RetrogeneDB ID: retro_mmus_1948

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:87236571..87237000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081853
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mxi1
• Ensembl ID: ENSMUSG00000025025
• Aliases: Mxi1, ENSMUSG00000067085, Gm10197, Mad2, bHLHc11
• Description: Max interacting protein 1 [Source:MGI Symbol;Acc:MGI:97245]

Sequence

>retro_mmus_1948
ATGGAGCAGGTGCAGATGATCAATGTGCAGTGCCTGCTGGAGACCGTGGAATTTTTGGAGCTCAGGTAGCGAGAGTGTGA
ACATGGCTATGTCTCATGTTTCCCCTCCATGCCGAACCCCTGGCTACAGCACTTGAAGCCCCCCACAGAGGTTGAGCCGG
CACAGAAACATAGCAGTGGGAGCAGCAACACCAGCACTGCCAACAGATCTACACACAATGAGTTCAAAAAGAACCGCCAA
GCTCACCTGCGCCTGTGTTTAAAACGCTTGAAAGCTCTGATCCCGCTGGGCCCAGACTGCACCAGGCACACAAGACTCGG
TTTGCCCAACAAAGCCAAAGCACACATCAAGAAACGTGAAGAAGCAGAGAGCCAGCACCAGCTCAAGAACTTGGAACGAG
AGCAGAGATTTTTAAAGCAGCAGCTAGAT

Alignment

ORF - retro_mmus_1948 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.62 %
• Parental protein coverage: 63.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERVRMINVQRLLEAAEFLERRERECEHGYASSFPSMPSPRLQHSKPPRRLSRAQKHSSGSSNTSTANRS
          ME.V.MINVQ.LLE..EFLE.R.RECEHGY.S.FPSMP.P.LQH.KPP.....AQKHSSGSSNTSTANRS
Retrocopy MEQVQMINVQCLLETVEFLELR*RECEHGYVSCFPSMPNPWLQHLKPPTEVEPAQKHSSGSSNTSTANRS

Parental  THNELEKNRRAHLRLCLERLKVLIPLGPDCTRHTTLGLLNKAKAHIKKLEEAERKSQHQLENLEREQRFL
          THNE..KNR.AHLRLCL.RLK.LIPLGPDCTRHT.LGL.NKAKAHIKK.EEAE..SQHQL.NLEREQRFL
Retrocopy THNEFKKNRQAHLRLCLKRLKALIPLGPDCTRHTRLGLPNKAKAHIKKREEAE--SQHQLKNLEREQRFL

Parental  KRRLE
          K..L.
Retrocopy KQQLD

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	48.66 RPM
SRP007412_cerebellum	0.00 RPM	71.56 RPM
SRP007412_heart	0.00 RPM	30.10 RPM
SRP007412_kidney	0.00 RPM	44.27 RPM
SRP007412_liver	0.03 RPM	18.49 RPM
SRP007412_testis	0.27 RPM	60.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1948 was not detected

EST

No EST(s) were mapped for retro_mmus_1948 retrocopy.

TSS

No TSS is located nearby retro_mmus_1948 retrocopy 5' end.

Lab

retro_mmus_1948 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1948 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350, retro_chof_1817,
Cavia porcellus	ENSCPOG00000022901	1 retrocopy	retro_cpor_574,
Dasypus novemcinctus	ENSDNOG00000002479	2 retrocopies	retro_dnov_1336, retro_dnov_668,
Mus musculus	ENSMUSG00000025025	1 retrocopy	retro_mmus_1948 ,
Sus scrofa	ENSSSCG00000022128	1 retrocopy	retro_sscr_947,
Vicugna pacos	ENSVPAG00000003400	2 retrocopies	retro_vpac_483, retro_vpac_595,