RetrogeneDB ID: retro_mmus_3469

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:74510945..74511527(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082447
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Chp1
• Ensembl ID: ENSMUSG00000014077
• Aliases: Chp1, 1500003O03Rik, AA960066, AI046351, Cahp, Chp, Sid470p, p24, vac
• Description: calcineurin-like EF hand protein 1 [Source:MGI Symbol;Acc:MGI:1927185]

Sequence

>retro_mmus_3469
GGGTCTCGAGCCTCCATGTTACTGTGGGTTGAAGAGCTCCAGGAGATCAAGAAGGAGACTGACTTTCCCCACAGCCTGAT
CACCTGCCTATACAGCCACTTCACCAGCCTGGACAAAGGAAAGAATGGGACTCTCAGCAGGGAAGATTTCTAGAGGATTC
CAGAACTTGCCATCAACCCATTGAGGGACCAGATCATCAATGCCTTCTTCTCAGAGGGAGAGGATCAGGTAAACTTTTGA
GGATTCATGGGAACTTTGGCTCATTTCTGACCCATTGAGGATAACAAAAAGAGCAATGATGTGAATCGACTGGAACCACT
CAACAGCTGGAGCAACAACTTGCACTTTACTTTCTGACTCTATGATTTGGATAAAGATGACAAGATCTCCCGTGATGAGC
TGTTATAGATACTGCGAATGATGGTCAGAGTGAATATTTCAGATGAGCTGCTAGGCAGTATTGCAGACAGGATCATCCAG
GAGGCTGACCAAGATGATGATAGTGCCATATCTTTTACAGAATTTTTTAACGTTTTAGAAAAGGTAGATGTAGAACAGAA
GATGAACATCAGACTTCTCCAC

Alignment

ORF - retro_mmus_3469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.47 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAFF
          GSRAS.LL..EEL.EIKKET.F.HS.IT.LYS.FTSLDKG.NGTLSREDF.RIPELAINPL.D.IINAFF
Retrocopy GSRASMLLWVEELQEIKKETDFPHSLITCLYSHFTSLDKGKNGTLSREDF*RIPELAINPLRDQIINAFF

Parental  SEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLRM
          SEGEDQVNF.GFM.TLAHF.PIEDN.KS.DVN..EPLNS.SN.LHF.F.LYDLDKDDKISRDELL..LRM
Retrocopy SEGEDQVNF*GFMGTLAHF*PIEDNKKSNDVNRLEPLNSWSNNLHFTF*LYDLDKDDKISRDELL*ILRM

Parental  MVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
          MV.VNISDE.LGSIADR.IQEADQD.DSAISFTEF..VLEKVDVEQKM.IR.LH
Retrocopy MVRVNISDELLGSIADRIIQEADQDDDSAISFTEFFNVLEKVDVEQKMNIRLLH

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	107.07 RPM
SRP007412_cerebellum	0.00 RPM	72.47 RPM
SRP007412_heart	0.00 RPM	68.24 RPM
SRP007412_kidney	0.00 RPM	111.34 RPM
SRP007412_liver	0.00 RPM	243.29 RPM
SRP007412_testis	0.00 RPM	16.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3469 was not detected

EST

No EST(s) were mapped for retro_mmus_3469 retrocopy.

TSS

No TSS is located nearby retro_mmus_3469 retrocopy 5' end.

Lab

retro_mmus_3469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3469 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469 ,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,