RetrogeneDB ID: retro_mmus_2694

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:121471556..121472164(-)
• Located in intron of: ENSMUSG00000029452

Retrocopy information

• Ensembl ID: ENSMUSG00000082760
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mapk3
• Ensembl ID: ENSMUSG00000063065
• Aliases: Mapk3, Erk-1, Erk1, Ert2, Esrk1, Mnk1, Mtap2k, Prkm3, p44, p44erk1, p44mapk
• Description: mitogen-activated protein kinase 3 [Source:MGI Symbol;Acc:MGI:1346859]

Sequence

>retro_mmus_2694
ATCAGCCCCTTTGAGCATCAAACCTACTGTCAGCGCACGCTGAGGGAAACCCAGATCTTGCTGTGATTCTGCCATGAGAA
TGTCATAGGCACCTGAGACATCCTCAGAGCACCCACCCTGGAAACCATGAGAGACATTTACATTGTTCAGGACCTCATGG
AGACAGACCTGTGCAAGCTGTTTAAGAGCCAGCCCCTGAGCAGTGACCACATCTGCTACTTCCTCTACCAGATCCTCTGG
GGCCTCAAGTGCATACACTCAGCCAATGTGCTGCACCGGGACCTGAAGCCTGCCAATCTGCTTTTCAACACCACCTGCGA
CCTTAAGGTCTGTGAGTTTGGCCTGGCCCGGATTGTTGACCCTGAACATGACCACACTGGCTTTCTGACAGAGTATGTGG
CCACATGCTGGTTCTGAGCCCCAGAGATCATGCTTAACTCCAAGGGCTACCCCAAATCCATTGACATCGGACTGTGGGCT
GCATTCTAGCTGAGATGCTCTCAAGCCGGCCCATCTTCCCGGGCAAGCACTACCTGGACCAGCTCAATCACATTCTAGGT
ATCCTGGATTCCCCATCCCAGAAGGACCTTAATTGTATCATTAAACTT

Alignment

ORF - retro_mmus_2694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 53.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRAPTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDH
          ISPFEHQTYCQRTLRE.QILL.F.HENVIG..DILRAPTLE.MRD.YIVQDLMETDL.KL.KSQ.LS.DH
Retrocopy ISPFEHQTYCQRTLRETQILL*FCHENVIGT*DILRAPTLETMRDIYIVQDLMETDLCKLFKSQPLSSDH

Parental  ICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRA
          ICYFLYQIL.GLK.IHSANVLHRDLKP.NLL.NTTCDLK.C.FGLARI.DPEHDHTGFLTEYVAT.W..A
Retrocopy ICYFLYQILWGLKCIHSANVLHRDLKPANLLFNTTCDLKVCEFGLARIVDPEHDHTGFLTEYVATCWF*A

Parental  PEIMLNSKGYTKSIDIW-SVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINM
          PEIMLNSKGY.KSIDI...VGCILAEMLS.RPIFPGKHYLDQLNHILGIL.SPSQ.DLNCII..
Retrocopy PEIMLNSKGYPKSIDIG<TVGCILAEMLSSRPIFPGKHYLDQLNHILGILDSPSQKDLNCIIKL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	109.62 RPM
SRP007412_cerebellum	0.00 RPM	73.43 RPM
SRP007412_heart	0.00 RPM	43.64 RPM
SRP007412_kidney	0.02 RPM	50.05 RPM
SRP007412_liver	0.00 RPM	24.66 RPM
SRP007412_testis	0.00 RPM	98.29 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_2694 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	5:121472537..121472567

EST

No EST(s) were mapped for retro_mmus_2694 retrocopy.

TSS

No TSS is located nearby retro_mmus_2694 retrocopy 5' end.

Lab

retro_mmus_2694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2694 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017108	1 retrocopy	retro_cfam_1254,
Loxodonta africana	ENSLAFG00000017904	1 retrocopy	retro_lafr_1022,
Mus musculus	ENSMUSG00000063065	1 retrocopy	retro_mmus_2694 ,
Rattus norvegicus	ENSRNOG00000019601	1 retrocopy	retro_rnor_831,