LARP1B La ribonucleoprotein 1B [Homo sapiens (human)] - Gene

Summary

Official Symbol: LARP1Bprovided by HGNC
Official Full Name: La ribonucleoprotein 1Bprovided by HGNC
Primary source: HGNC:HGNC:24704
See related: Ensembl:ENSG00000138709 MIM:620467; AllianceGenome:HGNC:24704
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LARP2
Summary: This gene encodes a protein containing domains found in the La related protein of Drosophila melanogaster. La motif-containing proteins are thought to be RNA-binding proteins, where the La motif and adjacent amino acids fold into an RNA recognition motif. The La motif is also found in proteins unrelated to the La protein. Alternative splicing has been observed at this locus and multiple variants, encoding distinct isoforms, are described. Additional splice variation has been identified but the full-length nature of these transcripts has not been determined. [provided by RefSeq, Jun 2013]
Expression: Broad expression in testis (RPKM 13.1), liver (RPKM 5.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q28.2

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (128060789..128222926)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (131364692..131527023)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (128981944..129144081)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The promoter of the gene of La ribonucleoprotein domain family (LARP2) was significantly hypermethylated in beta-thalassemia, and the expression of LARP2 was significantly lower in beta-thalassemia.
Title: Hypermethylation of the gene LARP2 for noninvasive prenatal diagnosis of β-thalassemia based on DNA methylation profile.
Review discusses the La motif, found in this protein.
Title: The La protein.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-X16707 (e-PCR)
- UniSTS:49165

SHGC-14401 (e-PCR)
- UniSTS:13370

SHGC-154468 (e-PCR)
- UniSTS:183874

SHGC-51061 (e-PCR)
- UniSTS:32071

NoName (e-PCR)
- UniSTS:236420

SHGC-24749 (e-PCR)
- UniSTS:16015

G01821 (e-PCR)
- UniSTS:9632

SHGC-50527 (e-PCR)
- UniSTS:31165

STS-H96643 (e-PCR)
- UniSTS:42691

RH80069 (e-PCR)
- UniSTS:89074

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA cap binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA stabilization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of translation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasmic stress granule	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	HDA more info	PubMed

General protein information

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Preferred Names: la-related protein 1B

Names: La ribonucleoprotein domain family member 1B; La ribonucleoprotein domain family, member 2; la-related protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_047161.1 RefSeqGene

Range

5047..155723

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001278604.2 → NP_001265533.1 la-related protein 1B isoform 4

See identical proteins and their annotated locations for NP_001265533.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. It encodes isoform 4 which is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK092764, BC110300, DA181086

Consensus CDS

CCDS64057.1

UniProtKB/Swiss-Prot

Q659C4

Related

ENSP00000377829.3, ENST00000394288.7

Conserved Domains (1) summary

cl02755
Location:216 → 288

LAM; LA motif RNA-binding domain
NM_001350531.2 → NP_001337460.1 la-related protein 1B isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, contains multiple coding region differences and uses a downstream start codon, compared to variant 1. It encodes isoform 5, which is shorter than isoform 1.

Source sequence(s)

AC096898, AK027164, AK092764, AL137759, BC018794, BX103089, BX537937

Conserved Domains (2) summary

smart00684
Location:468 → 506

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cl02755
Location:1 → 47

LAM; LA motif RNA-binding domain
NM_001410786.1 → NP_001397715.1 la-related protein 1B isoform 6

Status: REVIEWED

Source sequence(s)

AC096898, AC099340, AC108045, AC114735, AC124030

Consensus CDS

CCDS93633.1

UniProtKB/TrEMBL

A0A994J4H9, A0A994J4X5
NM_018078.4 → NP_060548.2 la-related protein 1B isoform 1

See identical proteins and their annotated locations for NP_060548.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC096898, AI374914, AK027164, AK092764, AL137759, DA181086, DB230609

Consensus CDS

CCDS3738.1

UniProtKB/Swiss-Prot

Q2YDB6, Q4W599, Q4W5B2, Q659A0, Q659C4, Q6P5X2, Q7Z3F7, Q86VK7, Q8N6F4, Q8N7H4, Q8NAF2, Q9H5E7, Q9NW12

UniProtKB/TrEMBL

A0A994J4H9

Related

ENSP00000321997.6, ENST00000326639.11

Conserved Domains (2) summary

smart00684
Location:748 → 786

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cd08038
Location:216 → 288

LARP_2; La RNA-binding domain of La-related protein 2
NM_032239.4 → NP_115615.2 la-related protein 1B isoform 3

See identical proteins and their annotated locations for NP_115615.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks several exons and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 3 which is much shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AA037692, AC108045, AK092764, AL832170, DA181086

Consensus CDS

CCDS47133.1

UniProtKB/TrEMBL

A0A3B3ISF8, G3V0E9

Related

ENSP00000390395.2, ENST00000432347.6

Conserved Domains (1) summary

cl02755
Location:216 → 288

LAM; LA motif RNA-binding domain
NM_178043.3 → NP_835144.1 la-related protein 1B isoform 2

See identical proteins and their annotated locations for NP_835144.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks several exons and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK001240, AK092764, BM129812, DA181086

UniProtKB/TrEMBL

D6R9W6

Related

ENSP00000424383.1, ENST00000507377.1

Conserved Domains (1) summary

cl02755
Location:216 → 288

LAM; LA motif RNA-binding domain

RNA

NR_146772.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks two internal exons and contains an alternate 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI652589, AI806546, AK027164, AK092764, AL137759, BC018794, BX537937

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

128060789..128222926

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017008340.2 → XP_016863829.1 la-related protein 1B isoform X13

UniProtKB/TrEMBL

A0A994J4H9

Conserved Domains (2) summary

smart00684
Location:776 → 814

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cl02755
Location:216 → 288

LAM; LA motif RNA-binding domain
XM_047415872.1 → XP_047271828.1 la-related protein 1B isoform X16

UniProtKB/Swiss-Prot

Q2YDB6, Q4W599, Q4W5B2, Q659A0, Q659C4, Q6P5X2, Q7Z3F7, Q86VK7, Q8N6F4, Q8N7H4, Q8NAF2, Q9H5E7, Q9NW12

UniProtKB/TrEMBL

A0A994J4H9
XM_011532057.3 → XP_011530359.2 la-related protein 1B isoform X2
XM_017008338.2 → XP_016863827.1 la-related protein 1B isoform X1
XM_011532059.3 → XP_011530361.2 la-related protein 1B isoform X4
XM_011532058.4 → XP_011530360.2 la-related protein 1B isoform X3
XM_011532062.3 → XP_011530364.2 la-related protein 1B isoform X8
XM_017008339.2 → XP_016863828.1 la-related protein 1B isoform X5

UniProtKB/TrEMBL

A0A3B3ISF0
XM_011532063.3 → XP_011530365.2 la-related protein 1B isoform X9
XM_011532060.3 → XP_011530362.2 la-related protein 1B isoform X6
XM_011532064.3 → XP_011530366.2 la-related protein 1B isoform X10
XM_047415870.1 → XP_047271826.1 la-related protein 1B isoform X12
XM_011532061.3 → XP_011530363.1 la-related protein 1B isoform X7

Conserved Domains (3) summary

smart00684
Location:930 → 968

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cd08038
Location:370 → 442

LARP_2; La RNA-binding domain of La-related protein 2

COG5193
Location:200 → 434

LHP1; La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]
XM_011532065.3 → XP_011530367.1 la-related protein 1B isoform X11

Conserved Domains (3) summary

smart00684
Location:890 → 928

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cd08038
Location:370 → 442

LARP_2; La RNA-binding domain of La-related protein 2

COG5193
Location:200 → 434

LHP1; La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]
XM_011532067.2 → XP_011530369.1 la-related protein 1B isoform X13

UniProtKB/TrEMBL

A0A994J4H9

Conserved Domains (2) summary

smart00684
Location:776 → 814

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cl02755
Location:216 → 288

LAM; LA motif RNA-binding domain
XM_047415871.1 → XP_047271827.1 la-related protein 1B isoform X15

UniProtKB/TrEMBL

A0A994J4H9
XM_047415873.1 → XP_047271829.1 la-related protein 1B isoform X19

UniProtKB/TrEMBL

A0A994J4H9
XM_047415874.1 → XP_047271830.1 la-related protein 1B isoform X20

UniProtKB/TrEMBL

A0A994J4H9
XM_017008343.2 → XP_016863832.1 la-related protein 1B isoform X17

UniProtKB/TrEMBL

A0A994J4H9, A0A994J4X5

Related

ENSP00000515817.1, ENST00000704292.1

Conserved Domains (2) summary

smart00684
Location:736 → 774

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cl02755
Location:216 → 288

LAM; LA motif RNA-binding domain
XM_047415875.1 → XP_047271831.1 la-related protein 1B isoform X21

UniProtKB/TrEMBL

A0A994J4H9
XM_047415877.1 → XP_047271833.1 la-related protein 1B isoform X24

UniProtKB/TrEMBL

A0A994J4H9
XM_011532068.2 → XP_011530370.1 la-related protein 1B isoform X18

Conserved Domains (3) summary

smart00684
Location:729 → 767

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

COG5193
Location:3 → 233

LHP1; La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]

cl02755
Location:169 → 241

LAM; LA motif RNA-binding domain
XM_011532069.2 → XP_011530371.1 la-related protein 1B isoform X22

UniProtKB/TrEMBL

A0A994J4H9

Conserved Domains (3) summary

smart00684
Location:689 → 727

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

COG5193
Location:5 → 233

LHP1; La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]

cl02755
Location:169 → 241

LAM; LA motif RNA-binding domain
XM_047415876.1 → XP_047271832.1 la-related protein 1B isoform X23

UniProtKB/TrEMBL

A0A994J4H9
XM_017008341.2 → XP_016863830.1 la-related protein 1B isoform X13

UniProtKB/TrEMBL

A0A994J4H9

Conserved Domains (2) summary

smart00684
Location:776 → 814

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cl02755
Location:216 → 288

LAM; LA motif RNA-binding domain
XM_047415879.1 → XP_047271835.1 la-related protein 1B isoform X27
XM_047415883.1 → XP_047271839.1 la-related protein 1B isoform X36
XM_011532070.3 → XP_011530372.2 la-related protein 1B isoform X25
XM_011532072.3 → XP_011530374.2 la-related protein 1B isoform X28
XM_047415878.1 → XP_047271834.1 la-related protein 1B isoform X26
XM_017008347.2 → XP_016863836.1 la-related protein 1B isoform X31
XM_047415882.1 → XP_047271838.1 la-related protein 1B isoform X33
XM_024454116.2 → XP_024309884.1 la-related protein 1B isoform X34

Conserved Domains (2) summary

cd08038
Location:417 → 489

LARP_2; La RNA-binding domain of La-related protein 2

COG5193
Location:311 → 481

LHP1; La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]
XM_017008345.2 → XP_016863834.1 la-related protein 1B isoform X30
XM_011532073.3 → XP_011530375.2 la-related protein 1B isoform X29
XM_047415881.1 → XP_047271837.1 la-related protein 1B isoform X32
XM_017008348.2 → XP_016863837.1 la-related protein 1B isoform X35
XM_047415886.1 → XP_047271842.1 la-related protein 1B isoform X38
XM_017008352.2 → XP_016863841.1 la-related protein 1B isoform X39

UniProtKB/TrEMBL

A0A3B3IT29
XM_047415887.1 → XP_047271843.1 la-related protein 1B isoform X40

Related

ENSP00000497514.2, ENST00000648358.2
XM_017008342.2 → XP_016863831.1 la-related protein 1B isoform X14

UniProtKB/TrEMBL

A0A994J4H9
XM_047415885.1 → XP_047271841.1 la-related protein 1B isoform X37
XM_011532077.3 → XP_011530379.1 la-related protein 1B isoform X37

See identical proteins and their annotated locations for XP_011530379.1

Conserved Domains (2) summary

smart00684
Location:535 → 573

DM15; Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function

cl02755
Location:1 → 47

LAM; LA motif RNA-binding domain
XM_047415884.1 → XP_047271840.1 la-related protein 1B isoform X37