RetrogeneDB ID: retro_mmus_1215

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:61558948..61559433(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Psma2
• Ensembl ID: ENSMUSG00000015671
• Aliases: Psma2, Lmpc3
• Description: proteasome (prosome, macropain) subunit, alpha type 2 [Source:MGI Symbol;Acc:MGI:104885]

Sequence

>retro_mmus_1215
GAAAAAAAGCAGAAATCCATCCTGTATGATGAAAGGAGTGTTCACAAGGTGGAGCCCATAACCAAACACATCGGTGTGGT
GTATAGTGGCATGGGCCCCGATTACAGAGCACTTGTACACAGAGCCCGGAAACTTGCTCAGCAATACTACTTGTTTACCA
AGATCCCATTCCCACAGCCCAGCTGGTACAGAGGGCAGCACCTGTGATGCAGGAGTACATGCAGGCAGGTGGTGTTCGTC
CATTCAGTGTTTCTTTACTTATCTGTGGGTGGAATGAGAGACCACCGTCTTTATTTCAGTCAGACCCATCTTGCTTTGCC
TGGAAGGCCACAGCAATGAGAAAGAACTATGTGAACTGGAAAACTGTCCTTGAGAAAAGATATGATGAAGACCTAGAACT
GGAAGATGCCATTCATACAGCCATCTTAACCCTAAAGGAAAGCTTTGAAGGGCAAATGACAGAAGATAACATAGAAGTTG
GGATC

Alignment

ORF - retro_mmus_1215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 70.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKKQKSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYY-LVYQEPIPTAQLVQRVASV
          EKKQKSILYDERSVHKVEPITKHIG.VYSGMGPDYR.LVHRARKLAQQYY.LVYQ.PIPTAQLVQR.A.V
Retrocopy EKKQKSILYDERSVHKVEPITKHIGVVYSGMGPDYRALVHRARKLAQQYY<LVYQDPIPTAQLVQRAAPV

Parental  MQEYTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLELEDA
          MQEY.Q.GGVRPF.VSLLICGWNE..P.LFQSDPS...FAWKATAM.KNYVN.KT.LEKRY.EDLELEDA
Retrocopy MQEYMQAGGVRPFSVSLLICGWNERPPSLFQSDPS--CFAWKATAMRKNYVNWKTVLEKRYDEDLELEDA

Parental  IHTAILTLKESFEGQMTEDNIEVGI
          IHTAILTLKESFEGQMTEDNIEVGI
Retrocopy IHTAILTLKESFEGQMTEDNIEVGI

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	0.07 RPM	53.83 RPM
SRP007412_cerebellum	0.13 RPM	49.89 RPM
SRP007412_heart	0.12 RPM	43.74 RPM
SRP007412_kidney	0.13 RPM	57.56 RPM
SRP007412_liver	0.05 RPM	44.27 RPM
SRP007412_testis	0.41 RPM	21.54 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1215 was not detected

EST

No EST(s) were mapped for retro_mmus_1215 retrocopy.

TSS

No TSS is located nearby retro_mmus_1215 retrocopy 5' end.

Lab

retro_mmus_1215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1215 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009433	3 retrocopies	retro_amel_1029, retro_amel_1336, retro_amel_1379,
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Mustela putorius furo	ENSMPUG00000018145	1 retrocopy	retro_mputfur_548,
Mus musculus	ENSMUSG00000015671	4 retrocopies	retro_mmus_1104, retro_mmus_1105, retro_mmus_1215 , retro_mmus_1320,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Otolemur garnettii	ENSOGAG00000016805	1 retrocopy	retro_ogar_197,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Rattus norvegicus	ENSRNOG00000049920	2 retrocopies	retro_rnor_2041, retro_rnor_2769,
Sus scrofa	ENSSSCG00000020769	3 retrocopies	retro_sscr_1082, retro_sscr_419, retro_sscr_440,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,