RetrogeneDB ID: retro_mmus_2388

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:115480967..115481273(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000086724
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Prkrip1
• Ensembl ID: ENSMUSG00000039737
• Aliases: None
• Description: Prkr interacting protein 1 (IL11 inducible) [Source:MGI Symbol;Acc:MGI:1914051]

Sequence

>retro_mmus_2388
ATGTATAGGCACCTACGGTGGAGAGAGTACCAGCGGCAGGACTACATGGATGCCATGGCTGAGAAGCAAAAACTGAGTGC
AGAGTTTCAGAAGAGACTAGAAAAGAGTAAAATTGCTGCAGAGGAGCAGATTGCAAAGCACCGGAAAAAGCGCCAGAAGT
TAAAAGAGAAGTTACTGGCAAAGAAGATGAAACTTGAGCAGAAGAAACAGAAGGAAGAACCCTGTCAGGGCCAGGAACTG
CATGCCAGCAGCTCTGAAGAGGCATCTGAAACATAGGAGGAAGAGGAGCCCAGCGTTGTCATCATG

Alignment

ORF - retro_mmus_2388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYRHLRRREYQRQDYMDAMAEKQKLDAEFQKRLEKNKIAAEEQTAKRRKKRQKLKEKKLLAKKMKLEQKK
          .YRHLR.REYQRQDYMDAMAEKQKL.AEFQKRLEK.KIAAEEQ.AK.RKKRQKLKE.KLLAKKMKLEQKK
Retrocopy MYRHLRWREYQRQDYMDAMAEKQKLSAEFQKRLEKSKIAAEEQIAKHRKKRQKLKE-KLLAKKMKLEQKK

Parental  QKEEPSQCQEQHASSSDEASETEEEEEEPSVVIM
          QKEEP.Q.QE.HASSS.EASET..EEEEPSVVIM
Retrocopy QKEEPCQGQELHASSSEEASET-*EEEEPSVVIM

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	15.61 RPM
SRP007412_cerebellum	0.00 RPM	16.07 RPM
SRP007412_heart	0.00 RPM	7.10 RPM
SRP007412_kidney	0.04 RPM	10.34 RPM
SRP007412_liver	0.00 RPM	5.84 RPM
SRP007412_testis	0.00 RPM	24.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2388 was not detected

EST

No EST(s) were mapped for retro_mmus_2388 retrocopy.

TSS

No TSS is located nearby retro_mmus_2388 retrocopy 5' end.

Lab

retro_mmus_2388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2388 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004106	1 retrocopy	retro_btau_1368,
Mus musculus	ENSMUSG00000039737	1 retrocopy	retro_mmus_2388 ,