RetrogeneDB ID: retro_mmus_3178

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:20556695..20557486(-)
• Located in intron of: ENSMUSG00000095403

Retrocopy information

• Ensembl ID: ENSMUSG00000095766
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pim2
• Ensembl ID: ENSMUSG00000031155
• Aliases: Pim2, DXCch3, Pim-2
• Description: proviral integration site 2 [Source:MGI Symbol;Acc:MGI:97587]

Sequence

>retro_mmus_3178
TTCACGGGACACAGCGTCACGGATAGACATCAGGTGGCCATCAAAGTAATCTCCTGGAACTGTGTGCTAGGCTGGTCCAC
CGTGTCAGACTCAGTCACCTGCCCACTTGAGGTTGCGTTGCTGTGGAAGGTGGGTGAAGACAATGGCCATTAGGGTGTGA
TACACCTGCTTGACTTCAAAACACCCGAAGGCTTCATGCTGGTCCTTGAGTGGCCTATGCCTGCTCAGGATCTCTTTGAC
TACATCACAGAGAAGGGGCTGCTGGGTGAAAGCTGTAGCTGCAGCTTCTTTACCCAAGTCGTGGCAGCTGTCCAGCACTG
CCATGCCTGTGGAGTTGTCCATTGGGATATCAAGGATGAGAACATCCTGATTGACCTATGCCAGGGTTCCATTAAACTCA
TTGATTTTGGTTCCCGTGCCCTGCTTCATGATGAGCCATACACTGACTTTGATGGGACAAGAGTGTATAGCCCTCCAAAG
TGGATCTTGCGACACCAGTACCATGCCCTGCCAGCGACCATCTGGTCACTAGGTGTCCTACTCTATGACATGCTCTGTGG
GGACATTCCCTTCAAGAGAGATCAGGAGATTCTGGAGGCTGAGCTAGACTTCCCTGCTCATGTCTCCCCAGATTGCTGTG
CCCTAATCCGCCGGTGCCTGGCCCCTAAACCCTGCTCCCGACCCTCACTGGAAGAGGTTCTGCTGAACCCCTGGATGCAA
ACACCAGCTGAAGAAAAGCCCATCAACTCCTCCAAAGGAAGCCCACCCCCTTGCCCTGGTCCCTGCTTCCC

Alignment

ORF - retro_mmus_3178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.85 %
• Parental protein coverage: 71.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FAGHRVTDRRQVAIKVISRNRVLGWSTVSDSVTCPLEVALLWKVGEGNGHPGVIRLLDWFETPEGFMLVL
          F.GH.VTDR.QVAIKVIS.N.VLGWSTVSDSVTCPLEVALLWKVGE.NGH.GVI.LLD.F.TPEGFMLVL
Retrocopy FTGHSVTDRHQVAIKVISWNCVLGWSTVSDSVTCPLEVALLWKVGEDNGH*GVIHLLD-FKTPEGFMLVL

Parental  ERPMPAQDLFDYITEKGPLGESCSRSFFTQVVAAVQHCHARGVVHRDIKDENILIDLCRGSIKLIDFGSG
          E.PMPAQDLFDYITEKG.LGESCS.SFFTQVVAAVQHCHA.GVVH.DIKDENILIDLC.GSIKLIDFGS.
Retrocopy EWPMPAQDLFDYITEKGLLGESCSCSFFTQVVAAVQHCHACGVVHWDIKDENILIDLCQGSIKLIDFGSR

Parental  ALLHDEPYTDFDGTRVYSPPEWISRHQYHALPATVWSLGVLLYDMVCGDIPFERDQEILEAELHFPAHVS
          ALLHDEPYTDFDGTRVYSPP.WI.RHQYHALPAT.WSLGVLLYDM.CGDIPF.RDQEILEAEL.FPAHVS
Retrocopy ALLHDEPYTDFDGTRVYSPPKWILRHQYHALPATIWSLGVLLYDMLCGDIPFKRDQEILEAELDFPAHVS

Parental  PDCCALIRRCLAPKPCSRPSLEEILLDPWMQSPAEEKPINSSKGS-PTPLPWSLLP
          PDCCALIRRCLAPKPCSRPSLEE.LL.PWMQ.PAEEKPINSSKGS.PTPLPWSLLP
Retrocopy PDCCALIRRCLAPKPCSRPSLEEVLLNPWMQTPAEEKPINSSKGS<PTPLPWSLLP

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	25.93 RPM
SRP007412_cerebellum	0.04 RPM	19.58 RPM
SRP007412_heart	0.00 RPM	2.49 RPM
SRP007412_kidney	0.02 RPM	3.27 RPM
SRP007412_liver	0.03 RPM	2.10 RPM
SRP007412_testis	0.00 RPM	1.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3178 was not detected

EST

No EST(s) were mapped for retro_mmus_3178 retrocopy.

TSS

No TSS is located nearby retro_mmus_3178 retrocopy 5' end.

Lab

retro_mmus_3178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007968	1 retrocopy	retro_etel_401,
Mus musculus	ENSMUSG00000031155	2 retrocopies	retro_mmus_2005, retro_mmus_3178 ,
Oryctolagus cuniculus	ENSOCUG00000015757	1 retrocopy	retro_ocun_1279,
Otolemur garnettii	ENSOGAG00000009613	1 retrocopy	retro_ogar_3049,
Sorex araneus	ENSSARG00000008832	3 retrocopies	retro_sara_222, retro_sara_223, retro_sara_395,