RetrogeneDB ID: retro_mmus_3224

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:81197629..81198354(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094615
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Coq10b
• Ensembl ID: ENSMUSG00000025981
• Aliases: Coq10b, 1500041J02Rik, 1700030I21Rik, 9530077A17Rik, AV002237, AW742641
• Description: coenzyme Q10 homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1915126]

Sequence

>retro_mmus_3224
ATGATCTTGGCAGCTGGTACCAGTCAGAGGGCCCTGGCGAGGGTGGCATCAGGGTGCCATCTGAAGTCGACCACCGTGAC
GGAAGCCCCGGCGCGGGGGTCTGCTCACGACGTCAGATACTTAGCTGCCTGTGTATACTGATGAACAGAACCCTTCCACC
ATGTGCCTCAGTTTTGCCTAAAGAGATCTGTGCAAGAACCTTCTTCAGAATCACTGCGCCATTAGTAAATAATCGAAAGG
ACTATTCAGAGAGAAGAATTGTAGGGTACTCAATGCAAGAAATGCATGACGTAGTATCAGGAATGGAGGACTATCAGCAT
TTCGTTCCTTGGTGTAAAAAGTCAGATATAATATCAAGGCGATCTGGATACTGTAAAACCAGATTAGAAGTTGGGTTCCC
CCCTGTTCTGGAGAGATACACATCAATAGTAACCTTGGTAAAACCACATTTGGTAAAGGCATCTTGTACTGACGGGAAAC
TTTTCAATCATTTGGAGACTATTTGGCGTTTTAGCCCAGGTCTTCCTGGCTATCCAAAAACTTGTACCTTGGATTTTTCA
ATTTCTTTTGAATTCTGCTCCCTTCTGCACTCTCAGCTCGCTACACTGTTCTTCGATGAAGTTGTGAAACAAATGGTAGC
AGCTTTTGAAAGAAGAGCATGTAAAATGTATGGTCCAGAGACAAACATCCCTCGGGAATTAATGCTTCATGAAATTCACC
ACACC

Alignment

ORF - retro_mmus_3224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIMAARTSQRALARVASGCHPKSTTVTEAPARGSARDVRHLAACG-VLINRTLPPCAAVLPKEICARTFF
          MI.AA.TSQRALARVASGCH.KSTTVTEAPARGSA.DVR.LAAC...L.NRTLPPCA.VLPKEICARTFF
Retrocopy MILAAGTSQRALARVASGCHLKSTTVTEAPARGSAHDVRYLAACV<ILMNRTLPPCASVLPKEICARTFF

Parental  RISAPLVNKRKEYSERRILGYSMQEMYDVVSGMEDYQHFVPWCKKSDIISRRSGYCKTRLEVGFPPVLER
          RI.APLVN.RK.YSERRI.GYSMQEM.DVVSGMEDYQHFVPWCKKSDIISRRSGYCKTRLEVGFPPVLER
Retrocopy RITAPLVNNRKDYSERRIVGYSMQEMHDVVSGMEDYQHFVPWCKKSDIISRRSGYCKTRLEVGFPPVLER

Parental  YTSIVTLVKPHLVKASCTDGKLFNHLETIWRFSPGLPGYPRTCTLDFSISFEFRSLLHSQLATLFFDEVV
          YTSIVTLVKPHLVKASCTDGKLFNHLETIWRFSPGLPGYP.TCTLDFSISFEF.SLLHSQLATLFFDEVV
Retrocopy YTSIVTLVKPHLVKASCTDGKLFNHLETIWRFSPGLPGYPKTCTLDFSISFEFCSLLHSQLATLFFDEVV

Parental  KQMVAAFERRACKLYGPETNIPRELMLHEIHHT
          KQMVAAFERRACK.YGPETNIPRELMLHEIHHT
Retrocopy KQMVAAFERRACKMYGPETNIPRELMLHEIHHT

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	18.64 RPM
SRP007412_cerebellum	0.00 RPM	11.85 RPM
SRP007412_heart	0.00 RPM	23.88 RPM
SRP007412_kidney	0.06 RPM	36.94 RPM
SRP007412_liver	0.08 RPM	50.41 RPM
SRP007412_testis	0.05 RPM	22.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3224 was not detected

EST

No EST(s) were mapped for retro_mmus_3224 retrocopy.

TSS

No TSS is located nearby retro_mmus_3224 retrocopy 5' end.

Lab

retro_mmus_3224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3224 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224 ,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,