RetrogeneDB ID: retro_mmus_1006

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:40496383..40497308(+)
• Located in intron of: None

Retrocopy information

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

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_1006
CCTGCAGCTGTGGCAGGCCGACCGCCGAAGGCCCCAGAGAACTTCTCTCAAAACTTGAAGGCGCTGCAAGAGCTGCTTAA
ACAAAAGTCACAGGCCCCAGAAAAACCTCTTGTCTCTCAGATGGATGACAAAATGCATCCCCAAATAATCCCGCAGAACA
GAAAAAGAGGCCTCAGATAAATCAAAGGGAGACAAGAAGTGGTCAGAAAAAGACAAGAGCACTAAGGGTTCTGTTACATC
TGCACCTAAGGACAGGAAGATGCTAGTACCTCCCACAGATACCTCTGGAACAGAGCCGTAGAAAGGACCCAAGAAGAGGA
CATATAGTGACATCTTTTCTCATCAAGAGGATCTCAAACCTAAGTGGAAAGCTACGGAGGCAGCTGTCATCTTGAATCAG
CCCACGCCCACTGAGGGAGACATCTGGTTTGATGATGTGGATGCAGATGATACTGAGGCTGCCATAGGGTCAGAGGCAGC
CATGCCGGTACAGAAGAGACTGCGCAGAGCGAGAGTACCATCTCCCTGGTGAAGGAACAAGCCTTTAGCGGCCTGACAAA
AGCCTTGGCCCTGGATTGTGAGATGGTAGGCGAGGGCCCCAAAGGAGAAGAAGGCATCATCGAAGCCGGTGTGTCCATCG
TGAACCAGTATGGGAAGTGCGTCTATGACAAGTACGTCAAGCCAACTGAGCCAGTGACTGACTATGGGACAGCCGTCAGT
GGGATCCAGCCTGAGAACCTGAAGCAGGGAGCAGAGTTTGAAGTTATGGAGAAGGAAATGGCAGAAATGTTGAACGGCAA
AATCCTGGTGGGGCACGCGCTACACAATGATTTAAAGGTTCTGTTTCTTGACCACCACCAACACCCCCCCAAAGAAAATC
AGGAACACCCAAAAATTCAAACCATTCCAGAGTCCAGTAAAGAGT

Alignment

ORF - retro_mmus_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 70.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PAAVAGRPPKAPENFSQNWKALQELLKQKSQAAEKPLVSQMDDKMHPQIIQQNRKK-ASDKSKGDKQRTE
          PAAVAGRPPKAPENFSQN.KALQELLKQKSQA.EKPLVSQMDDKMHPQII.QNRK..ASDKSKGDK...E
Retrocopy PAAVAGRPPKAPENFSQNLKALQELLKQKSQAPEKPLVSQMDDKMHPQIIPQNRKR>ASDKSKGDKKWSE

Parental  KAKSTRGSVTSAPTDRKILVPPTDTSGTEQKKGAKKRTYSDISSHQGALKPKWKATEAAVILNQPTPTEE
          K.KST.GSVTSAP.DRK.LVPPTDTSGTE..KG.KKRTYSDI.SHQ..LKPKWKATEAAVILNQPTPTE.
Retrocopy KDKSTKGSVTSAPKDRKMLVPPTDTSGTEP*KGPKKRTYSDIFSHQEDLKPKWKATEAAVILNQPTPTEG

Parental  DIWFDDVDPDDIEDAIGPEAAMLVRKRL-GQKKRTISLEKEQAFGGLTKALALDCEMVGVGPKGEES-IA
          DIWFDDVD.DD.E.AIG.EAAM.V.KRL..Q...TISL.KEQAF.GLTKALALDCEMVG.GPKGEE..I.
Retrocopy DIWFDDVDADDTEAAIGSEAAMPVQKRL<AQSESTISLVKEQAFSGLTKALALDCEMVGEGPKGEEGIIE

Parental  ARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILVGHALHNDL
          A.VSIVNQYGKCVYDKYVKPTEPVTDY.TAVSGI.PENLKQG.EFEV..KE.AEML.G.ILVGHALHNDL
Retrocopy AGVSIVNQYGKCVYDKYVKPTEPVTDYGTAVSGIQPENLKQGAEFEVMEKEMAEMLNGKILVGHALHNDL

Parental  KVLFLDH---PKKK-IRDTQKFKPFRSRVKS
          KVLFLDH...P.K..IR.TQKFKPF.S.VKS
Retrocopy KVLFLDHHQHPPKE>IRNTQKFKPFQSPVKS

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	42.73 RPM
SRP007412_cerebellum	0.00 RPM	56.62 RPM
SRP007412_heart	0.00 RPM	15.10 RPM
SRP007412_kidney	0.00 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_1006 was not detected

EST

No EST(s) were mapped for retro_mmus_1006 retrocopy.

TSS

No TSS is located nearby retro_mmus_1006 retrocopy 5' end.

Lab

retro_mmus_1006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1006 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,