RetrogeneDB ID: retro_mmus_339

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:79957579..79958057(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rtfdc1
• Ensembl ID: ENSMUSG00000027502
• Aliases: Rtfdc1, 1700067C04Rik, 2410001C21Rik, 5730427M17Rik, AA589417
• Description: replication termination factor 2 domain containing 1 [Source:MGI Symbol;Acc:MGI:1913654]

Sequence

>retro_mmus_339
ATGGGTTGCGACGGAGGCACCATCCCCAAGAGGCACGAGCTGGTGAAGGGGCCGAAGAAGGTCGAGAAGGTTGACAAAAG
ACGCTGAACTGGTAGCCCAATGGAACTACTGTACTCTAAGTCAGGAAATCCTGAGGCGCCCAATAGTTGCCTGTGAGCTT
GGCAGACTGTATAACAAAGATGCAGTCATCGAGTTTCTGTTGGACAAATCTGCTGAGAAGGCCCTGGGGAAGGCGGCATC
ACACATCAGAAGCATCAAGAATGTGACAGAGCTCAGGCTTTTTGACAACCCCGCCTGGGAAGGAGATAAAGGGAACACCA
AGGGCGACAAGCATGATGACCTCCAGTGAGCGCAGTTCATCTGCCCTGTGGTGGGCTTGGAGATGAACGGCCGGCACAGG
TTTTGCTTCCTCCGATGCTGCGGTTGTGTGTTTTCTGAACGCGACTTGAAGGAGATAAAAGCTGAAGTGTGTCACACG

Alignment

ORF - retro_mmus_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.88 %
• Parental protein coverage: 51.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGCDGGTIPKRHELVKGPKKVEKVD-KDAELVAQWNYCTLSQEILRRPIVACELGRLYNKDAVIEFLLDK
          MGCDGGTIPKRHELVKGPKKVEKVD.KDAELVAQWNYCTLSQEILRRPIVACELGRLYNKDAVIEFLLDK
Retrocopy MGCDGGTIPKRHELVKGPKKVEKVD>KDAELVAQWNYCTLSQEILRRPIVACELGRLYNKDAVIEFLLDK

Parental  SAEKALGKAASHIRSIKNVTELRLSDNPAWEGDKGNTKGDKHDDLQRARFICPVVGLEMNGRHRFCFLRC
          SAEKALGKAASHIRSIKNVTELRL.DNPAWEGDKGNTKGDKHDDLQ.A.FICPVVGLEMNGRHRFCFLRC
Retrocopy SAEKALGKAASHIRSIKNVTELRLFDNPAWEGDKGNTKGDKHDDLQ*AQFICPVVGLEMNGRHRFCFLRC

Parental  CGCVFSERALKEIKAEVCHT
          CGCVFSER.LKEIKAEVCHT
Retrocopy CGCVFSERDLKEIKAEVCHT

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	56.58 RPM
SRP007412_cerebellum	0.00 RPM	59.96 RPM
SRP007412_heart	0.00 RPM	29.39 RPM
SRP007412_kidney	0.29 RPM	47.60 RPM
SRP007412_liver	0.05 RPM	50.03 RPM
SRP007412_testis	0.27 RPM	54.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_339 was not detected

EST

No EST(s) were mapped for retro_mmus_339 retrocopy.

TSS

No TSS is located nearby retro_mmus_339 retrocopy 5' end.

Lab

retro_mmus_339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_339 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027390	1 retrocopy	retro_btau_1076,
Echinops telfairi	ENSETEG00000003143	1 retrocopy	retro_etel_2095,
Mus musculus	ENSMUSG00000027502	1 retrocopy	retro_mmus_339 ,
Ornithorhynchus anatinus	ENSOANG00000009249	1 retrocopy	retro_oana_124,
Otolemur garnettii	ENSOGAG00000004444	1 retrocopy	retro_ogar_3150,