RetrogeneDB ID: retro_mmus_1479

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:70665304..70665647(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Med31
• Ensembl ID: ENSMUSG00000020801
• Aliases: Med31, 3110004H13Rik, CGI-125, l11Jus15
• Description: mediator of RNA polymerase II transcription, subunit 31 homolog (yeast) [Source:MGI Symbol;Acc:MGI:1914529]

Sequence

>retro_mmus_1479
ATGCCAATGGCTGTTGCTATGAAGATAGGTGATGCTAGAAATTGACTTTGGATTTAGTTGGAGTTGAAATTTGTGCAGTG
TTTAGTCAACCCAAATTATCTTAATTTTCCTGTCCAAAGAGGTTACTTCAAAAGCAAAGCTTTTGTTAATTAAGTACTTG
CTTTACTGGAAAGAACCAGAATTTGCTAAATAACTAAAGTGCCCTCAGTGTTTATGTATGTTAGAACTGTTCCAACATTT
TCAAAAGGAGCTGGTGAATGCTCTGCGTGTGAAATTTATTGACAAAGAGAAGATTCTACACTGGTAGCACTATTTGTAGA
AGCAGTTGCATCTTCAGCAAGCC

Alignment

ORF - retro_mmus_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.5 %
• Parental protein coverage: 90.08 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAVAMETDDAGNRLRFQLELEFVQCLANPNYLN-FLAQRGYFKDKAFVNYLKYLLYWKEPEYAKYLKY
          M..AVAM...DA.N.L...LEL.FVQCL.NPNYLN.FL......K.K......KYLLYWKEPE.AK.LK.
Retrocopy MPMAVAMKIGDARN*LWI*LELKFVQCLVNPNYLN>FLSKEVTSKAKLLL--IKYLLYWKEPEFAK*LKC

Parental  PQCLHMLELLQYEHFRKELVNAQCAKFIDEQQILHWQHYSRKRVRLQQA
          PQCL.MLEL....HF.KELVNA...KFID...ILHW.HY..K...LQQA
Retrocopy PQCLCMLEL--FQHFQKELVNALRVKFIDKEKILHW*HYL*KQLHLQQA

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	5.75 RPM
SRP007412_cerebellum	0.00 RPM	5.60 RPM
SRP007412_heart	0.00 RPM	4.20 RPM
SRP007412_kidney	0.00 RPM	3.75 RPM
SRP007412_liver	0.00 RPM	1.83 RPM
SRP007412_testis	0.00 RPM	10.75 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1479 was not detected

EST

No EST(s) were mapped for retro_mmus_1479 retrocopy.

TSS

No TSS is located nearby retro_mmus_1479 retrocopy 5' end.

Lab

retro_mmus_1479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1479 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023445	1 retrocopy	retro_cfam_863,
Myotis lucifugus	ENSMLUG00000010814	1 retrocopy	retro_mluc_1682,
Mus musculus	ENSMUSG00000020801	2 retrocopies	retro_mmus_1479 , retro_mmus_3201,