RetrogeneDB ID: retro_mmus_927

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:32929153..32929775(-)
• Located in intron of: ENSMUSG00000097494

Retrocopy information

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

Parental gene information

• Parental gene symbol: Metrnl
• Ensembl ID: ENSMUSG00000039208
• Aliases: None
• Description: meteorin, glial cell differentiation regulator-like [Source:MGI Symbol;Acc:MGI:2384806]

Sequence

>retro_mmus_927
GTGTGTATATAGCCATTCAGGGCTTCCACCTGGGCCAGTATTGGGGAAAAAAAACCCTAGAGAACTGAGACTGTTGGTGT
GGGACATCGGTGCTGAGCCTGGCCAGATGCAGTAGTTCAGTCTAGAGCAGGGTGGTCTGTTTGTGGAGGTAACATCCCAA
CAGGATATTCAGCAGGAGGACTACAGGCTTCTAGTATGAGCTGTTGAGTGGACAGAGAGGACTGGACACCCGTGTGCCGT
CTGCTCAACACCAGCCTTGCAGTGACATCGAGGTTGTCCTTGCCATCTGCACCAGTGACTTAATCAACCGAGGCTTCATC
CAGGATGTCACCCATGTGCCAGAGCAACAAGTGTTGGTCATCTGCCTGCCAGTGAGTAGGCTCCATTGGAAGGAGAAAAG
AATCCTCCAGACAGCTCCTGAGGGCAGTGGCCACTGGCAGGATCACATCACTATACTGCTGGGGTGTGGTGTATAGCCAG
GGTATGGGAAAGTACTTTCCACTGGACATGTGAACATTGGGGAGGGCACAGTTTGTATGTCCTGCATGGTTTAGTGGCTT
TCAAAGGATGTATAGGAGTAGAAAGGAGAGGGGCATAAAACCTTGTCAAGATCAATATGGAG

Alignment

ORF - retro_mmus_927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.24 %
• Parental protein coverage: 89.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VCIKPFRDSS-GANIYLEKTGELRLLVRDIRGEPGQVQCFSLEQGGLFVEATPQQDI-SRRTTGFQYELM
          VCI.PFR.S..G.........ELRLLV.DI..EPGQ.Q.FSLEQGGLFVE.T.QQDI.SRRTTGF.YEL.
Retrocopy VCI*PFRAST>GPVLGXXXPRELRLLVWDIGAEPGQMQ*FSLEQGGLFVEVTSQQDI>SRRTTGF*YELL

Parental  SGQRGLDLHVLSAPCRPCSDTEVLLAICTSDFVVRGFIEDVTHVPEQQVSVIYLRVNRLHRQKSRVFQPA
          SGQRGLD..V.SA...PCSD.EV.LAICTSD...RGFI.DVTHVPEQQV.VI.L.V.RLH....R..Q.A
Retrocopy SGQRGLDTRVPSAQHQPCSDIEVVLAICTSDLINRGFIQDVTHVPEQQVLVICLPVSRLHWKEKRILQTA

Parental  PEDSGHWLGHVTTLLQCGVRPGHGEFLFTGHVHFGE-AQLGCAPRFSDFQRMYRKAEEMGINPCE-INME
          PE.SGHW..H.T.LL.CGV.PG.G..L.TGHV..GE.AQ..C...FS.FQRMYR...E.GI.PC..INME
Retrocopy PEGSGHWQDHITILLGCGV*PGYGKVLSTGHVNIGE>AQFVCPAWFSGFQRMYRSRKERGIKPCQ>INME

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	0.09 RPM	5.33 RPM
SRP007412_cerebellum	0.09 RPM	4.73 RPM
SRP007412_heart	0.03 RPM	11.33 RPM
SRP007412_kidney	0.10 RPM	13.74 RPM
SRP007412_liver	0.03 RPM	3.93 RPM
SRP007412_testis	3.25 RPM	4.07 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_927 was not detected

EST

No EST(s) were mapped for retro_mmus_927 retrocopy.

TSS

No TSS is located nearby retro_mmus_927 retrocopy 5' end.

Lab

retro_mmus_927 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_927 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2366

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000039208	1 retrocopy	retro_mmus_927 ,
Rattus norvegicus	ENSRNOG00000046202	1 retrocopy	retro_rnor_2366,