RetrogeneDB ID: retro_mmus_2454

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:40775261..40775564(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000056412
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2454
ATGAACTTGGAGCGGGTATCCAATGAGGAGAAGTTGAACCTGTGCCGGAAGTACTATCTTGGTGGATTTGCGTTCCTGCC
TTTTCTTTGGTTAGTCAACATTTTCTGGTTCTTCAGAGAGGCGTTCCTCGCCCCAGCCTACACAGAGCAGAGCCAAATCA
AAGGCTATGTTTGGCGCTCAGCTGTGGGCTTCCTCTTCTGGGTGATCATTCTCGCCACCTGGATCACCATCTTCCAGATC
TACCGGCCCCGCTGGGGCGCTCTTGGGGACTACCTCTCCTTCACCATTCCCCTGGGCACTCCC

Alignment

ORF - retro_mmus_2454 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLAPAYTEQSQIKGYVWRSAVGFLFWVII
          MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLAPAYTEQSQIKGYVWRSAVGFLFWVII
Retrocopy MNLERVSNEEKLNLCRKYYLGGFAFLPFLWLVNIFWFFREAFLAPAYTEQSQIKGYVWRSAVGFLFWVII

Parental  LATWITIFQIYRPRWGALGDYLSFTIPLGTP
          LATWITIFQIYRPRWGALGDYLSFTIPLGTP
Retrocopy LATWITIFQIYRPRWGALGDYLSFTIPLGTP

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	7.43 RPM
SRP007412_cerebellum	0.00 RPM	6.56 RPM
SRP007412_heart	0.09 RPM	8.62 RPM
SRP007412_kidney	0.04 RPM	12.03 RPM
SRP007412_liver	0.00 RPM	11.03 RPM
SRP007412_testis	0.14 RPM	13.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2454 was not detected

EST

No EST(s) were mapped for retro_mmus_2454 retrocopy.

TSS

No TSS is located nearby retro_mmus_2454 retrocopy 5' end.

Lab

retro_mmus_2454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2454 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,