)EnsemblGRCm39 Ensembl
GRCm38269,861,562 - 69,871,846 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl269,861,562 - 69,871,846 (+)EnsemblGRCm38mm10GRCm38
MGSCv37269,699,619 - 69,709,903 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36269,662,467 - 69,672,643 (+)NCBIMGSCv36mm8
Celera271,531,605 - 71,541,890 (+)NCBICelera
Cytogenetic Map2C2NCBI
cM Map240.95NCBI
Ssb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8375,024,385 - 75,034,016 (+)NCBIGRCr8
mRatBN7.2354,616,616 - 54,626,203 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl354,616,619 - 54,626,203 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx358,018,226 - 58,027,720 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0366,601,821 - 66,611,315 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0364,364,199 - 64,373,694 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0356,092,425 - 56,102,008 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl356,092,501 - 56,102,001 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0362,727,433 - 62,737,034 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4352,001,106 - 52,010,611 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1351,897,477 - 51,906,978 (+)NCBI
Celera354,176,184 - 54,185,689 (+)NCBICelera
Cytogenetic Map3q21NCBI
Ssb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554494,806,468 - 4,815,175 (-)NCBIChiLan1.0ChiLan1.0
SSB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21372,459,193 - 72,472,464 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B72,474,165 - 72,487,436 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B57,071,158 - 57,084,428 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B174,536,382 - 174,549,609 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B174,536,382 - 174,549,604 (+)Ensemblpanpan1.1panPan2
Ssb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303131,732,490 - 131,741,876 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936509286,398 - 298,147 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936509286,397 - 295,779 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SSB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1576,088,641 - 76,100,785 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11576,088,587 - 76,099,517 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21585,205,395 - 85,216,312 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SSB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11055,325,975 - 55,339,317 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1055,262,897 - 55,339,008 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040144,196,826 - 144,210,322 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ssb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247877,292,549 - 7,301,190 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SSB
114 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 22 16 6 6 6 6 33 22 12 14 10

Sequence


Ensembl Acc Id: ENSCAFT00000038572   ⟹   ENSCAFP00000034314
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3614,465,129 - 14,476,609 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845042377   ⟹   ENSCAFP00845033222
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl3614,584,083 - 14,597,026 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845042454   ⟹   ENSCAFP00845033280
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl3614,584,114 - 14,597,032 (+)Ensembl
RefSeq Acc Id: XM_022414678   ⟹   XP_022270386
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13614,465,859 - 14,476,786 (+)NCBI
Dog10K_Boxer_Tasha3614,477,795 - 14,488,515 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038446997   ⟹   XP_038302925
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.03614,584,035 - 14,595,782 (+)NCBI
RefSeq Acc Id: XM_038446998   ⟹   XP_038302926
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.03614,584,614 - 14,595,782 (+)NCBI
RefSeq Acc Id: XM_038521072   ⟹   XP_038377000
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.13614,667,144 - 14,678,600 (+)NCBI
RefSeq Acc Id: XM_038521073   ⟹   XP_038377001
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.13614,667,724 - 14,678,600 (+)NCBI
RefSeq Acc Id: XM_038584773   ⟹   XP_038440701
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.03614,770,849 - 14,782,579 (+)NCBI
RefSeq Acc Id: XM_038584774   ⟹   XP_038440702
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.03614,771,428 - 14,782,579 (+)NCBI
RefSeq Acc Id: XM_038649189   ⟹   XP_038505117
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.03614,659,402 - 14,670,867 (+)NCBI
RefSeq Acc Id: XM_038649190   ⟹   XP_038505118
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.03614,659,982 - 14,670,867 (+)NCBI
RefSeq Acc Id: XM_535952   ⟹   XP_535952
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13614,465,088 - 14,476,786 (+)NCBI
Dog10K_Boxer_Tasha3614,477,215 - 14,488,515 (+)NCBI
Sequence:
RefSeq Acc Id: XP_535952   ⟸   XM_535952
- UniProtKB: A0A8C0TUD6 (UniProtKB/TrEMBL),   A0A8C0QUD0 (UniProtKB/TrEMBL),   A0A8I3PZQ3 (UniProtKB/TrEMBL),   A0A8C0MPL8 (UniProtKB/TrEMBL),   A0A8I3S7X5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022270386   ⟸   XM_022414678
- UniProtKB: A0A8C0TUD6 (UniProtKB/TrEMBL),   A0A8C0QUD0 (UniProtKB/TrEMBL),   A0A8I3PZQ3 (UniProtKB/TrEMBL),   A0A8C0MPL8 (UniProtKB/TrEMBL),   A0A8I3S7X5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000034314   ⟸   ENSCAFT00000038572
RefSeq Acc Id: XP_038377000   ⟸   XM_038521072
RefSeq Acc Id: XP_038377001   ⟸   XM_038521073
RefSeq Acc Id: XP_038505117   ⟸   XM_038649189
RefSeq Acc Id: XP_038505118   ⟸   XM_038649190
RefSeq Acc Id: XP_038302925   ⟸   XM_038446997
- UniProtKB: A0A8C0TUD6 (UniProtKB/TrEMBL),   A0A8C0QUD0 (UniProtKB/TrEMBL),   A0A8I3PZQ3 (UniProtKB/TrEMBL),   A0A8C0MPL8 (UniProtKB/TrEMBL),   A0A8I3S7X5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038302926   ⟸   XM_038446998
- UniProtKB: A0A8C0TUD6 (UniProtKB/TrEMBL),   A0A8C0QUD0 (UniProtKB/TrEMBL),   A0A8I3PZQ3 (UniProtKB/TrEMBL),   A0A8C0MPL8 (UniProtKB/TrEMBL),   A0A8I3S7X5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038440701   ⟸   XM_038584773
- UniProtKB: A0A8C0MPL8 (UniProtKB/TrEMBL),   A0A8C0QUD0 (UniProtKB/TrEMBL),   A0A8C0TUD6 (UniProtKB/TrEMBL),   A0A8I3PZQ3 (UniProtKB/TrEMBL),   A0A8I3S7X5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038440702   ⟸   XM_038584774
- UniProtKB: A0A8C0MPL8 (UniProtKB/TrEMBL),   A0A8C0QUD0 (UniProtKB/TrEMBL),   A0A8C0TUD6 (UniProtKB/TrEMBL),   A0A8I3PZQ3 (UniProtKB/TrEMBL),   A0A8I3S7X5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845033280   ⟸   ENSCAFT00845042454
Ensembl Acc Id: ENSCAFP00845033222   ⟸   ENSCAFT00845042377
Protein Domains
HTH La-type RNA-binding   RRM   XRRM

Promoters
RGD ID:13689068
Promoter ID:EPDNEW_C7135
Type:initiation region
Name:SSB_1
Description:Sjogren syndrome antigen B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13614,465,149 - 14,465,209EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000012418 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030007775 UniProtKB/TrEMBL
  ENSCAFG00040025841 UniProtKB/TrEMBL
  ENSCAFG00845024004 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000038572.4 UniProtKB/TrEMBL
  ENSCAFT00000105055.1 UniProtKB/TrEMBL
  ENSCAFT00030014250.1 UniProtKB/TrEMBL
  ENSCAFT00030014369.1 UniProtKB/TrEMBL
  ENSCAFT00030014449.1 UniProtKB/TrEMBL
  ENSCAFT00040048290.1 UniProtKB/TrEMBL
  ENSCAFT00040048293.1 UniProtKB/TrEMBL
  ENSCAFT00845042377.1 UniProtKB/TrEMBL
  ENSCAFT00845042454 ENTREZGENE
  ENSCAFT00845042454.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  3.30.70.330 UniProtKB/TrEMBL
InterPro La_dom_prot UniProtKB/TrEMBL
  La_HTH UniProtKB/TrEMBL
  La_xRRM UniProtKB/TrEMBL
  Lupus_La UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene SSB ENTREZGENE
PANTHER LUPUS LA PROTEIN UniProtKB/TrEMBL
  LUPUS LA PROTEIN HOMOLOG UniProtKB/TrEMBL
  PTHR22792 UniProtKB/TrEMBL
Pfam PF05383 UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
  RRM_3 UniProtKB/TrEMBL
PRINTS LUPUSLA UniProtKB/TrEMBL
PROSITE HTH_LA UniProtKB/TrEMBL
  RRM UniProtKB/TrEMBL
  XRRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
  SM00715 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
  SSF54928 UniProtKB/TrEMBL
UniProt A0A8C0MPL8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0QUD0 ENTREZGENE
  A0A8C0RF64_CANLF UniProtKB/TrEMBL
  A0A8C0TUD6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0Z7A0_CANLF UniProtKB/TrEMBL
  A0A8I3PZQ3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3S7X5 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:58552 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-22 SSB  small RNA binding exonuclease protection factor La    Sjogren syndrome antigen B  Symbol and/or name change 5135510 APPROVED