RetrogeneDB ID: retro_mmus_3086

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:128016465..128017220(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Yipf5
• Ensembl ID: ENSMUSG00000024487
• Aliases: Yipf5, 2610311I19Rik, AA408236, Yip1a
• Description: Yip1 domain family, member 5 [Source:MGI Symbol;Acc:MGI:1914430]

Sequence

>retro_mmus_3086
ATGTCAGGCTTTGATAACTTAAACAGCAGTTTCTACCAGATGAGTTACAGCATCGACGAGCAATCTCAGCAGTCCTATGA
CTATGGAGGAGGTGGAGGACCCCACGGCAAGCAGTATGCTGGCTGTGACTGCTCGCAGCAAGGCCGATTTGTCCCTCCAG
ACATGATGCAGCCACAGCAGACATACACTGGGCAGATTTACCAGCCAACTGAGGCCTATCCTCCAACAACACCTCAACCA
GCCATTCTATGGAGACAGCTTTGAGGAGGAGCCCCCTCTGTTAGAAGAGTTGGGCATCAATTTTGACATTTGGCAAAAAA
AACGCTAACGGTGCTACACCCTCTGAGGGCAGCTGACGGCAGCATCATGAATGAGACGGACTTGGCAGGGTCAGTGGTGT
TCTGCCTTGCCTTTGGGGCCACGCTGTTATTATTGGCTGGAAAATCCAGTTTGGCTACGTATATGGGATCAGTGCAATTG
GATACTTAGGAATGTTTTATTTGTTAAATTTAGTGAGTATGACAGGTGTGTCATTTGGTTGTGTGGCAAGTGTCCTGGGG
TATTATCTTCTTCCCATGATCCTGTTGTCCAACTTTGCAGTGGTATTTTCTTTACAAGGTATGGTAGGAATTCTTCTCAT
TGCCACAATTATTGGATGGTGTAGTTTTTCCGCTTCCAAAATTTTTATTTCTGCATTAGCTATGGATGGACAACAACTTT
TAGTGGCATGTCCCTGTGCTGTGTTGTATGCAGTC

Alignment

ORF - retro_mmus_3086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 97.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGFDNLNSGFYQTSYSIDEQSQQSYDYGGSGGPYSKQYAGCDYSQQGRFVPPDMMQPQQTYTGQIYQPT
          MSGFDNLNS.FYQ.SYSIDEQSQQSYDYGG.GGP..KQYAGCD.SQQGRFVPPDMMQPQQTYTGQIYQPT
Retrocopy MSGFDNLNSSFYQMSYSIDEQSQQSYDYGGGGGPHGKQYAGCDCSQQGRFVPPDMMQPQQTYTGQIYQPT

Parental  QAY-PPTTP-QPFYGDSFEEEPPLLEELGINFD-HIWQKTLTVLHPLRAADGSIMNETDLAGPVVFCLAF
          .AY.P.T...QPFYGDSFEEEPPLLEELGINFD.H.....LTVLHPLRAADGSIMNETDLAG.VVFCLAF
Retrocopy EAYPPTTPQ>QPFYGDSFEEEPPLLEELGINFD<HLXXXXLTVLHPLRAADGSIMNETDLAGSVVFCLAF

Parental  GATLLL-AGK-IQFGYVYGISAIGCLGMFCLLNLMSMTGVSFGCVASVLGYCLLPMILLSSFAVVFSLQG
          GATLLL.AGK.IQFGYVYGISAIG.LGMF.LLNL.SMTGVSFGCVASVLGY.LLPMILLS.FAVVFSLQG
Retrocopy GATLLLLAGK<IQFGYVYGISAIGYLGMFYLLNLVSMTGVSFGCVASVLGYYLLPMILLSNFAVVFSLQG

Parental  MVGILLTATIIGWCSFSASKIFISALAMDGQQLLVAYPCALLYGV
          MVGILL.ATIIGWCSFSASKIFISALAMDGQQLLVA.PCA.LY.V
Retrocopy MVGILLIATIIGWCSFSASKIFISALAMDGQQLLVACPCAVLYAV

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	0.05 RPM	29.25 RPM
SRP007412_cerebellum	0.04 RPM	24.23 RPM
SRP007412_heart	0.03 RPM	9.81 RPM
SRP007412_kidney	0.04 RPM	20.31 RPM
SRP007412_liver	0.00 RPM	23.21 RPM
SRP007412_testis	0.05 RPM	23.69 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_3086 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	7:128016666..128017026

EST

No EST(s) were mapped for retro_mmus_3086 retrocopy.

TSS

No TSS is located nearby retro_mmus_3086 retrocopy 5' end.

Lab

retro_mmus_3086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3086 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014497	1 retrocopy	retro_dnov_16,
Mus musculus	ENSMUSG00000024487	1 retrocopy	retro_mmus_3086 ,
Sorex araneus	ENSSARG00000013838	1 retrocopy	retro_sara_516,
Tarsius syrichta	ENSTSYG00000008071	1 retrocopy	retro_tsyr_16,