RetrogeneDB ID: retro_mmus_1415

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:84182708..84183015(-)
• Located in intron of: ENSMUSG00000041653

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psenen
• Ensembl ID: ENSMUSG00000036835
• Aliases: Psenen, 1700023M09Rik, Pen-2
• Description: presenilin enhancer 2 homolog (C. elegans) [Source:MGI Symbol;Acc:MGI:1913590]

Sequence

>retro_mmus_1415
ATGAACTTGGAGCGGGTATCCAATGAGGAGAAGTTGAACCTGTGCCGGAAGTACTATCTTGGTGGATTTGCGTTCCTGCC
TTTTCTTTGGTTGGTCAACATTTTCTGGTTCTTTAGAGAGGCTTTCCTCGCCCCAGCCTACACAGAGCAGAGCCAAATCA
AAGGCTATGTTTGGCGCTCAGCTGTGGGCTTCCTCTTCTTGGTGATCATTCATTCTCACCACCTGGATCACCATCTTCCA
GATCTACCGGCCCCGCTGGGGCGCTCTTGGGGACTACCTCTCCTTCACCATTCCCCTGGGCACTCCC

Alignment

ORF - retro_mmus_1415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLAPAYTEQSQIKGYVWRSAVGFLF-W-V
          MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLAPAYTEQSQIKGYVWRSAVGFLF.W..
Retrocopy MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLAPAYTEQSQIKGYVWRSAVGFLF>W*S

Parental  IILATWITIFQIYRPRWGALGDYLSFTIPLGTP
          .IL.TWITIFQIYRPRWGALGDYLSFTIPLGTP
Retrocopy FILTTWITIFQIYRPRWGALGDYLSFTIPLGTP

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	7.43 RPM
SRP007412_cerebellum	0.09 RPM	6.56 RPM
SRP007412_heart	0.00 RPM	8.62 RPM
SRP007412_kidney	0.02 RPM	12.03 RPM
SRP007412_liver	0.00 RPM	11.03 RPM
SRP007412_testis	0.00 RPM	13.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1415 was not detected

EST

No EST(s) were mapped for retro_mmus_1415 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_43200	575 libraries	251 libraries	242 libraries	4 libraries	0 libraries

The graphical summary, for retro_mmus_1415 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_1415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1415 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002930	1 retrocopy	retro_eeur_7,
Macropus eugenii	ENSMEUG00000012358	1 retrocopy	retro_meug_524,
Myotis lucifugus	ENSMLUG00000011528	2 retrocopies	retro_mluc_1385, retro_mluc_1860,
Mus musculus	ENSMUSG00000036835	2 retrocopies	retro_mmus_1415 , retro_mmus_2454,
Sorex araneus	ENSSARG00000002056	1 retrocopy	retro_sara_708,
Sus scrofa	ENSSSCG00000024330	1 retrocopy	retro_sscr_664,
Tupaia belangeri	ENSTBEG00000001589	1 retrocopy	retro_tbel_447,