RetrogeneDB ID: retro_mmus_1826

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:37784265..37785584(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmc1
• Ensembl ID: ENSMUSG00000021178
• Aliases: Psmc1, AI325227, P26s4, S4
• Description: protease (prosome, macropain) 26S subunit, ATPase 1 [Source:MGI Symbol;Acc:MGI:106054]

Sequence

>retro_mmus_1826
ATGGGTCAAAGTCAGAGTGGTGGCCATGGTCCTGGGGGTGGCAAGAAGGATGACAAGGACAAGAAAAAGGAATATGAACC
TCCTGTCCCAACTAGAGTGGGGAAAAAGAAGAAGAAAACGAAGGGACCAGCTGCTGCCAGCAAACTTCCACTGGTAACAA
CTCACACCCAGTGCCACCTGAAATTACTAAAGCTAGAGAGAATAAAAGACTATCTTCTCATGGAGGAGGAATTCATTAGA
AATCAGGAACAGATGAAACCATTAGAAGAAAAGCAAGAAGAGGAAAGATCAAAAATGGATGATCCCAGGGGGACCCCCAT
GTCTGTAGGAACCTTGGAAGAGATCATTGATGATAATCATGCCATTGTGTCCACATCTGTGGGCTCAGAACACTACAGTC
AGCATCCTGCCATTTGTAGACAAGGATCTGCTGGAACCAGGCTGTTCAGTCCTGCTCAACCACAAGGTGCATGCTGTGAT
AGGGGTGCTAATGGATGACACGGATCCCCTGATCACGGTGATGAAGGTGGAAAAGGACCCCCAGGAAACCTATGCAGATA
TTGGGGGACTGGACAACCAGATCCAAGAAATTAAGGAGTCTGTGGAGCTTGCTCTTACCCATCCTGGCTATTACGAAGAG
ATGGGGATAAAGCCCCCTAAGGGGGTCATTCTCTACGGTCCACCAGGAACAGGTAAAGCTCTATTGGCCAAAGCAGTAGC
GAACCAGACTTCAGCCATTCTCTTGCGAGTGGTTGGCTCAGAGCTTATCCAGAAGTATGTAGGTGACGCGGCCCAAACTT
GTCCGGGAGCTCTTCCGGGTTGCTGAGGAGCACACACCGTCCATCGTGTTCATTGATGAGATCGACACCATTGGGACCAA
AAGATATGATTCAAACTCTGGAGGTGAGAGAGAAATTCGACGAACAATGTTGGAACTGTTGAACCAGTTGGATGGATTTG
ATTCAAGGGGAGATGTAAAAGTTATCACGGCCACAAACCAAATAGAAACTTTGGATCCAGCACTTATCAGGCCAGGCCCC
ATTGACAGAAAGATCGAGTTCCCCCTGCCTGATGAGACCAAGAAGCATATCTTCCAGATTCACACCAGCAGGATGACACT
GGCTGATGATGTAACCTTGGATGACTTGATCATGGCAAAGGATGACCTCTCTGGGGCCGACATCAAGGCAATCTGTACAG
AAGCTGGCTTGATGGCCTTACGGGGACGCAGAATGAAAGTAACAAATGAAGACTACAAAAAATCTAAAGAGAATGTTCTT
TATAAAAAACAAGAAGGCACCCCCAAGGGATTCGGTCTC

Alignment

ORF - retro_mmus_1826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIKD
          MGQSQSGGHGPGGGKKDDKDKKK.YEPPVPTRVGKKKKKTKGP.AASKLPLVT.HTQC.LKLLKLERIKD
Retrocopy MGQSQSGGHGPGGGKKDDKDKKKEYEPPVPTRVGKKKKKTKGPAAASKLPLVTTHTQCHLKLLKLERIKD

Parental  YLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHY-VSILSFV
          YLLMEEEFIRNQEQMKPLEEKQEEERSK.DD.RGTPMSVGTLEEIIDDNHAIVSTSVGSEHY.VSIL.FV
Retrocopy YLLMEEEFIRNQEQMKPLEEKQEEERSKMDDPRGTPMSVGTLEEIIDDNHAIVSTSVGSEHY>VSILPFV

Parental  DKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPE
          DKDLLEPGCSVLLNHKVHAVIGVLMDDTDPL.TVMKVEK.PQETYADIGGLDNQIQEIKESVEL.LTHP.
Retrocopy DKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLITVMKVEKDPQETYADIGGLDNQIQEIKESVELALTHPG

Parental  YYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDG-PKLVRELFRVAEEHA
          YYEEMGIKPPKGVILYGPPGTGK.LLAKAVANQTSA..LRVVGSELIQKY.GD..PKLVRELFRVAEEH.
Retrocopy YYEEMGIKPPKGVILYGPPGTGKALLAKAVANQTSAILLRVVGSELIQKYVGDA>PKLVRELFRVAEEHT

Parental  PSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRID
          PSIVFIDEID.IGTKRYDSNSGGEREI.RTMLELLNQLDGFDSRGDVKVI.ATN.IETLDPALIRPG.ID
Retrocopy PSIVFIDEIDTIGTKRYDSNSGGEREIRRTMLELLNQLDGFDSRGDVKVITATNQIETLDPALIRPGPID

Parental  RKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNED
          RKIEFPLPDE.TKK.IFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALR.RRMKVTNED
Retrocopy RKIEFPLPDE-TKKHIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRGRRMKVTNED

Parental  FKKSKENVLYKKQEGTPEGLYL
          .KKSKENVLYKKQEGTP.G..L
Retrocopy YKKSKENVLYKKQEGTPKGFGL

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	96.00 RPM
SRP007412_cerebellum	0.09 RPM	109.38 RPM
SRP007412_heart	0.09 RPM	87.29 RPM
SRP007412_kidney	0.08 RPM	101.66 RPM
SRP007412_liver	0.00 RPM	96.81 RPM
SRP007412_testis	0.09 RPM	60.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1826 was not detected

EST

No EST(s) were mapped for retro_mmus_1826 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_64288	319 libraries	234 libraries	455 libraries	55 libraries	9 libraries

The graphical summary, for retro_mmus_1826 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_1826 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1826 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001839	4 retrocopies	retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Equus caballus	ENSECAG00000003601	1 retrocopy	retro_ecab_355,
Echinops telfairi	ENSETEG00000002661	1 retrocopy	retro_etel_580,
Felis catus	ENSFCAG00000011310	8 retrocopies	retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Myotis lucifugus	ENSMLUG00000007471	2 retrocopies	retro_mluc_2490, retro_mluc_508,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Mustela putorius furo	ENSMPUG00000008150	4 retrocopies	retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus	ENSMUSG00000021178	3 retrocopies	retro_mmus_1517, retro_mmus_1826 , retro_mmus_812,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pteropus vampyrus	ENSPVAG00000010020	3 retrocopies	retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Tursiops truncatus	ENSTTRG00000013582	1 retrocopy	retro_ttru_239,