RetrogeneDB ID: retro_mmus_2758

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:87093574..87093930(+)
• 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_2758
TTAATAATCGGCTACGTCCATCCATTTTGTTGTTGGTATCGGTCTTCGGCAACCATGCTGGAACACCTGAGTTCGATGCC
CACCCAGATGGATTACAAGGGGCAGAAACTAGCTGAACAGATGTTTCAGGGGATCATTCTTTTTTCTGCATTGGGTTTAT
CTACGGGTACGTGGCTGAACAGTTTGGGTGGACTGTCTATCTAGTTATGGCCGGACTTGCTTTCTCCTGTCTGCTGACAC
TTCTTCCATGGCCTATCTACCGCCGCCATCCCCTAAAGTGGTTACCTGTTCAAGACTTAGGCACAAAAGACAAGAAATCA
GGGGACAGAAAAATTAAGAGGCATGCTAAAAATAAC

Alignment

ORF - retro_mmus_2758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLNNRLRPFRCRYRSSATMLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYG-YVAEQFGWTVYI
          L......PF.C.YRSSATMLEHLSS.PTQMDYKGQKLAEQMFQGIILFSA..G...G.YVAEQFGWTVY.
Retrocopy LIIGYVHPFCCWYRSSATMLEHLSSMPTQMDYKGQKLAEQMFQGIILFSAL-GLSTG<YVAEQFGWTVYL

Parental  VMAGFAFSCLLTLPPWPIYRRHPLKWLPVQDLGTEDKKSGDRKIKRHAKNN
          VMAG.AFSCLLTL.PWPIYRRHPLKWLPVQDLGT.DKKSGDRKIKRHAKNN
Retrocopy VMAGLAFSCLLTLLPWPIYRRHPLKWLPVQDLGTKDKKSGDRKIKRHAKNN

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	33.36 RPM
SRP007412_cerebellum	0.00 RPM	26.53 RPM
SRP007412_heart	0.00 RPM	29.85 RPM
SRP007412_kidney	0.06 RPM	40.50 RPM
SRP007412_liver	0.03 RPM	38.40 RPM
SRP007412_testis	0.14 RPM	115.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2758 was not detected

EST

No EST(s) were mapped for retro_mmus_2758 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_125406	337 libraries	265 libraries	420 libraries	47 libraries	3 libraries

The graphical summary, for retro_mmus_2758 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_2758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2758 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,