RetrogeneDB ID: retro_mmus_2004

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:179364293..179364815(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081882
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl8
• Ensembl ID: ENSMUSG00000003970
• Aliases: None
• Description: ribosomal protein L8 [Source:MGI Symbol;Acc:MGI:1350927]

Sequence

>retro_mmus_2004
ATGGGCCATGAGATCTGAGGTCAGAGGAAAGGCACCTGGGTTGTGTATTCTGCAGTCAGACACATGAAACACCAGCTTGT
CTGCGTGCTGTGGACTTTGCTGAGCAACACGGCCATATTAAGTGCATTGCAAAGAACATCATTCATGACCCTGGCTATGG
CACTCCCTTGTAAAGGGTGGCCTTTCATGATCCCTACCCATCTAAGAAGCGGAGGAAGCTGTTCACCCCTGCAGGGGGAA
TCCACACCTGGCAATCTGTGTACTGAGGCACAAAGGCCCACACAGTAGCAGCAATGCTTTGCCCATGGGCACTACTGCTG
AAGGTACTGTGATGTGTTGTCTGGAGGAGAATCCTGGGAAGAGGCAAGCTGGCACAAGCCTCCAGGATTTCTCCCACAAT
CATCTCCCATGACTGTGGAGCCCAAGAAGACCCAACTAAAGCTTCCTTCAGGATCCAAGGTGATTTTCTCAGCCATGAGA
GCTATTGTTGGCATGGTTGCCAGGGGAGACAGAATTGACAAA

Alignment

ORF - retro_mmus_2004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.56 %
• Parental protein coverage: 68.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGRVIRGQRKGAGSVFRAHVKHRKGA-ARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRF
          MG..I.GQRKG...V..A.V.H.K...A.LRAVDFAE.HG.IK.I.K.IIHDPG.G.PL..V.F.DPY..
Retrocopy MGHEI*GQRKGTWVVYSA-VRHMKHQ<ACLRAVDFAEQHGHIKCIAKNIIHDPGYGTPL*RVAFHDPYPS

Parental  KKRTELFIAAEGIHTGQFVYCGKKAQL-NIGNVLPVGTMPEGTIVCCLEEKPGD-RGKLARASGNYATVI
          KKR..LF..A.GIHT.Q.VY.G.KA......N.LP.GT..EGT.V.C..E.....RGKLA.AS....T.I
Retrocopy KKRRKLFTPAGGIHTWQSVY*GTKAHT<SSSNALPMGTTAEGT-VMCCLEENPG>RGKLAQASRISPTII

Parental  SHN-PETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDK
          SH...E.KKT..KLPSGSK.VI.SA.RA.VG.VA.G.RIDK
Retrocopy SHD>VEPKKTQLKLPSGSK-VIFSAMRAIVGMVARGDRIDK

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	123.99 RPM
SRP007412_cerebellum	0.00 RPM	178.07 RPM
SRP007412_heart	0.00 RPM	251.66 RPM
SRP007412_kidney	0.00 RPM	251.61 RPM
SRP007412_liver	0.00 RPM	224.72 RPM
SRP007412_testis	0.00 RPM	201.71 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2004 was not detected

EST

No EST(s) were mapped for retro_mmus_2004 retrocopy.

TSS

No TSS is located nearby retro_mmus_2004 retrocopy 5' end.

Lab

retro_mmus_2004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2004 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Gorilla gorilla	ENSGGOG00000008164	1 retrocopy	retro_ggor_1974,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Mus musculus	ENSMUSG00000003970	2 retrocopies	retro_mmus_2004 , retro_mmus_2112,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Pan troglodytes	ENSPTRG00000020716	1 retrocopy	retro_ptro_1931,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,