RetrogeneDB ID: retro_mmus_468

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:94468717..94469887(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ppm1b
• Ensembl ID: ENSMUSG00000061130
• Aliases: Ppm1b, PP2CB
• Description: protein phosphatase 1B, magnesium dependent, beta isoform [Source:MGI Symbol;Acc:MGI:101841]

Sequence

>retro_mmus_468
ATGGGTGCATTTTTGGATAAACCCAAAACTGAAAAGCACAATGCTCACGGTGCTGGGAATGGTCTGCGTTATGGCCTGAG
CAGTATGCAAGGATGGAGAGTAGAAATGGAAGATGTACACACAGCTGTTGTGGGTATTCCTCATGGCTTGGACAACTGGT
CGTTTTTTGCAGTTTATGATGGTCATGCTGGATCCCGAGTGGCAAATTACTGTTCAACACATCTATTAGAACACATCACC
ACCAATGAAGACTTCAGGGCAGCTGACAAATCAGGCTCTGCTCTCGAGCCTTCAGTAGAAAGTGTGAAGACTGGTATCAG
GACTGGCTTTTTGAAAATTGATGAATATATGCGCAACTTCTCAGACCTGAGGAACGGGATGGACAGGAGCGGCTCGACTG
CAGTGGGCGTGATGGTCTCCCCTACACACATGTACTTCATCAACTGTGGTGACTCTTGAGCTGTTCTGTGTAGGAACGGA
CAGGTCTGCTTTTCTACCCAGGATCACAAACCTTGTAATCCAGTGGAGAAGGAGCGCATCCAAAACGCAGGAGACAGTGT
GATGATCCAGCGTGTGAACGGCTCACTAGCAGTGTCTCGGGCTCTGGGGGACTATGACTACAAGTGTGTGGATGGCAAGG
GCCCTACAGGGCAGCTTGTTTCTCCAGAGCCTGAGGTTTATGAGATTGTGAGAGCAGAAGAGGATGAGTTTGTCGTCTTG
GCCTGTGATGGGATCTGGGATGTGATGAGCAATGAGGAGCTCTGTGAGTTTGTTAAGTCTAGGCTTGAGGTGTCGGACGA
CCTGGAGAATGTGTGCAATTGGGTAGTGGACACTTGTTTACATAAGGGAAGTCGAGATAACATGAGTGTTGTATTAGTTT
GCTTTTCAAATGCCCCCAAGGTCTCAGAGGAAGCCGTGAAGAGAGATTCAGAGTTGTATAAGCACTTGGAATCACGGGTT
GAAGAAATCATGCAGAAGTCTGGGGAGGAAGGAATGCCTGATCTTGCCCATGTGATGCGCATTTTGTCTGCAGAAAATAT
CCCAAATTTACCTCCCGGGGGAGGTCTCGCTGGCAAGCGCCATGTTATTGAAGCTGTTTATAGTAGACTTAATCCACACA
AAGACAATGATGGGGGCGCTGGCGATCTAGAAGACTCATTGGTAGCCTTA

Alignment

ORF - retro_mmus_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAFLDKPKTEKHNAHGAGNGLRYGLSSMQGWRVEMEDAHTAVVGIPHGLDNWSFFAVYDGHAGSRVANY
          MGAFLDKPKTEKHNAHGAGNGLRYGLSSMQGWRVEMED.HTAVVGIPHGLDNWSFFAVYDGHAGSRVANY
Retrocopy MGAFLDKPKTEKHNAHGAGNGLRYGLSSMQGWRVEMEDVHTAVVGIPHGLDNWSFFAVYDGHAGSRVANY

Parental  CSTHLLEHITTNEDFRAADKSGSALEPSVESVKTGIRTGFLKIDEYMRNFSDLRNGMDRSGSTAVGVMVS
          CSTHLLEHITTNEDFRAADKSGSALEPSVESVKTGIRTGFLKIDEYMRNFSDLRNGMDRSGSTAVGVMVS
Retrocopy CSTHLLEHITTNEDFRAADKSGSALEPSVESVKTGIRTGFLKIDEYMRNFSDLRNGMDRSGSTAVGVMVS

Parental  PTHMYFINCGDSRAVLCRNGQVCFSTQDHKPCNPVEKERIQNAGGSVMIQRVNGSLAVSRALGDYDYKCV
          PTHMYFINCGDS.AVLCRNGQVCFSTQDHKPCNPVEKERIQNAG.SVMIQRVNGSLAVSRALGDYDYKCV
Retrocopy PTHMYFINCGDS*AVLCRNGQVCFSTQDHKPCNPVEKERIQNAGDSVMIQRVNGSLAVSRALGDYDYKCV

Parental  DGKGPTEQLVSPEPEVYEIVRAEEDEFVVLACDGIWDVMSNEELCEFVKSRLEVSDDLENVCNWVVDTCL
          DGKGPT.QLVSPEPEVYEIVRAEEDEFVVLACDGIWDVMSNEELCEFVKSRLEVSDDLENVCNWVVDTCL
Retrocopy DGKGPTGQLVSPEPEVYEIVRAEEDEFVVLACDGIWDVMSNEELCEFVKSRLEVSDDLENVCNWVVDTCL

Parental  HKGSRDNMSVVLVCFSNAPKVSEEAVKRDSELDKHLESRVEEIMQKSGEEGMPDLAHVMRILSAENIPNL
          HKGSRDNMSVVLVCFSNAPKVSEEAVKRDSEL.KHLESRVEEIMQKSGEEGMPDLAHVMRILSAENIPNL
Retrocopy HKGSRDNMSVVLVCFSNAPKVSEEAVKRDSELYKHLESRVEEIMQKSGEEGMPDLAHVMRILSAENIPNL

Parental  PPGGGLAGKRHVIEAVYSRLNPHKDNDGGAGDLEDSLVAL
          PPGGGLAGKRHVIEAVYSRLNPHKDNDGGAGDLEDSLVAL
Retrocopy PPGGGLAGKRHVIEAVYSRLNPHKDNDGGAGDLEDSLVAL

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	0.14 RPM	55.70 RPM
SRP007412_cerebellum	0.09 RPM	90.23 RPM
SRP007412_heart	0.28 RPM	70.54 RPM
SRP007412_kidney	0.48 RPM	75.54 RPM
SRP007412_liver	0.11 RPM	73.46 RPM
SRP007412_testis	0.59 RPM	136.99 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_468 was not detected

EST

No EST(s) were mapped for retro_mmus_468 retrocopy.

TSS

No TSS is located nearby retro_mmus_468 retrocopy 5' end.

Lab

retro_mmus_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_468 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021096	2 retrocopies	retro_mmus_2925, retro_mmus_2926,
Mus musculus	ENSMUSG00000061130	1 retrocopy	retro_mmus_468 ,
Oryctolagus cuniculus	ENSOCUG00000005461	1 retrocopy	retro_ocun_1094,
Drosophila melanogaster	FBgn0035425	1 retrocopy	retro_dmel_64,
Drosophila melanogaster	FBgn0086361	1 retrocopy	retro_dmel_66,