RetrogeneDB ID: retro_mmus_790

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:52116491..52116743(-)
• Located in intron of: ENSMUSG00000097219

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lyrm2
• Ensembl ID: ENSMUSG00000045854
• Aliases: None
• Description: LYR motif containing 2 [Source:MGI Symbol;Acc:MGI:1917573]

Sequence

>retro_mmus_790
GCGGCTTCCCGCTTGCCTCCTGCGGCCCTGACGCTGAAGCAGTTCATGAGAAGGCAGCAAGTTCTCCTCCTCTACAGAAA
GATTTTGCGAGCGATTAGGCAAGTTCCAAGTGATTCTGACTAAAAATACCTTTAGGACTGGGCCAGGAAAGAATTTAAAA
GAAACAAAAGTGCCATAGAAGAGGATACAATGATGATTACCCAAGGCAATATGCAGCTAAAGGAACTAGAAAGGACGCTT
GCTTTAGCCAAC

Alignment

ORF - retro_mmus_790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.02 %
• Parental protein coverage: 97.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSDRKYLQDWAREEFKRNKSATEEDTIRMMITQ
          AASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSD.KYL.DWAR.EFKRNKSA.EEDT..MMITQ
Retrocopy AASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSD*KYL*DWARKEFKRNKSAIEEDT--MMITQ

Parental  GNMQLKELERTLALAN
          GNMQLKELERTLALAN
Retrocopy GNMQLKELERTLALAN

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	8.32 RPM
SRP007412_cerebellum	0.09 RPM	5.78 RPM
SRP007412_heart	0.00 RPM	15.07 RPM
SRP007412_kidney	0.06 RPM	18.27 RPM
SRP007412_liver	0.08 RPM	7.13 RPM
SRP007412_testis	0.00 RPM	11.94 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_790 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	11:52117260..52118181

EST

No EST(s) were mapped for retro_mmus_790 retrocopy.

TSS

No TSS is located nearby retro_mmus_790 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: GAAGTAGCCCTTCAGTACTTTG (22 nt long)
• Reverse primer: CTTCATTTACATTCTTGATTAGAGTG (26 nt long)
• Anneling temperature: 53 °C
• (Expected) product size: 417
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_790 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009916	1 retrocopy	retro_meug_2134,
Microcebus murinus	ENSMICG00000012230	2 retrocopies	retro_mmur_631, retro_mmur_650,
Mus musculus	ENSMUSG00000045854	2 retrocopies	retro_mmus_474, retro_mmus_790 ,
Otolemur garnettii	ENSOGAG00000034900	1 retrocopy	retro_ogar_508,
Sus scrofa	ENSSSCG00000004324	1 retrocopy	retro_sscr_686,
Ictidomys tridecemlineatus	ENSSTOG00000016198	1 retrocopy	retro_itri_1279,
Tursiops truncatus	ENSTTRG00000007420	1 retrocopy	retro_ttru_1516,