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

Name: Lin28b
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Lin28b (lin-28 homolog B) Chinchilla lanigera

Analyze

Symbol:

Lin28b

Name:

lin-28 homolog B

RGD ID:

8939234

Description:

ENCODES a protein that exhibits RNA binding (ortholog); sequence-specific double-stranded DNA binding (ortholog); INVOLVED IN miRNA catabolic process (ortholog); negative regulation of pre-miRNA processing (ortholog); negative regulation of primary miRNA processing (ortholog); ASSOCIATED WITH disease of cellular proliferation (ortholog); genetic disease (ortholog); Neoplastic Cell Transformation (ortholog); FOUND IN cytosol (ortholog); nucleolus (ortholog); nucleoplasm (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

lin-28 homolog B (C. elegans)

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	LIN28B (lin-28 homolog B)	NCBI	Ortholog
Mus musculus (house mouse):	Lin28b (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Lin28b (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LIN28B (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LIN28B (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lin28b (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LIN28B (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LIN28B (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lin28b (lin-28 homolog B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955411	30,381,208 - 30,499,678 (+)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

disease of cellular proliferation (ISO)

genetic disease (ISO)

Neoplastic Cell Transformation (ISO)

neuroblastoma (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

miRNA catabolic process (ISO)

negative regulation of pre-miRNA processing (ISO)

negative regulation of primary miRNA processing (ISO)

positive regulation of miRNA catabolic process (ISO)

pre-miRNA processing (ISO)

RNA 3'-end processing (ISO)

RNA destabilization (ISO)

Cellular Component

cytosol (ISO)

nucleolus (ISO)

nucleoplasm (ISO)

Molecular Function

protein binding (ISO)

RNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:22301074

Genomics

Comparative Map Data

Lin28b
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955411	30,381,208 - 30,499,678 (+)	NCBI	ChiLan1.0	ChiLan1.0

LIN28B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	104,937,026 - 105,083,332 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	104,936,616 - 105,083,332 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	105,404,982 - 105,531,207 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	105,511,616 - 105,637,899 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	6	106,027,398 - 106,153,711 (+)	NCBI		Celera
Cytogenetic Map	6	q16.3-q21	NCBI
HuRef	6	102,848,044 - 102,974,520 (+)	NCBI		HuRef
CHM1_1	6	105,666,790 - 105,793,230 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	6	106,113,007 - 106,259,422 (+)	NCBI		T2T-CHM13v2.0

Lin28b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	45,252,713 - 45,362,410 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	10	45,252,716 - 45,362,491 (-)	Ensembl		GRCm39 Ensembl
GRCm38	10	45,376,617 - 45,486,314 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	45,376,620 - 45,486,395 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	45,096,425 - 45,190,007 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	10	45,065,048 - 45,158,616 (-)	NCBI		MGSCv36	mm8
Celera	10	46,249,152 - 46,342,378 (-)	NCBI		Celera
Cytogenetic Map	10	B2	NCBI
cM Map	10	23.5	NCBI

Lin28b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	20	50,447,700 - 50,547,135 (-)	NCBI		GRCr8
mRatBN7.2	20	48,865,329 - 48,964,769 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	48,869,485 - 48,955,077 (-)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	20	50,482,536 - 50,580,273 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	50,486,809 - 50,564,987 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	52,094,397 - 52,182,964 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	49,685,524 - 49,765,967 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	20	51,065,112 - 51,157,124 (+)	NCBI		Celera
Cytogenetic Map	20	q13	NCBI

LIN28B
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	5	124,960,620 - 125,103,365 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	122,847,067 - 122,989,850 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	102,755,256 - 102,897,739 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	106,646,991 - 106,772,374 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	106,640,448 - 106,772,374 (+)	Ensembl	panpan1.1		panPan2

LIN28B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	62,403,831 - 62,529,435 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	62,403,333 - 62,524,838 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	62,192,981 - 62,315,060 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	12	63,254,885 - 63,380,812 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	12	63,245,774 - 63,376,607 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	12	62,610,319 - 62,736,100 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	12	62,451,489 - 62,577,218 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	12	62,730,358 - 62,855,996 (+)	NCBI		UU_Cfam_GSD_1.0

Lin28b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404946	97,371,614 - 97,497,852 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936564	1,663,068 - 1,768,283 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936564	1,646,469 - 1,768,879 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LIN28B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	71,159,251 - 71,296,217 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	71,173,291 - 71,296,131 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	80,544,640 - 80,620,604 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LIN28B
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	13	68,721,209 - 68,859,257 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	13	68,725,392 - 68,839,811 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666040	41,068,949 - 41,187,159 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lin28b
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624952	193,395 - 309,102 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_013510789	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01012257	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDF01020583	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_013510789 ⟹ XP_013366243

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955411	30,381,208 - 30,499,678 (+)	NCBI

Sequence:

show sequence

AGGAAGTGACCCACGTGCGGACGCGTTCACCGACCGCTGCAACCCCGCGTGAGGGTGTTTTACG
AGGATTTGCACTCCAAAAAACTTTTTTTTTTTTTATATCACACATTCGTAAATATTGAGTGTTT
CCGAGTAACATCCTAGAGTATGTATTCGGAGCTCTCAGTGCGGAAATTTCTTAAATGTTCTTCA
GAAGACGATGAGGTCATTCAACCAGGTTTCATCAGCCCCAGGCGGGGCAAGCAAAGGTGGTGGA
GAAGAGTCCGGGAAGCTGCCGGAGCAGGCAGAGGAGGAATCCCAGGTTTTGCACGGAACTGGCC
ACTGTAAGTGGTTCAATGTGCGAATGGGATTTGGATTCATCTCCATGATAAACCGAGAGGGGAG
CCCCTTGGATATTCCAGTGGATGTATTTGTACACCAAAGCAAACTATTCATGGAAGGATTTAGA
AGCCTGAAAGAAGGAGAACCAGTGGAATTCACATTTAAAAAATCTTCCAAAGGCCTTGAATCGA
TACGGGTAACAGGACCTGGTGGGACCCCCTGTTTAGGAAGTGAAAGAAGACCCAAAGGGAAGAC
ACTACAAAAAAGAAAACCAAAGGGAGATAGGTGGAGACGGCAGGATTTACTGATGGATCAGAAG
TGGACTGTGAGAGAAGAAGAGTCCAGGATGACTCCAAGATGCTACAACTGTGGTGGCCTTGATC
ATCATGCAAAGGAATGTAGTCTACCTCCTCAGCCAAAGAAGTGCCATTACTGTCAGAGCATCAT
GCACATGGTGGCAAACTGCCCACACAAAACTGTTGCACAGCTACCCGCCAGTTCTCAGGGAAGA
CAGGAAGCAGAATCCCAGCCGTGCACTTCAGCCTCCCCCAGAGAAGGGGGAGGAGGACACGGCT
GCGCTCCGCCACTGCTTCCTCAGGAGGCTAGGTCAGAGGGCTCGGAACGGCCAGGCAGGTCACC
TCAAGAAGTTTCCTCCGCGAAGGCATCTGCGGCTCCAGAAGAGCAAAACAAAAAGGGGCCTTCT
GTTCAAAAACGAAAAAAGACATAGTCCTTCTTAACATACTGTTTTCCCTACCTGGTTGGGAAGT
CTACCTCATGCAAGTACAGGGAAACAGTATTTCACAGATAGCAGCTGACCTGGAATTTTTAACT
ACTGTTGAGGAACTGTGGATTTTTTTAAACAGACAAATCACTCTAAGCAAATTACATTTGAGCA
AGTTGTCGTGTTTTATGTAATTTAGAGAATGAGGAACTATATACATCAATATATGCTCATGTGC
GAGGGAGGGAGCCTGGCTCTGTGTGCGTGTGTGTGCGGATTTTACTAGGAATGTAGACATATGT
AAAAAGAGGGTTTGTCTTTATATATCTGTGTATGTGGATAAGCACACACCCTCCCTCACATAAT
TGAACATCTCTAAGACCCTGAAAATCCATGTGAAGTATTTAAAATGGTTTAGAAAATAATCCCT
TGAATTTTTCTTACCATGTCACCTTTTTTATAGTACATTTATATTTCATTTCATAAGAATGAAA
ACATGACTGTTACCTTTTGTGTGAACCAAAGGAAACTTCAAATCTCAGAGCTGCCAATCATATG
GTACTAAAGGTTTTTTAAGACATCCAGTTTCTACCAAGTTTGGGATTGCCTCTTTTTCTTGCTC
TCTATGGAGTGGTTTTTTTCTCCCTTTTGAAGGTAATACCTTAAGCCCAAATGCCTCTGCCATA
GCTTTTCTGATTCTGGGATACACAGCTCCAGAAAAGACAATGAATGTGAAATTTCTGTGCTGAC
ATTTCAGTGTTTTTAATTCTATGTTTTGATTGTAAATTACATGCCTAATACGAGAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_013366243	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000015300.1

RefSeq Acc Id:

XP_013366243 ⟸ XM_013510789

- UniProtKB:

A0A8C2VGI2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MRSFNQVSSAPGGASKGGGEESGKLPEQAEEESQVLHGTGHCKWFNVRMGFGFISMINREGSPL
DIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTGPGGTPCLGSERRPKGKTLQ
KRKPKGDRWRRQDLLMDQKWTVREEESRMTPRCYNCGGLDHHAKECSLPPQPKKCHYCQSIMHM
VANCPHKTVAQLPASSQGRQEAESQPCTSASPREGGGGHGCAPPLLPQEARSEGSERPGRSPQE
VSSAKASAAPEEQNKKGPSVQKRKKT

hide sequence

Protein Domains

CCHC-type CSD

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000010534	UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000015460.1	UniProtKB/TrEMBL
Gene3D-CATH	Nucleic acid-binding proteins	UniProtKB/TrEMBL
	Zinc finger, CCHC-type	UniProtKB/TrEMBL
InterPro	CSD	UniProtKB/TrEMBL
	CSP_DNA-bd	UniProtKB/TrEMBL
	NA-bd_OB-fold	UniProtKB/TrEMBL
	Znf_CCHC	UniProtKB/TrEMBL
	Znf_CCHC_sf	UniProtKB/TrEMBL
NCBI Gene	Lin28b	ENTREZGENE
PANTHER	PROTEIN LIN-28	UniProtKB/TrEMBL
	PROTEIN LIN-28 HOMOLOG B	UniProtKB/TrEMBL
Pfam	CSD	UniProtKB/TrEMBL
	zf-CCHC	UniProtKB/TrEMBL
PRINTS	COLDSHOCK	UniProtKB/TrEMBL
PROSITE	CSD_2	UniProtKB/TrEMBL
	ZF_CCHC	UniProtKB/TrEMBL
SMART	CSP	UniProtKB/TrEMBL
	ZnF_C2HC	UniProtKB/TrEMBL
Superfamily-SCOP	Nucleic acid-binding proteins	UniProtKB/TrEMBL
	Retrovirus zinc finger-like domains	UniProtKB/TrEMBL
UniProt	A0A8C2VGI2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-03	Lin28b	lin-28 homolog B		lin-28 homolog B (C. elegans)	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar

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