RetrogeneDB ID: retro_mmus_354

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:112151088..112151753(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gemin2
• Ensembl ID: ENSMUSG00000060121
• Aliases: None
• Description: gem (nuclear organelle) associated protein 2 [Source:MGI Symbol;Acc:MGI:1913853]

Sequence

>retro_mmus_354
AGGATCGAAGCAGCCCAGTGTCCAGATGTTGTGATAGCCCAGACTGACCCAAATAAATTGAAAAAGAATTAAAGTGTGAA
CATTTCTCTTTCCGGATGCCAGCCTGCTCCTGAAGGTTATTACCCAACACTTCAGTGGCATCAACAAGTGGCACATTTTT
CAACTGTTCGACAGAGTGTGTACAAGCATAGAAATCATTGGAAATCTCAACATTTGGATAGTAATGTGGCAATGCCAAAA
TCTGAAGATGAAGAAGGCTGGAAAAATTTTTGTCTAGGTGAAAGATTATGTGCTGAAGGAGCTACTGAACCATCTACAGA
TAAAAGCCCTGGGATTGATTATGTACAAGTTGGTTTTCTTCCCTGGCTTAGTATTTTAAGCAGAATGAATCAGGCAACCA
TTACTAATATCTTGGAATATCTAAGTAATTAATTGGAGAAAGAGACTTTACTCCATAATTGGGAGGATGATTTTATGCTT
TGTTGGCCTGTCTTGAAAAGCCTTTATTACCTGAGGTATATTGACTAATTCGACAGCTTACAAGATGTTCTGAAGTGAGG
CTCCTGGTGGGCAGTAAAGAAGACCAAAGAGTCTAGGCTTTGAATCTGCTGATCTGCTTAGTTAGCAGGTATTTTGATCA
ACATGATTTAGCTGATGAGCCATCT

Alignment

ORF - retro_mmus_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 83.27 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QIEAAQCPDVVVAQIDPKKLKRKQSVNISLSGCQPAPEGYSPTLQWQQQQVAHFSTVRQSVHKHRNHWKS
          .IEAAQCPDVV.AQ.DP.KLK...SVNISLSGCQPAPEGY.PTLQW.QQ.VAHFSTVRQSV.KHRNHWKS
Retrocopy RIEAAQCPDVVIAQTDPNKLKKN*SVNISLSGCQPAPEGYYPTLQWHQQ-VAHFSTVRQSVYKHRNHWKS

Parental  QQLDSNVAMPKSEDEEGWKKFCLGERLCAEGATGPSTEESPGIDYVQVGFPPLLSIVSRMNQTTITSVLE
          Q.LDSNVAMPKSEDEEGWK.FCLGERLCAEGAT.PST..SPGIDYVQVGF.P.LSI.SRMNQ.TIT..LE
Retrocopy QHLDSNVAMPKSEDEEGWKNFCLGERLCAEGATEPSTDKSPGIDYVQVGFLPWLSILSRMNQATITNILE

Parental  YLSN-WFGERDFTPELGRWFYALLACLEKPLLPEAHSLIRQLARRCSEVRLLVGSKDDERVPALNLLICL
          YLSN...GERDFTP.LG..FYALLACLEKPLLPE...LIRQL..RCSEVRLLVGSK.D.RV.ALNLLICL
Retrocopy YLSN<LIGERDFTP*LGG*FYALLACLEKPLLPEVY*LIRQLT-RCSEVRLLVGSKEDQRV*ALNLLICL

Parental  VSRYFDQRDLADEPS
          VSRYFDQ.DLADEPS
Retrocopy VSRYFDQHDLADEPS

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	4.28 RPM
SRP007412_cerebellum	0.00 RPM	5.30 RPM
SRP007412_heart	0.00 RPM	4.45 RPM
SRP007412_kidney	0.00 RPM	4.93 RPM
SRP007412_liver	0.00 RPM	11.03 RPM
SRP007412_testis	0.00 RPM	8.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_354 was not detected

EST

No EST(s) were mapped for retro_mmus_354 retrocopy.

TSS

No TSS is located nearby retro_mmus_354 retrocopy 5' end.

Lab

retro_mmus_354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_354 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016248	1 retrocopy	retro_cjac_2630,
Dasypus novemcinctus	ENSDNOG00000018278	1 retrocopy	retro_dnov_1040,
Homo sapiens	ENSG00000092208	1 retrocopy	retro_hsap_455,
Gorilla gorilla	ENSGGOG00000016691	2 retrocopies	retro_ggor_1844, retro_ggor_438,
Microcebus murinus	ENSMICG00000004811	1 retrocopy	retro_mmur_1221,
Myotis lucifugus	ENSMLUG00000002619	1 retrocopy	retro_mluc_1005,
Mus musculus	ENSMUSG00000060121	1 retrocopy	retro_mmus_354 ,
Pongo abelii	ENSPPYG00000005764	1 retrocopy	retro_pabe_278,
Pan troglodytes	ENSPTRG00000006291	1 retrocopy	retro_ptro_342,