RetrogeneDB ID: retro_mmus_891

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:97663449..97663874(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pqbp1
• Ensembl ID: ENSMUSG00000031157
• Aliases: Pqbp1, PQBP-1, Sfc2, npw38
• Description: polyglutamine binding protein 1 [Source:MGI Symbol;Acc:MGI:1859638]

Sequence

>retro_mmus_891
GTGCCCCTCCCTGTTGCACTGCAGACCTGCTTGGCATAGAGGAGCTATCCTCAAACATCGGAATCGGAGCCAGATGAAGA
GATTATTGCTGAAGAATATGATCATCATCCTGTCGACTATGAGCCACCCAGACAGAGGGCCTGCCACGGCGCTGGTACAA
GGTGTTTGAACTCTCTTGTGAACTCCCTCACTATTGGCATGTGTTGACAGACCTCAAGTCCTGGCTCTCATCACATGATC
ATAACTTTGTTGTTACCAAATCTGCCAATAAACTCAGGAACGATAATGCAGATGCTGAGGACAAGCTGGACTGGAATCAT
GAGAAGCTGAACAGAAATTTTGAGAAGTCAGATCTTAGTCGCGAGAAGCCAGACAGGAGCCATGACAAGGCAGACAGAAG
CCACCATAAATGACCGAGAATGAGA

Alignment

ORF - retro_mmus_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.24 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPLPVALQTRLAKRGILKHLEPEPEEEIIAEDYDDDPVDYE-ATRIEGLPPSWYKVFDPSCGLPYYWNVE
          .PLPVALQT.LA.R......E.EP.EEIIAE.YD..PVDYE.AT..EGLP..WYKVF..SC.LP.YW.V.
Retrocopy VPLPVALQTCLA*RSYPQTSESEPDEEIIAEEYDHHPVDYE<ATQTEGLPRRWYKVFELSCELPHYWHVL

Parental  TDLVSWLSPHDPNFVVTKSAKKVRNNNADAEDKSDRNLEKVDRNHEKSDRSHEKPDRSHEKADRNHEKND
          TDL.SWLS.HD.NFVVTKSA.K.RN.NADAED...............SD.S.EKPDRSH.KADR.H.K..
Retrocopy TDLKSWLSSHDHNFVVTKSANKLRNDNADAEDXXXXXXXXXXXXXXXSDLSREKPDRSHDKADRSHHK*P

Parental  RER
          R.R
Retrocopy RMR

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	43.64 RPM
SRP007412_cerebellum	0.00 RPM	66.00 RPM
SRP007412_heart	0.00 RPM	17.62 RPM
SRP007412_kidney	0.00 RPM	28.49 RPM
SRP007412_liver	0.00 RPM	27.06 RPM
SRP007412_testis	0.00 RPM	4.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_891 was not detected

EST

No EST(s) were mapped for retro_mmus_891 retrocopy.

TSS

No TSS is located nearby retro_mmus_891 retrocopy 5' end.

Lab

retro_mmus_891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_891 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2326

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004165	2 retrocopies	retro_meug_1293, retro_meug_435,
Mus musculus	ENSMUSG00000031157	1 retrocopy	retro_mmus_891 ,
Rattus norvegicus	ENSRNOG00000007766	1 retrocopy	retro_rnor_2326,
Tupaia belangeri	ENSTBEG00000008669	1 retrocopy	retro_tbel_1908,