RetrogeneDB ID: retro_mmus_32

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:48939788..48940127(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000068537
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Cox7a2l
• Ensembl ID: ENSMUSG00000024248
• Aliases: Cox7a2l, COX7AR, COX7RP, EB1, SIG-81, SIG81, Silg81
• Description: cytochrome c oxidase subunit VIIa polypeptide 2-like [Source:MGI Symbol;Acc:MGI:106015]

Sequence

>retro_mmus_32
GTGTACTATAAGTTTAGCAGGTCCACGCAGAAGTTGGCTAGAGCTTGGGCTTCGAAAGCCTATACTCCGCAGGGGTTACA
GCTGGTTTCCATGGAAACACCACCTACCACATTTGCTACACCAACCAAACTGACCTCCAGTGCAACAGCATATGATTATG
CTGGGAAGAACAAAGTTCCAGAGCTGCAGAAGTTCTTCCAGAAGGCTGATGGCATGCCCATTCACCTGAAAGGAGGCCTT
CCGGACCAAATGCTTTACCAGACCACCATGGCTCTGACAATGGGAGGGACCATCTACTGCCTGACTCTACATGGCCTTGC
AGCCCAGAAACTTGCTTGC

Alignment

ORF - retro_mmus_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.06 %
• Parental protein coverage: 96.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYYKFSSFTQKLAGAWASEAYTPQGLKPVSTEAPPIIFATPTKLTSSVTAYDYSGKNKVPELQKFFQKAD
          .YYKFS..TQKLA.AWAS.AYTPQGL..VS.E.PP..FATPTKLTSS.TAYDY.GKNKVPELQKFFQKAD
Retrocopy VYYKFSRSTQKLARAWASKAYTPQGLQLVSMETPPTTFATPTKLTSSATAYDYAGKNKVPELQKFFQKAD

Parental  G--FHLKRGLPDQMLYRTTMALTLGGTIYCLIALYMASQ
          G...HLK.GLPDQMLY.TTMALT.GGTIYCL.....A.Q
Retrocopy GMPIHLKGGLPDQMLYQTTMALTMGGTIYCLTLHGLAAQ

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	41.17 RPM
SRP007412_cerebellum	0.00 RPM	28.01 RPM
SRP007412_heart	0.00 RPM	67.74 RPM
SRP007412_kidney	0.00 RPM	44.62 RPM
SRP007412_liver	0.00 RPM	28.76 RPM
SRP007412_testis	0.00 RPM	22.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_32 was not detected

EST

No EST(s) were mapped for retro_mmus_32 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_122929	324 libraries	580 libraries	166 libraries	0 libraries	2 libraries

The graphical summary, for retro_mmus_32 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_32 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_32 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032040	1 retrocopy	retro_cfam_1847,
Callithrix jacchus	ENSCJAG00000014705	1 retrocopy	retro_cjac_1492,
Echinops telfairi	ENSETEG00000011940	1 retrocopy	retro_etel_650,
Homo sapiens	ENSG00000115944	1 retrocopy	retro_hsap_825,
Gorilla gorilla	ENSGGOG00000010739	1 retrocopy	retro_ggor_674,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Mustela putorius furo	ENSMPUG00000008875	1 retrocopy	retro_mputfur_97,
Mus musculus	ENSMUSG00000024248	2 retrocopies	retro_mmus_32 , retro_mmus_926,
Nomascus leucogenys	ENSNLEG00000016666	1 retrocopy	retro_nleu_258,
Oryctolagus cuniculus	ENSOCUG00000027189	3 retrocopies	retro_ocun_1617, retro_ocun_1781, retro_ocun_28,
Otolemur garnettii	ENSOGAG00000016029	1 retrocopy	retro_ogar_114,
Pan troglodytes	ENSPTRG00000011865	1 retrocopy	retro_ptro_575,
Sarcophilus harrisii	ENSSHAG00000012014	1 retrocopy	retro_shar_479,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21,
Tupaia belangeri	ENSTBEG00000014124	3 retrocopies	retro_tbel_2384, retro_tbel_4472, retro_tbel_4545,