RetrogeneDB ID: retro_mmus_450

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:64454361..64454577(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Smim7
• Ensembl ID: ENSMUSG00000044600
• Aliases: Smim7, 9130011J15Rik
• Description: small integral membrane protein 7 [Source:MGI Symbol;Acc:MGI:1914068]

Sequence

>retro_mmus_450
ATGATCGGAGACATACTGCTGTTCCAGATGCTGCTGATGAACGTTGGGGGCTGTGCTCAACTTTAAACTGAAAAAGAAGG
ACATGCAAGGCTTTGGGGGGAGGAATTGAGGGAACCCAGCACAGGAGACAACATCCGGGAATTCCTAGTGAGCCTGAGGT
ACTTCCGGATCTTCACCACCCTGTGGAATGTGTTCATGGTCATACTGTTCGGCTCT

Alignment

ORF - retro_mmus_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIGDILLFGTLLMNAGAVLNFKLKKKD-TQGFGEESKEPSTGDNIREFLLSLRYFRIFIALWNVFMMLCM
          MIGDILLF..LLMN.G........K.......GEE..EPSTGDNIREFL.SLRYFRIF..LWNVFM....
Retrocopy MIGDILLFQMLLMNVGGCAQL*TEKEGHARLWGEELREPSTGDNIREFLVSLRYFRIFTTLWNVFM----

Parental  IVLFGS
          ..LFGS
Retrocopy VILFGS

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	63.20 RPM
SRP007412_cerebellum	0.00 RPM	36.60 RPM
SRP007412_heart	0.00 RPM	60.58 RPM
SRP007412_kidney	0.00 RPM	48.37 RPM
SRP007412_liver	0.00 RPM	32.22 RPM
SRP007412_testis	0.00 RPM	11.80 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_450 was not detected

EST

No EST(s) were mapped for retro_mmus_450 retrocopy.

TSS

No TSS is located nearby retro_mmus_450 retrocopy 5' end.

Lab

retro_mmus_450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_450 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2694

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010105	1 retrocopy	retro_amel_1688,
Canis familiaris	ENSCAFG00000015643	1 retrocopy	retro_cfam_1927,
Callithrix jacchus	ENSCJAG00000013936	1 retrocopy	retro_cjac_1223,
Equus caballus	ENSECAG00000026861	1 retrocopy	retro_ecab_640,
Felis catus	ENSFCAG00000016411	1 retrocopy	retro_fcat_934,
Homo sapiens	ENSG00000214046	1 retrocopy	retro_hsap_2244,
Mus musculus	ENSMUSG00000044600	1 retrocopy	retro_mmus_450 ,
Nomascus leucogenys	ENSNLEG00000005569	1 retrocopy	retro_nleu_1315,
Pongo abelii	ENSPPYG00000009694	2 retrocopies	retro_pabe_1964, retro_pabe_2031,
Pan troglodytes	ENSPTRG00000010650	1 retrocopy	retro_ptro_1589,
Rattus norvegicus	ENSRNOG00000042037	1 retrocopy	retro_rnor_2694,
Sus scrofa	ENSSSCG00000013863	1 retrocopy	retro_sscr_955,
Tarsius syrichta	ENSTSYG00000009556	1 retrocopy	retro_tsyr_1550,
Tursiops truncatus	ENSTTRG00000015020	2 retrocopies	retro_ttru_136, retro_ttru_597,
Vicugna pacos	ENSVPAG00000006699	1 retrocopy	retro_vpac_65,