RetrogeneDB ID: retro_mmus_2610

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:137615626..137615959(+)
• Located in intron of: ENSMUSG00000089984

Retrocopy information

• Ensembl ID: ENSMUSG00000081228
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uqcrb
• Ensembl ID: ENSMUSG00000021520
• Aliases: Uqcrb, 2210415M14Rik, QP-C, QPC, UQBC, UQBP, UQPC
• Description: ubiquinol-cytochrome c reductase binding protein [Source:MGI Symbol;Acc:MGI:1914780]

Sequence

>retro_mmus_2610
ATGGCGGGCCGATCTGCTGTTGCAGCATCAAGCAAGTGGCTGGATGGTTTTCGAAAGTGGTATTATAATGCTGTGGGATT
CAATCAACTGGGGTTAATGTGAGATGCTACACTACATGAAACTGAAGATGTAAAAGAAGCCATAAGAAGGCTTCCTGAGG
ACCTTTATAATGACAGGATGTTTCGAATTAAGAGAGTCCTGGACCTGACTATGAGGCATCAGATCTTGCCTAAGGATCAG
TGGACAAAATATGAGGAGGACAAATTCTACCTTGAACCCTATCTAAAAGAGGTTATTCGGGAAAGAAAGGAGAGAGAAGA
GTGGGCAAAGAAG

Alignment

ORF - retro_mmus_2610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRSAVSASSKWLDGFRKWYYNAAGFNKLGLMRDDTLHETEDVKEAIRRLPEDLYNDRMFRIKRALDLT
          MAGRSAV.ASSKWLDGFRKWYYNA.GFN.LGLM.D.TLHETEDVKEAIRRLPEDLYNDRMFRIKR.LDLT
Retrocopy MAGRSAVAASSKWLDGFRKWYYNAVGFNQLGLM*DATLHETEDVKEAIRRLPEDLYNDRMFRIKRVLDLT

Parental  MRHQILPKDQWTKYEEDKFYLEPYLKEVIRERKEREEWAKK
          MRHQILPKDQWTKYEEDKFYLEPYLKEVIRERKEREEWAKK
Retrocopy MRHQILPKDQWTKYEEDKFYLEPYLKEVIRERKEREEWAKK

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	0.02 RPM	29.53 RPM
SRP007412_cerebellum	0.04 RPM	23.45 RPM
SRP007412_heart	0.34 RPM	157.95 RPM
SRP007412_kidney	0.10 RPM	96.36 RPM
SRP007412_liver	0.03 RPM	59.56 RPM
SRP007412_testis	0.18 RPM	16.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2610 was not detected

EST

No EST(s) were mapped for retro_mmus_2610 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_111075	329 libraries	165 libraries	420 libraries	126 libraries	32 libraries

The graphical summary, for retro_mmus_2610 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2610 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007287	1 retrocopy	retro_amel_985,
Canis familiaris	ENSCAFG00000009449	4 retrocopies	retro_cfam_1504, retro_cfam_1509, retro_cfam_1531, retro_cfam_792,
Callithrix jacchus	ENSCJAG00000020560	2 retrocopies	retro_cjac_2206, retro_cjac_894,
Cavia porcellus	ENSCPOG00000012149	2 retrocopies	retro_cpor_1086, retro_cpor_866,
Erinaceus europaeus	ENSEEUG00000001312	1 retrocopy	retro_eeur_224,
Felis catus	ENSFCAG00000026302	5 retrocopies	retro_fcat_1292, retro_fcat_178, retro_fcat_1780, retro_fcat_378, retro_fcat_558,
Homo sapiens	ENSG00000156467	2 retrocopies	retro_hsap_3261, retro_hsap_4838,
Gorilla gorilla	ENSGGOG00000026528	1 retrocopy	retro_ggor_3017,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127,
Loxodonta africana	ENSLAFG00000002542	1 retrocopy	retro_lafr_727,
Myotis lucifugus	ENSMLUG00000007182	1 retrocopy	retro_mluc_1601,
Macaca mulatta	ENSMMUG00000008804	3 retrocopies	retro_mmul_2053, retro_mmul_2065, retro_mmul_2581,
Mus musculus	ENSMUSG00000021520	4 retrocopies	retro_mmus_1175, retro_mmus_1628, retro_mmus_2610 , retro_mmus_514,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Oryctolagus cuniculus	ENSOCUG00000008113	3 retrocopies	retro_ocun_1149, retro_ocun_345, retro_ocun_570,
Otolemur garnettii	ENSOGAG00000004302	1 retrocopy	retro_ogar_1451,
Ochotona princeps	ENSOPRG00000008892	2 retrocopies	retro_opri_109, retro_opri_688,
Pongo abelii	ENSPPYG00000018763	2 retrocopies	retro_pabe_2703, retro_pabe_3762,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Sorex araneus	ENSSARG00000002999	3 retrocopies	retro_sara_460, retro_sara_52, retro_sara_704,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Tarsius syrichta	ENSTSYG00000010502	2 retrocopies	retro_tsyr_1114, retro_tsyr_898,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,