RetrogeneDB ID: retro_mmus_3487

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:93931601..93931834(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081573
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ccdc167
• Ensembl ID: ENSMUSG00000024018
• Aliases: Ccdc167, 1110021J02Rik
• Description: coiled-coil domain containing 167 [Source:MGI Symbol;Acc:MGI:1915847]

Sequence

>retro_mmus_3487
GAAAAACTGTCTCAGTGTAGGAAGGACCTGGAGGCCATGACCTCCCAGCTCTACAGGGCAGACCGAGTCCTGAGGACAGG
AGGTCTCTGGAGAAGGAGAAAAACACCCTCAGGAACAAAGCCTCCAAGTATGAGAAGGAGCTGAAGCTGCTTTGACAAGA
GAACCGGCAGAACATGCTCCTCTCGGTGGCCATCTTCATAGTCTTCACCGTGCTCCATGCTCCCTGGACTATG

Alignment

ORF - retro_mmus_3487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.75 %
• Parental protein coverage: 80.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKLSRCRKDLEAVTSQLYRAEL-SPEDRRSLEKEKHTLMNKASKYEKELKLLRHENRKNTLLSVAIFTVF
          EKLS.CRKDLEA.TSQLYRA...SPEDRRSLEKEK.TL.NKASKYEKELKLL..ENR.N.LLSVAIF.VF
Retrocopy EKLSQCRKDLEAMTSQLYRADR<SPEDRRSLEKEKNTLRNKASKYEKELKLL*QENRQNMLLSVAIFIVF

Parental  ALLYAYWTM
          ..L.A.WTM
Retrocopy TVLHAPWTM

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	7.36 RPM
SRP007412_cerebellum	0.00 RPM	17.28 RPM
SRP007412_heart	0.00 RPM	6.26 RPM
SRP007412_kidney	0.00 RPM	4.60 RPM
SRP007412_liver	0.00 RPM	3.03 RPM
SRP007412_testis	0.00 RPM	1.97 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3487 was not detected

EST

No EST(s) were mapped for retro_mmus_3487 retrocopy.

TSS

No TSS is located nearby retro_mmus_3487 retrocopy 5' end.

Lab

retro_mmus_3487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3487 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012069	2 retrocopies	retro_btau_30, retro_btau_517,
Canis familiaris	ENSCAFG00000030835	1 retrocopy	retro_cfam_1854,
Callithrix jacchus	ENSCJAG00000005622	2 retrocopies	retro_cjac_3293, retro_cjac_960,
Felis catus	ENSFCAG00000006745	1 retrocopy	retro_fcat_1558,
Mus musculus	ENSMUSG00000024018	1 retrocopy	retro_mmus_3487 ,
Otolemur garnettii	ENSOGAG00000000921	1 retrocopy	retro_ogar_880,
Pongo abelii	ENSPPYG00000016563	1 retrocopy	retro_pabe_2092,