RetrogeneDB ID: retro_mmus_2928

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:43863794..43864183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Spcs1
• Ensembl ID: ENSMUSG00000021917
• Aliases: Spcs1, 1810004F21Rik
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1916269]

Sequence

>retro_mmus_2928
TGCCTTTGGTATCACACCCTACAAACCATACTCCTTAAGAATCTGCTAGCCTGTTTCACTGTCAGTATCAGTCTTCTGCA
ACCACGCTGGAGCACCTGAGTTCCCGGCCCACCCAGATGGATTACAACGGGCAGAAGCTAGCTGAACAGATGTCTCAGGG
AATTATTCTTTTTTCTGCAATAGCTGGGTTTATCTATGGGTACGTGACTGAACAGTTTGGGTGGAATGTCTACATAGTTA
TGTCGGATTTGCTTTCTCGTATCTGATGACATTTCCTCCGTGGCCTATCTACAGCCACTATCCCCTAAAGCGGGTTACCT
GTTCAAGACTTAGGCACAGAAGACAAGAAATCAGGGGATAGAAAAATGAAGAGGCTTGCTAAAAATAAC

Alignment

ORF - retro_mmus_2928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.19 %
• Parental protein coverage: 80.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CSRYRPPQTLLLNNRLRPF-RCRYRSSATMLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYV
          C..Y...QT.LL.N.L..F..C.Y.SSAT.LEHLSS.PTQMDY.GQKLAEQM.QGIILFSAI.GFIYGYV
Retrocopy CLWYHTLQTILLKNLLACF<HCQYQSSATTLEHLSSRPTQMDYNGQKLAEQMSQGIILFSAIAGFIYGYV

Parental  AEQFGWTVYIVMA-GFAFSCLLTLPPWPIYRRHPLK-WLPVQDLGTEDKKSGDRKIKRHAKNN
          .EQFGW.VYIVM..GFAFS.L.T.PPWPIY...PLK..LPVQDLGTEDKKSGDRK.KR.AKNN
Retrocopy TEQFGWNVYIVMS<GFAFSYLMTFPPWPIYSHYPLK>GLPVQDLGTEDKKSGDRKMKRLAKNN

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	0.00 RPM	33.36 RPM
SRP007412_cerebellum	0.00 RPM	26.53 RPM
SRP007412_heart	0.00 RPM	29.85 RPM
SRP007412_kidney	0.00 RPM	40.50 RPM
SRP007412_liver	0.00 RPM	38.40 RPM
SRP007412_testis	0.00 RPM	115.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2928 was not detected

EST

No EST(s) were mapped for retro_mmus_2928 retrocopy.

TSS

No TSS is located nearby retro_mmus_2928 retrocopy 5' end.

Lab

retro_mmus_2928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2928 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245, retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686, retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575, retro_lafr_625,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928 ,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,