RetrogeneDB ID: retro_mmus_466

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:91171651..91172148(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psme1
• Ensembl ID: ENSMUSG00000022216
• Aliases: Psme1, AW413925, PA28a
• Description: proteasome (prosome, macropain) 28 subunit, alpha [Source:MGI Symbol;Acc:MGI:1096367]

Sequence

>retro_mmus_466
ATGGCCACACTGAGGGTCCATCCTGAAACCAAGCCAAGGTGGATGTGTTCCGTGAAGACCTGTGTAGCAAGACAGAGAAC
CTGCTTGGGAGCTATTTTCCCAAGAAGATCTCAGAGCTGGATGTGTTCTTAAAGAAGCCAGCTCTCAATGACGCCAACCT
GAGCAATCTGAAGGCTCTGTTGGACATCCCAGCACCTGATCCAGTCAAGGAGAAAGAGGAGGAGGAGCAGAAGCACCATC
ATGAGAAGGATGAAAAGAAGAAAGGGGACAAAGATGACAAAGGTCCTCCCTGTGGCCCAGTGAACTGCAATGAGAAGATC
GTGGTCCTCCTGAAACACCTAAAACCTGAGATCAAGGATGCCATCGAGCAACTCAATCTGGTCACTACCTGGTTGCTGCT
ACAGATACCTCGGATAGAGGATGGGAATAATTTTGGCGTGGCTGTCCAGGAAAAGGTGTTTGAGTTGGTGACCAGCCTTC
ATACCAAGCTGGAAGGA

Alignment

ORF - retro_mmus_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.88 %
• Parental protein coverage: 71.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATLRVHPEA-QAKVDVFREDLCSKTENLLGSYFPKKISELDAFLKEPALNEANLSNLKAPLDIPVPDPV
          MATLRVHPE..QAKVDVFREDLCSKTENLLGSYFPKKISELD.FLK.PALN.ANLSNLKA.LDIP.PDPV
Retrocopy MATLRVHPET<QAKVDVFREDLCSKTENLLGSYFPKKISELDVFLKKPALNDANLSNLKALLDIPAPDPV

Parental  KEKEKEERKKQQEKEEKEEKKKGDEDDKGPPCGPVNCNEKIVVLLQRLKPEIKDVTEQLNLVTTWLQLQI
          KEKE.EE.K......EK.EKKKGD.DDKGPPCGPVNCNEKIVVLL..LKPEIKD..EQLNLVTTWL.LQI
Retrocopy KEKEEEEQKHHH---EKDEKKKGDKDDKGPPCGPVNCNEKIVVLLKHLKPEIKDAIEQLNLVTTWLLLQI

Parental  PRIEDGNNFGVAVQEKVFELMTNLHTKLEG
          PRIEDGNNFGVAVQEKVFEL.T.LHTKLEG
Retrocopy PRIEDGNNFGVAVQEKVFELVTSLHTKLEG

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	0.12 RPM	21.54 RPM
SRP007412_cerebellum	0.00 RPM	20.36 RPM
SRP007412_heart	0.03 RPM	80.56 RPM
SRP007412_kidney	0.23 RPM	79.40 RPM
SRP007412_liver	0.30 RPM	84.19 RPM
SRP007412_testis	0.18 RPM	8.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_466 was not detected

EST

No EST(s) were mapped for retro_mmus_466 retrocopy.

TSS

No TSS is located nearby retro_mmus_466 retrocopy 5' end.

Lab

retro_mmus_466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016433	1 retrocopy	retro_amel_637,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Canis familiaris	ENSCAFG00000011924	1 retrocopy	retro_cfam_246,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001,
Felis catus	ENSFCAG00000005583	1 retrocopy	retro_fcat_1567,
Macropus eugenii	ENSMEUG00000014712	1 retrocopy	retro_meug_1052,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466 ,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Rattus norvegicus	ENSRNOG00000019041	1 retrocopy	retro_rnor_50,
Tursiops truncatus	ENSTTRG00000008620	1 retrocopy	retro_ttru_569,