RetrogeneDB ID: retro_mmus_1463

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:45411580..45412346(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080715
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psma3
• Ensembl ID: ENSMUSG00000060073
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type 3 [Source:MGI Symbol;Acc:MGI:104883]

Sequence

>retro_mmus_1463
ATGAGCTCCATTGGCACTGGGTATGACTTGTCAGCCTCTATGTTCTCTCCTGATGGAAGAGTTTTCCAAATTGAATATGC
CATGAAGGCTATGGAAAACAGTAGTACAGCTATTGGGATCAGATGTAAAGACGATGTTGTGTTTGGAGTAGAAAAAGTAG
TCCTTTCTAAACTTTATGAAGAAGGCTCCAGTAAACGTCTTTTTAATGTTGATCGACATGTTGCAATGGCAGTTGCAGGA
TGGCTGGCAGATGCTCGTTCACTAGCAGACATAGCAAGAGAAGAAGCATCCAACTTTAGGTCCAACTTTGGCTATAACAT
TCCTCTAAAACGTCTTGCACACAGAGTGGCCATGTATGTACACGCCTATACACTCTACAGCGCTGTTAGACCTTTTGGCT
GCAGTTTCTTGTTGGGGTCTTACAGTGCGAATGATGGTGCACAGCTCTATATGATCGACCCATCAGGTGTTTCATATGGT
TGCTGGGGCTGTGCGATTGGCGAAGCCAGGCAGGCTGCAAAGACAGAGATAGAAAAGCTTCAGATGAAGGAAATGACTTG
CCGTGATGTAGTTAAAGAAGTTGCAAAAAATAATTTACATAGTACACGATGGAGTTAAGGATAAAGCTTTTGAACTGGAG
CTCAGCTGGGTTGGTGAATTAACTAAAGGAAGACATGAAATTGTTCCCAAAGACATAAGCGAGGAAGCAGAAAAATGTGC
CAAGGAACCTTTGAAGGAAGAAGATGAATCAGATGGTGACAATATG

Alignment

ORF - retro_mmus_1463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNV
          MSSIGTGYDLSAS.FSPDGRVFQ.EYAMKA.ENSSTAIGIRCKD.VVFGVEK.VLSKLYEEGS.KRLFNV
Retrocopy MSSIGTGYDLSASMFSPDGRVFQIEYAMKAMENSSTAIGIRCKDDVVFGVEKVVLSKLYEEGSSKRLFNV

Parental  DRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGS
          DRHV.MAVAG.LADARSLADIAREEASNFRSNFGYNIPLK.LA.RVAMYVHAYTLYSAVRPFGCSF.LGS
Retrocopy DRHVAMAVAGWLADARSLADIAREEASNFRSNFGYNIPLKRLAHRVAMYVHAYTLYSAVRPFGCSFLLGS

Parental  YSANDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDVVKEVA-KIIYIVHDEVKDKA
          YSANDGAQLYMIDPSGVSYG.WGCAIG.ARQAAKTEIEKLQMKEMTCRDVVKEVA.KIIYIVHD.VKDKA
Retrocopy YSANDGAQLYMIDPSGVSYGCWGCAIGEARQAAKTEIEKLQMKEMTCRDVVKEVA>KIIYIVHDGVKDKA

Parental  FELELSWVGELTKGRHEIVPKDIREEAEKYAKESLKEEDESDDDNM
          FELELSWVGELTKGRHEIVPKDI.EEAEK.AKE.LKEEDESD.DNM
Retrocopy FELELSWVGELTKGRHEIVPKDISEEAEKCAKEPLKEEDESDGDNM

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	0.16 RPM	42.68 RPM
SRP007412_cerebellum	0.00 RPM	29.44 RPM
SRP007412_heart	0.03 RPM	29.42 RPM
SRP007412_kidney	0.00 RPM	36.23 RPM
SRP007412_liver	0.08 RPM	48.75 RPM
SRP007412_testis	0.50 RPM	22.55 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1463 was not detected

EST

No EST(s) were mapped for retro_mmus_1463 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_47681	398 libraries	584 libraries	87 libraries	2 libraries	1 library

The graphical summary, for retro_mmus_1463 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_1463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1463 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015287	1 retrocopy	retro_cfam_1331,
Callithrix jacchus	ENSCJAG00000018732	1 retrocopy	retro_cjac_3974,
Dasypus novemcinctus	ENSDNOG00000004077	27 retrocopies	retro_dnov_1089, retro_dnov_1115, retro_dnov_1156, retro_dnov_1240, retro_dnov_1252, retro_dnov_1285, retro_dnov_1347, retro_dnov_1473, retro_dnov_1542, retro_dnov_1604, retro_dnov_1650, retro_dnov_1662, retro_dnov_1783, retro_dnov_1785, retro_dnov_1791, retro_dnov_1880, retro_dnov_1896, retro_dnov_198, retro_dnov_2030, retro_dnov_2125, retro_dnov_2128, retro_dnov_2334, retro_dnov_2507, retro_dnov_2578, retro_dnov_447, retro_dnov_765, retro_dnov_992,
Dipodomys ordii	ENSDORG00000002167	1 retrocopy	retro_dord_402,
Homo sapiens	ENSG00000100567	1 retrocopy	retro_hsap_1348,
Gorilla gorilla	ENSGGOG00000015814	1 retrocopy	retro_ggor_1049,
Macaca mulatta	ENSMMUG00000003509	2 retrocopies	retro_mmul_2187, retro_mmul_564,
Monodelphis domestica	ENSMODG00000007839	1 retrocopy	retro_mdom_544,
Mustela putorius furo	ENSMPUG00000006126	2 retrocopies	retro_mputfur_1549, retro_mputfur_414,
Mus musculus	ENSMUSG00000060073	3 retrocopies	retro_mmus_1277, retro_mmus_1463 , retro_mmus_2810,
Nomascus leucogenys	ENSNLEG00000013092	1 retrocopy	retro_nleu_1831,
Oryctolagus cuniculus	ENSOCUG00000010316	1 retrocopy	retro_ocun_667,
Otolemur garnettii	ENSOGAG00000000382	2 retrocopies	retro_ogar_1764, retro_ogar_2857,
Ochotona princeps	ENSOPRG00000002835	2 retrocopies	retro_opri_67, retro_opri_991,
Pongo abelii	ENSPPYG00000005855	2 retrocopies	retro_pabe_1120, retro_pabe_339,
Pan troglodytes	ENSPTRG00000006390	1 retrocopy	retro_ptro_923,
Rattus norvegicus	ENSRNOG00000007851	1 retrocopy	retro_rnor_183,
Sorex araneus	ENSSARG00000002670	2 retrocopies	retro_sara_437, retro_sara_573,
Ictidomys tridecemlineatus	ENSSTOG00000013539	1 retrocopy	retro_itri_1317,
Tupaia belangeri	ENSTBEG00000016910	1 retrocopy	retro_tbel_1947,
Tursiops truncatus	ENSTTRG00000013526	1 retrocopy	retro_ttru_545,