RetrogeneDB ID: retro_mmus_1777

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:57116729..57117103(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl35
• Ensembl ID: ENSMUSG00000052962
• Aliases: Mrpl35, 1110066C01Rik
• Description: mitochondrial ribosomal protein L35 [Source:MGI Symbol;Acc:MGI:1913473]

Sequence

>retro_mmus_1777
CTGTCAAACACCTGGCACATGGGCATAGTGCACCAGTCAGTCCTTAATAGAGTATTGGTTCCCAGTGTCCTGGAGCCACC
AGTCAGAACTCTAACATCCTGAAACACACGGAAGGCAAGAGAAAGACAGTAAGAGTGGTCGTGAAATGCTTCCTTTGATT
TCATCCTGGCTTTTGGCTAAGGAGAAATGCTGGCTAGAAGAAAAAAATATGGAAAAAGTCAACTGTAAGAAAGAAGCTCT
TGAGGGAATTTGTATCCTGCAACAAGACCCAGAGTAAACTCCCAGATAAAATGATGATGTCTTTCTGGAAGAGCTGCAAC
TGGTGCCCTGGTGATCCTTACCAGATGCACCATGATTGTACAAGCCTGACAGTA

Alignment

ORF - retro_mmus_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.34 %
• Parental protein coverage: 68.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTSVGHLAYGHTTTVLNRVATLVPSVLKPPVRALTYCSTRK-GKRKTVKSVVHRFLRLHSGLWLRRKAGY
          .....H....H...VLNRV..LVPSVL.PPVR.LT...TRK.GKRKTV..VV..FL..H.G.WLRR.AG.
Retrocopy LSNTWHMGIVHQS-VLNRV--LVPSVLEPPVRTLTS*NTRK<GKRKTVRVVVKCFL*FHPGFWLRRNAG*

Parental  KKKLWKKSTARKKRLREFVFCSKTQSKLLDKMTTSFWKRRNWYAGDPYQMYHDRTNLRV
          KKK.WKKST.RKK.LREFV.C.KTQSKL.DKM..SFWK..NW..GDPYQM.HD.T.L.V
Retrocopy KKKIWKKSTVRKKLLREFVSCNKTQSKLPDKMMMSFWKSCNWCPGDPYQMHHDCTSLTV

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	23.50 RPM
SRP007412_cerebellum	0.00 RPM	17.93 RPM
SRP007412_heart	0.00 RPM	22.54 RPM
SRP007412_kidney	0.00 RPM	19.31 RPM
SRP007412_liver	0.00 RPM	15.29 RPM
SRP007412_testis	0.00 RPM	24.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1777 was not detected

EST

No EST(s) were mapped for retro_mmus_1777 retrocopy.

TSS

No TSS is located nearby retro_mmus_1777 retrocopy 5' end.

Lab

retro_mmus_1777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1777 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1399

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Homo sapiens	ENSG00000132313	4 retrocopies	retro_hsap_3424, retro_hsap_4784, retro_hsap_595, retro_hsap_681,
Gorilla gorilla	ENSGGOG00000026769	3 retrocopies	retro_ggor_2315, retro_ggor_2979, retro_ggor_526,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777 ,
Nomascus leucogenys	ENSNLEG00000002756	4 retrocopies	retro_nleu_1103, retro_nleu_1362, retro_nleu_2217, retro_nleu_781,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pongo abelii	ENSPPYG00000012214	5 retrocopies	retro_pabe_1817, retro_pabe_2837, retro_pabe_3724, retro_pabe_541, retro_pabe_595,
Pan troglodytes	ENSPTRG00000012152	4 retrocopies	retro_ptro_2325, retro_ptro_3185, retro_ptro_438, retro_ptro_489,
Rattus norvegicus	ENSRNOG00000008546	1 retrocopy	retro_rnor_1399,
Tupaia belangeri	ENSTBEG00000015366	10 retrocopies	retro_tbel_1143, retro_tbel_146, retro_tbel_2647, retro_tbel_289, retro_tbel_2892, retro_tbel_3789, retro_tbel_3828, retro_tbel_428, retro_tbel_4379, retro_tbel_627,
Tarsius syrichta	ENSTSYG00000007713	2 retrocopies	retro_tsyr_1128, retro_tsyr_264,