RetrogeneDB ID: retro_mmus_975

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:106886523..106886921(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083861
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 0610037L13Rik
• Ensembl ID: ENSMUSG00000028608
• Aliases: 0610037L13Rik, 1110008H16Rik
• Description: RIKEN cDNA 0610037L13 gene [Source:MGI Symbol;Acc:MGI:1921348]

Sequence

>retro_mmus_975
GGGGAAATGTTGCTGAAGCTCACAGCCACACTGAAGAGCGTCATCAATCTTCAGCCAGTGGGTGAGGACTTCCGGTGGTA
CCTGAAGATAAAATGTGGCAGCTGTGGTGAGACTTCAGAGAAGTGACAATATTTCTGGCTGATGGACGACGGCGTGGCAT
TGAAAGGAGGTGGAGGCAGTATCTTCATGGTCCAGAAGAGCACATCGTGTGCATGGGAAAACTCCATTGAGATCATGAGC
AGAACTATCAAGTCTTTAACACTGAAAACAGTAAGACGCTTCAGACTATTGTACAGTTTAAGTGTTAGGACCTTGAACCA
ATTGACTTCCAGATCCACGCTGGATTTGTTGGTGAAGCGGAGGAGGCAGGGACAGTCTTTAGGGACAGGAACCTGCAG

Alignment

ORF - retro_mmus_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.19 %
• Parental protein coverage: 82.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKIALQLKATLENVTNLRPVGEDFRWYLKMKCGNCGEISEKWQYIRLM-DSVALKGGRGSASMVQKCKLC
          G...L.L.ATL..V.NL.PVGEDFRWYLK.KCG.CGE.SEK.QY..LM.D.VALKGG.GS..MVQK...C
Retrocopy GEMLLKLTATLKSVINLQPVGEDFRWYLKIKCGSCGETSEK*QYFWLMDDGVALKGGGGSIFMVQKSTSC

Parental  ARENSIDILSSTIKA-YNAEDNEKFKTIVEFECRGLEPVDFQPQAGFAADGVESGTVFSDINLQ
          A.ENSI.I.S.TIK...N.E......TIV.F.C..LEP.DFQ..AGF.....E.GTVF.D.NLQ
Retrocopy AWENSIEIMSRTIKS<FNTENSKTLQTIVQFKC*DLEPIDFQIHAGFVGEAEEAGTVFRDRNLQ

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	35.00 RPM
SRP007412_cerebellum	0.00 RPM	32.87 RPM
SRP007412_heart	0.00 RPM	33.59 RPM
SRP007412_kidney	0.00 RPM	25.97 RPM
SRP007412_liver	0.00 RPM	20.21 RPM
SRP007412_testis	0.00 RPM	46.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_975 was not detected

EST

No EST(s) were mapped for retro_mmus_975 retrocopy.

TSS

No TSS is located nearby retro_mmus_975 retrocopy 5' end.

Lab

retro_mmus_975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_975 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2403

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975 ,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351, retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999, retro_rnor_2403, retro_rnor_2705,