Lin28b (lin-28 homolog B) - Rat Genome Database

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Gene: Lin28b (lin-28 homolog B) Rattus norvegicus
Analyze
Symbol: Lin28b
Name: lin-28 homolog B
RGD ID: 1597432
Description: Predicted to enable mRNA binding activity and sequence-specific double-stranded DNA binding activity. Predicted to be involved in RNA metabolic process and regulation of RNA metabolic process. Predicted to be located in cytosol; nucleolus; and nucleoplasm. Predicted to be active in cytoplasm and nucleus. Orthologous to human LIN28B (lin-28 homolog B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; atrazine.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lin-28 homolog B (C. elegans); LOC683611; LOC689054; similar to lin-28 homolog b
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82050,447,700 - 50,547,135 (-)NCBIGRCr8
mRatBN7.22048,865,329 - 48,964,769 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2048,869,485 - 48,955,077 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02050,482,536 - 50,580,273 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2050,486,809 - 50,564,987 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02052,094,397 - 52,182,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42049,685,524 - 49,765,967 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2051,065,112 - 51,157,124 (+)NCBICelera
Cytogenetic Map20q13NCBI
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

Cellular Component
cytoplasm  (IBA)
cytosol  (IEA,ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:18951094   PMID:19703396   PMID:22681889   PMID:27384999  


Genomics

Comparative Map Data
Lin28b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82050,447,700 - 50,547,135 (-)NCBIGRCr8
mRatBN7.22048,865,329 - 48,964,769 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2048,869,485 - 48,955,077 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02050,482,536 - 50,580,273 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2050,486,809 - 50,564,987 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02052,094,397 - 52,182,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42049,685,524 - 49,765,967 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2051,065,112 - 51,157,124 (+)NCBICelera
Cytogenetic Map20q13NCBI
LIN28B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386104,937,026 - 105,083,332 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6104,936,616 - 105,083,332 (+)EnsemblGRCh38hg38GRCh38
GRCh376105,404,982 - 105,531,207 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366105,511,616 - 105,637,899 (+)NCBINCBI36Build 36hg18NCBI36
Celera6106,027,398 - 106,153,711 (+)NCBICelera
Cytogenetic Map6q16.3-q21NCBI
HuRef6102,848,044 - 102,974,520 (+)NCBIHuRef
CHM1_16105,666,790 - 105,793,230 (+)NCBICHM1_1
T2T-CHM13v2.06106,113,007 - 106,259,422 (+)NCBIT2T-CHM13v2.0
Lin28b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391045,252,713 - 45,362,410 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1045,252,716 - 45,362,491 (-)EnsemblGRCm39 Ensembl
GRCm381045,376,617 - 45,486,314 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1045,376,620 - 45,486,395 (-)EnsemblGRCm38mm10GRCm38
MGSCv371045,096,425 - 45,190,007 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361045,065,048 - 45,158,616 (-)NCBIMGSCv36mm8
Celera1046,249,152 - 46,342,378 (-)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.5NCBI
Lin28b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541130,381,208 - 30,499,678 (+)NCBIChiLan1.0ChiLan1.0
LIN28B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25124,960,620 - 125,103,365 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16122,847,067 - 122,989,850 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06102,755,256 - 102,897,739 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16106,646,991 - 106,772,374 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6106,640,448 - 106,772,374 (+)Ensemblpanpan1.1panPan2
LIN28B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11262,403,831 - 62,529,435 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1262,403,333 - 62,524,838 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1262,192,981 - 62,315,060 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01263,254,885 - 63,380,812 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1263,245,774 - 63,376,607 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11262,610,319 - 62,736,100 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01262,451,489 - 62,577,218 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01262,730,358 - 62,855,996 (+)NCBIUU_Cfam_GSD_1.0
Lin28b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494697,371,614 - 97,497,852 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365641,663,068 - 1,768,283 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365641,646,469 - 1,768,879 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIN28B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl171,159,251 - 71,296,217 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1171,173,291 - 71,296,131 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2180,544,640 - 80,620,604 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LIN28B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11368,721,209 - 68,859,257 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1368,725,392 - 68,839,811 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604041,068,949 - 41,187,159 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lin28b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624952193,395 - 309,102 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lin28b
633 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:287
Count of miRNA genes:166
Interacting mature miRNAs:182
Transcripts:ENSRNOT00000034485, ENSRNOT00000057064, ENSRNOT00000064466, ENSRNOT00000065438
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat


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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4 6 6 6 10 6
Low 16 16 16 2 16 62 12 30
Below cutoff 3 15 12 4 12 3 5 2 5 2 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034485   ⟹   ENSRNOP00000037788
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2048,869,485 - 48,955,077 (-)Ensembl
Rnor_6.0 Ensembl2050,486,809 - 50,564,987 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000064466   ⟹   ENSRNOP00000059027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2050,486,809 - 50,564,987 (-)Ensembl
RefSeq Acc Id: XM_039099150   ⟹   XP_038955078
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,447,700 - 50,547,135 (-)NCBI
mRatBN7.22048,865,329 - 48,964,769 (-)NCBI
RefSeq Acc Id: XM_063279641   ⟹   XP_063135711
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,447,700 - 50,532,501 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038955078 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135711 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99668 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037788.4
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000037788   ⟸   ENSRNOT00000034485
RefSeq Acc Id: ENSRNOP00000059027   ⟸   ENSRNOT00000064466
RefSeq Acc Id: XP_038955078   ⟸   XM_039099150
- Peptide Label: isoform X1
- UniProtKB: A6K6U9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135711   ⟸   XM_063279641
- Peptide Label: isoform X2
Protein Domains
CCHC-type   CSD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZIK1-F1-model_v2 AlphaFold D3ZIK1 1-271 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1597432 AgrOrtholog
BioCyc Gene G2FUF-3262 BioCyc
Ensembl Genes ENSRNOG00000025938 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034485.7 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.140 UniProtKB/TrEMBL
  Zinc finger, CCHC-type UniProtKB/TrEMBL
InterPro Cold_shock_prot UniProtKB/TrEMBL
  CSP_DNA-bd UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/TrEMBL
  Znf_CCHC UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/TrEMBL
NCBI Gene 689054 ENTREZGENE
PANTHER PROTEIN LIN-28 UniProtKB/TrEMBL
  PROTEIN LIN-28 HOMOLOG B UniProtKB/TrEMBL
Pfam CSD UniProtKB/TrEMBL
  zf-CCHC UniProtKB/TrEMBL
PhenoGen Lin28b PhenoGen
PRINTS COLDSHOCK UniProtKB/TrEMBL
PROSITE CSD_2 UniProtKB/TrEMBL
  ZF_CCHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025938 RatGTEx
SMART CSP UniProtKB/TrEMBL
  ZnF_C2HC UniProtKB/TrEMBL
Superfamily-SCOP Nucleic_acid_OB UniProtKB/TrEMBL
  SSF57756 UniProtKB/TrEMBL
UniProt A6K6U9 ENTREZGENE, UniProtKB/TrEMBL
  D3ZIK1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-01 Lin28b  lin-28 homolog B  Lin28b  lin-28 homolog B (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-07-01 Lin28b  lin-28 homolog B (C. elegans)  LOC683611  similar to lin-28 homolog b  Data merged from RGD:1584540 737654 APPROVED
2008-03-06 Lin28b  lin-28 homolog B (C. elegans)  LOC689054  similar to lin-28 homolog b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC689054  similar to lin-28 homolog b      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC683611  similar to lin-28 homolog b      Symbol and Name status set to provisional 70820 PROVISIONAL