Mycbp2 MYC binding protein 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Mycbp2provided by RGD
Full Name: MYC binding protein 2provided by RGD
Primary source: RGD:1312048
See related: EnsemblRapid:ENSRNOG00000010479 AllianceGenome:RGD:1312048
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Pam; Phr1
Summary: Predicted to enable several functions, including guanyl-nucleotide exchange factor activity; small GTPase binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including circadian regulation of gene expression; protein K48-linked ubiquitination; and regulation of synaptic assembly at neuromuscular junction. Predicted to act upstream of or within several processes, including axonogenesis; negative regulation of protein catabolic process; and regulation of cytoskeleton organization. Predicted to be located in several cellular components, including axon; microtubule cytoskeleton; and nucleoplasm. Predicted to be active in nucleus and plasma membrane. Orthologous to human MYCBP2 (MYC binding protein 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 368.4), Brain (RPKM 313.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15q21

Exon count:: 86

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (86352061..86590126, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (79937354..80175432, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (93678062..93901556, complement) , (87405472..87450812, complement)

Chromosome 15 - NC_086033.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Protein network profiles associated with PAM during the modulation of synaptic strength, was studied.
Title: Toponomics analysis of functional interactions of the ubiquitin ligase PAM (Protein Associated with Myc) during spinal nociceptive processing.
Pam, through its interaction with tuberin, could regulate the ubiquitination and proteasomal degradation of the tuberin-hamartin complex particularly in the CNS [Mycbp2]
Title: Pam and its ortholog highwire interact with and may negatively regulate the TSC1.TSC2 complex.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BM386386 (e-PCR)
- UniSTS:261259

RH143902 (e-PCR)
- UniSTS:233148

AI102336 (e-PCR)
- UniSTS:261079

RH125194 (e-PCR)
- UniSTS:162016

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables small GTPase binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within branchiomotor neuron axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell morphogenesis involved in neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system projection neuron axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in central nervous system projection neuron axonogenesis	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K48-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in regulation of axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cytoskeleton organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic assembly at neuromuscular junction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in axon	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in microtubule cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase MYCBP2

Names: E3 ubiquitin-protein ligase MYCBP2-like; MYC binding protein 2, E3 ubiquitin protein ligase; pam, highwire, rpm 1; probable E3 ubiquitin-protein ligase MYCBP2; probable E3 ubiquitin-protein ligase MYCBP2-like; protein associated with Myc

NP_001099525.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949112.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949114.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949115.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949116.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949117.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949118.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949119.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949120.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949121.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949122.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949123.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949124.2

EC 2.3.2.27

EC 2.3.2.33

XP_038949125.1

EC 2.3.2.27

EC 2.3.2.33

XP_038949126.1

EC 2.3.2.27

EC 2.3.2.33

XP_063130239.1

EC 2.3.2.27

EC 2.3.2.33

XP_063130241.1

EC 2.3.2.27

EC 2.3.2.33

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.

mRNA and Protein(s)

NM_001106055.2 → NP_001099525.2 E3 ubiquitin-protein ligase MYCBP2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A0A8I6A2N3, A0A8I6A4L1

Related

ENSRNOP00000085907.2, ENSRNOT00000099831.2

Conserved Domains (8) summary

smart00557
Location:2392 → 2443

IG_FLMN; Filamin-type immunoglobulin domains

COG5184
Location:683 → 1024

ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]

pfam00415
Location:958 → 1006

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam08005
Location:1724 → 1879

PHR; PHR domain

pfam08239
Location:2477 → 2537

SH3_3; Bacterial SH3 domain

pfam13540
Location:943 → 971

RCC1_2; Regulator of chromosome condensation (RCC1) repeat

pfam13639
Location:4497 → 4550

zf-RING_2; Ring finger domain

cl02148
Location:3822 → 3914

APC10-like; APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086033.1 Reference GRCr8

Range

86352061..86590126 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063274171.1 → XP_063130241.1 E3 ubiquitin-protein ligase MYCBP2 isoform X14

Related

ENSRNOP00000092896.1, ENSRNOT00000109278.2
XM_039093195.2 → XP_038949123.2 E3 ubiquitin-protein ligase MYCBP2 isoform X12
XM_039093194.2 → XP_038949122.2 E3 ubiquitin-protein ligase MYCBP2 isoform X11

Related

ENSRNOP00000076173.2, ENSRNOT00000093546.3
XM_039093192.2 → XP_038949120.2 E3 ubiquitin-protein ligase MYCBP2 isoform X9

Related

ENSRNOP00000085773.1, ENSRNOT00000112777.2
XM_039093191.2 → XP_038949119.2 E3 ubiquitin-protein ligase MYCBP2 isoform X8
XM_039093196.2 → XP_038949124.2 E3 ubiquitin-protein ligase MYCBP2 isoform X13
XM_039093193.2 → XP_038949121.2 E3 ubiquitin-protein ligase MYCBP2 isoform X10
XM_039093190.2 → XP_038949118.2 E3 ubiquitin-protein ligase MYCBP2 isoform X7

Related

ENSRNOP00000076104.2, ENSRNOT00000093370.3
XM_039093189.2 → XP_038949117.2 E3 ubiquitin-protein ligase MYCBP2 isoform X6
XM_039093188.2 → XP_038949116.2 E3 ubiquitin-protein ligase MYCBP2 isoform X5
XM_063274169.1 → XP_063130239.1 E3 ubiquitin-protein ligase MYCBP2 isoform X4
XM_039093186.2 → XP_038949114.2 E3 ubiquitin-protein ligase MYCBP2 isoform X2
XM_039093187.2 → XP_038949115.2 E3 ubiquitin-protein ligase MYCBP2 isoform X3
XM_039093184.2 → XP_038949112.2 E3 ubiquitin-protein ligase MYCBP2 isoform X1
XM_039093197.2 → XP_038949125.1 E3 ubiquitin-protein ligase MYCBP2 isoform X15

UniProtKB/TrEMBL

A0A1W2Q616

Conserved Domains (8) summary

COG5184
Location:683 → 988

ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]

cd16463
Location:4475 → 4529

RING-H2_PHR; RING finger, H2 subclass, found in the PHR protein family

cd19799
Location:4309 → 4357

Bbox2_MYCBP2; B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins

cl02148
Location:3798 → 3890

APC10-like; APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination

pfam00415
Location:922 → 970

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam08005
Location:1199 → 1349

PHR; PHR domain

pfam08239
Location:2442 → 2504

SH3_3; Bacterial SH3 domain

cl27659
Location:2359 → 2410

Filamin; Filamin/ABP280 repeat
XM_039093198.2 → XP_038949126.1 E3 ubiquitin-protein ligase MYCBP2 isoform X16

Conserved Domains (5) summary

cd16463
Location:2314 → 2368

RING-H2_PHR; RING finger, H2 subclass, found in the PHR protein family

cd19799
Location:2148 → 2196

Bbox2_MYCBP2; B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins

cl02148
Location:1637 → 1729

APC10-like; APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination

pfam08239
Location:281 → 343

SH3_3; Bacterial SH3 domain

cl27659
Location:198 → 249

Filamin; Filamin/ABP280 repeat