RetrogeneDB ID: retro_mmus_2516

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:132801930..132802254(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081647
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atpif1
• Ensembl ID: ENSMUSG00000054428
• Aliases: Atpif1, Atpi, If1
• Description: ATPase inhibitory factor 1 [Source:MGI Symbol;Acc:MGI:1196457]

Sequence

>retro_mmus_2516
ATGGCAGGCTTGGCGTTGGTGGTTCGGCTCGGCTCGGTGTCTGGGGTATGAGGGTCCTGTGAACCCGAGGCTTCGTCTCA
GACTCGTCGGAGAGCATAGATATGGGCGCTGGCTCCAACCGAGAAGCTGGTGGAGCCTTCAGAAAAGGAGAAAAGGCTGA
AGAGGGTCGGTACTTCCGAGAGAAGACTAGAGTACAGCTGGCTGCCCTGAAAAAAACACCATGAAGATGAGATTGACCAC
CATTCAAAGGCGATAGAGCGTCTGCAGAAGCCGATTGAACGCCGCTGCCGCCGTAGGAAGATTCAAAGCCTAAAGAGTGG
TCAT

Alignment

ORF - retro_mmus_2516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGSALAVR-ARFGVWGMKVLQTRGFVSDSSDSMDTGAGSIREAGGAFGKREKAEEDRYFREKTKEQLAA
          MAG.AL.VR.AR.GVWGM.VL.TRGFVSDSS.S.D.GAGS.REAGGAF.K.EKAEE.RYFREKT..QLAA
Retrocopy MAGLALVVR<ARLGVWGMRVL*TRGFVSDSSESIDMGAGSNREAGGAFRKGEKAEEGRYFREKTRVQLAA

Parental  L-RKHHEDEIDHHSKEIERLQKQIER--HKKKIQQLKNNH
          L..KHHEDEIDHHSK.IERLQK.IER.....KIQ.LK..H
Retrocopy L>KKHHEDEIDHHSKAIERLQKPIERRCRRRKIQSLKSGH

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	52.59 RPM
SRP007412_cerebellum	0.00 RPM	39.90 RPM
SRP007412_heart	0.00 RPM	36.58 RPM
SRP007412_kidney	0.02 RPM	77.60 RPM
SRP007412_liver	0.00 RPM	7.54 RPM
SRP007412_testis	0.00 RPM	58.23 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_2516 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	4:132801468..132802707
ENCFF001YKA	POLR2A	4:132801629..132802671

EST

No EST(s) were mapped for retro_mmus_2516 retrocopy.

TSS

No TSS is located nearby retro_mmus_2516 retrocopy 5' end.

Lab

retro_mmus_2516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032458	2 retrocopies	retro_cfam_1777, retro_cfam_651,
Callithrix jacchus	ENSCJAG00000009581	1 retrocopy	retro_cjac_1406,
Dasypus novemcinctus	ENSDNOG00000015460	1 retrocopy	retro_dnov_2592,
Myotis lucifugus	ENSMLUG00000000170	1 retrocopy	retro_mluc_363,
Mustela putorius furo	ENSMPUG00000015536	1 retrocopy	retro_mputfur_1570,
Mus musculus	ENSMUSG00000054428	2 retrocopies	retro_mmus_2516 , retro_mmus_908,
Otolemur garnettii	ENSOGAG00000010337	2 retrocopies	retro_ogar_116, retro_ogar_268,
Pteropus vampyrus	ENSPVAG00000017615	1 retrocopy	retro_pvam_817,
Rattus norvegicus	ENSRNOG00000013300	1 retrocopy	retro_rnor_2655,
Sorex araneus	ENSSARG00000010860	1 retrocopy	retro_sara_458,
Ictidomys tridecemlineatus	ENSSTOG00000020766	1 retrocopy	retro_itri_1240,