RetrogeneDB ID: retro_mmus_145

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:48945398..48946118(-)
• Located in intron of: ENSMUSG00000048852

Retrocopy information

• Ensembl ID: ENSMUSG00000078153
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Psme2
• Ensembl ID: ENSMUSG00000079197
• Aliases: Psme2, AA589371, AI788882, PA28b
• Description: proteasome (prosome, macropain) 28 subunit, beta [Source:MGI Symbol;Acc:MGI:1096365]

Sequence

>retro_mmus_145
ATGGCCAAGCCTTGTGGGGTCCGCTTGAGTGGAGAAGCCCGAAAACAGGTGGATGTCTTCAGACAAAATCTTTTCCAGGA
GGCTGATGACTTCCTCTGCACTTTCTTGCCACGGAAAATCATATCCCTGAGTCAGCTCTTGCAGGAGGATTCCCTCAATG
TGGCCGACCTCTCCTCCCTCCGGGCTCCTCTGGACATCCCTATCCCAGATCCTCCACCCAAGGATGACGAGATGGAAACA
GACAAGCAGGAGAAGAAGGAAGTCCCTAAGTGTGGCTACCTCCCGGGGAACGAGAAGCTTCTGGCCTTGCTTGCTTTGGT
TAAGCCAGAAGTCTGGACTCTCAAAGAGAAGTGCATTCTGGTAATCACGTGGATCCAGCACCTGATCCCCAAGATTGAGG
ATGGAAATGATTTTGGGGTGGCAATTCAGGAGAAGGTGCTGGAGAGAGTGAATGCTGTCAAGACCAAAGTAGAAGCTTTC
CAGACAACTATTTCCAAGTACTTCTCAGAACGAGGGGATGCTGTAGCCAAGGCTTCCAAGGATACCCATGTAATGGATTA
CCGGGCCTTGGTGCATGAGCGAGATGAAGCAGCCTATGGGGCGCTTAGGGCCATGGTGCTGGACCTGAGGGCCTTCTATG
CTGAGCTTTATCATATCATCAGCAGCAACCTAGAGAAAATCGTCAACCCGAAGGGTGAAGAAAAGCCATCGATGTACTGA

Alignment

ORF - retro_mmus_145 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAKPCGVRLSGEARKQVDVFRQNLFQEADDFLCTFLPRKIISLSQLLQEDSLNVADLSSLRAPLDIPIPD
          MAKPCGVRLSGEARKQVDVFRQNLFQEADDFLCTFLPRKIISLSQLLQEDSLNVADLSSLRAPLDIPIPD
Retrocopy MAKPCGVRLSGEARKQVDVFRQNLFQEADDFLCTFLPRKIISLSQLLQEDSLNVADLSSLRAPLDIPIPD

Parental  PPPKDDEMETDKQEKKEVPKCGYLPGNEKLLALLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGV
          PPPKDDEMETDKQEKKEVPKCGYLPGNEKLLALLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGV
Retrocopy PPPKDDEMETDKQEKKEVPKCGYLPGNEKLLALLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGV

Parental  AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKDTHVMDYRALVHERDEAAYGALRAMVLDLR
          AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKDTHVMDYRALVHERDEAAYGALRAMVLDLR
Retrocopy AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKDTHVMDYRALVHERDEAAYGALRAMVLDLR

Parental  AFYAELYHIISSNLEKIVNPKGEEKPSMY
          AFYAELYHIISSNLEKIVNPKGEEKPSMY
Retrocopy AFYAELYHIISSNLEKIVNPKGEEKPSMY

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	0.19 RPM	12.69 RPM
SRP007412_cerebellum	0.17 RPM	15.37 RPM
SRP007412_heart	0.75 RPM	31.32 RPM
SRP007412_kidney	0.94 RPM	44.41 RPM
SRP007412_liver	0.85 RPM	67.97 RPM
SRP007412_testis	0.09 RPM	6.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_145 was not detected

EST

No EST(s) were mapped for retro_mmus_145 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_13011	635 libraries	309 libraries	115 libraries	13 libraries	0 libraries

The graphical summary, for retro_mmus_145 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_145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_145 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Felis catus	ENSFCAG00000005585	1 retrocopy	retro_fcat_1605,
Homo sapiens	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
Gorilla gorilla	ENSGGOG00000016025	4 retrocopies	retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Myotis lucifugus	ENSMLUG00000009769	1 retrocopy	retro_mluc_2172,
Macaca mulatta	ENSMMUG00000012473	4 retrocopies	retro_mmul_1229, retro_mmul_1919, retro_mmul_1940, retro_mmul_2281,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145 ,
Nomascus leucogenys	ENSNLEG00000015260	4 retrocopies	retro_nleu_2086, retro_nleu_2726, retro_nleu_3086, retro_nleu_844,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Pongo abelii	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,
Sus scrofa	ENSSSCG00000002004	1 retrocopy	retro_sscr_302,