RetrogeneDB ID: retro_mmus_2104

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:150110596..150111620(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083055
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rexo4
• Ensembl ID: ENSMUSG00000052406
• Aliases: Rexo4, Gm111, Xpmc2h
• Description: REX4, RNA exonuclease 4 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2684957]

Sequence

>retro_mmus_2104
GTCTCTGTGTCTTCCCTGTGGTTCGGACTGTGGAGAGCAGGGAGATGAAAACAAAGGCCTTGGCGTCAGTGCCCCAGCCT
GGGCCTATCAGGAAGAAAGCCAAAAGAAGTTCAGGAAGAGCAAAGCTCTGGCAGGAAGTGGGGCTCCAGGAAGCCGCCCT
GTGGCTGTGGTGGGCGGACCACCGAAGGCCCCAGAGAACTTTTCTCAAAATTGGAAGGCGCTACAAGAGCTGCTGAAACA
AACGTCACAGGCCGTAGAAAAACCTCTTGTCTCTCAGATGGATGACAAAATGCACCCCCAAATAATCCAGCAGAACAGAA
AAAAGGCCTCAGATAAATCAAAGGGAGACAAGCAGAGGACAGAAAAAGCCAAGAGCACTAGGGGTTCTGTTACATCTGCA
CCTAAGGACAGGAAGATACTAGTACCTTCCACAGTTACCTCTGGAACAGAGCAGAAGAAAGGAGCCAAGAAGAGGACATA
TAGTGACATCTCTTCTAATCAAGGGGATCTCAAGCCTAAGTGGAAAGCTACAGAGGCAGCTGTTATCTTGAATCAGCCCA
CGCCCACTGAGGAAGACATCTGGTTTGATGATGTGGATCCAGATGATATTGAGGCTGCCATAGGCCCAGAGGCAGCCATG
CTGGTACGGAAGAGGCTGGGGCAGAAGAAGAGGACCATCTCTCTGGTGAAGGAACAAGCCTTTGGTGGCCTGACAAAAGC
CTTGGCCCTGGATTGTGAGATGGTAGGCGTGGGTCCCAAAGGAGAAGAGAGCATCGCAGCCTGTGTGTCCAATGTGAACC
AGTATGGGAAGTGTGTTTATGACAAGTACATCAAGCCAACTGAGCCAGTGTCTGACTACAGGACAGTCGTCAGTGGGATC
CAGCCTGAGAACCTGAAGCAGGGAGAAGAGTTTGAAGTTGTGAAGAAGGTGGCAGAAGTATTGAAGTGCAGAATCCTGGT
GGGGCATGCACTACACAATGATCTAAAGGTTTTGTCCATCCAAAAAAAGAAAATCAGGGACACT

Alignment

ORF - retro_mmus_2104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.6 %
• Parental protein coverage: 80.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAVSSL-VVPTAESGEMKTKATAPVPQPGPIRKLARKKAK-KKFRKSKALAGSGVPGSHPAAVAGRPPKA
          V.VSSL.VV.T.ES.EMKTKA.A.VPQPGPI....RKKAK.KKFRKSKALAGSG.PGS.P.AV.G.PPKA
Retrocopy VSVSSL<VVRTVESREMKTKALASVPQPGPI----RKKAK<KKFRKSKALAGSGAPGSRPVAVVGGPPKA

Parental  PENFSQNWKALQELLKQKSQAAEKPLVSQMDDKMHPQIIQQNRKKASDKSKGDKQRTEKAKSTRGSVTSA
          PENFSQNWKALQELLKQ.SQA.EKPLVSQMDDKMHPQIIQQNRKKASDKSKGDKQRTEKAKSTRGSVTSA
Retrocopy PENFSQNWKALQELLKQTSQAVEKPLVSQMDDKMHPQIIQQNRKKASDKSKGDKQRTEKAKSTRGSVTSA

Parental  PTDRKILVPPTDTSGTEQKKGAKKRTYSDISSHQGALKPKWKATEAAVILNQPTPTEEDIWFDDVDPDDI
          P.DRKILVP.T.TSGTEQKKGAKKRTYSDISS.QG.LKPKWKATEAAVILNQPTPTEEDIWFDDVDPDDI
Retrocopy PKDRKILVPSTVTSGTEQKKGAKKRTYSDISSNQGDLKPKWKATEAAVILNQPTPTEEDIWFDDVDPDDI

Parental  EDAIGPEAAMLVRKRLGQKKRTISLEKEQAFGGLTKALALDCEMVGVGPKGEESIAARVSIVNQYGKCVY
          E.AIGPEAAMLVRKRLGQKKRTISL.KEQAFGGLTKALALDCEMVGVGPKGEESIAA.VS.VNQYGKCVY
Retrocopy EAAIGPEAAMLVRKRLGQKKRTISLVKEQAFGGLTKALALDCEMVGVGPKGEESIAACVSNVNQYGKCVY

Parental  DKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILVGHALHNDLKVLFLDHPKKKIRD
          DKY.KPTEPV.DYRT.VSGI.PENLKQGEEFEVVKK.VAE.LK.RILVGHALHNDLKVL.....KKKIRD
Retrocopy DKYIKPTEPVSDYRTVVSGIQPENLKQGEEFEVVKK-VAEVLKCRILVGHALHNDLKVLSIQ--KKKIRD

Parental  T
          T
Retrocopy T

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	0.05 RPM	42.73 RPM
SRP007412_cerebellum	0.00 RPM	56.62 RPM
SRP007412_heart	0.00 RPM	15.10 RPM
SRP007412_kidney	0.08 RPM	27.78 RPM
SRP007412_liver	0.00 RPM	27.72 RPM
SRP007412_testis	0.00 RPM	18.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2104 was not detected

EST

No EST(s) were mapped for retro_mmus_2104 retrocopy.

TSS

No TSS is located nearby retro_mmus_2104 retrocopy 5' end.

Lab

retro_mmus_2104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000012817	1 retrocopy	retro_mdom_1839,
Mus musculus	ENSMUSG00000052406	2 retrocopies	retro_mmus_1006, retro_mmus_2104 ,
Nomascus leucogenys	ENSNLEG00000013130	1 retrocopy	retro_nleu_2930,
Pongo abelii	ENSPPYG00000019735	1 retrocopy	retro_pabe_1278,