RetrogeneDB ID: retro_mmus_2676

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:102416663..102416930(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fdx1l
• Ensembl ID: ENSMUSG00000079677
• Aliases: Fdx1l, B230118G17Rik
• Description: ferredoxin 1-like [Source:MGI Symbol;Acc:MGI:1915415]

Sequence

>retro_mmus_2676
GGGGGATCTTGGGGACCCAGGACCAGGCACGCGACAATAACATCTAGGACATTCGAGACTACAGGTGAGTGGCGTGCTGG
CGAGGAGGAGGCAGACTGCCCGGAGCTGCCCTGGGACGTGGTCAATGTGGTGTTCGTGGACTGCTCGGGCAAGCAGATCC
CGGAGAGGGGCAGAGTCGAGGACAATGTTCTCTACCTGGCCCAGCGCCACTGGGTGGACCTGGAAAGGGCCTGCAAAGCA
TCCCTGGCATGTTCCACCTGCCATGTA

Alignment

ORF - retro_mmus_2676 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.9 %
• Parental protein coverage: 51.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGSWGPRAGHAAVTSRTFGTTGERRAGEEAADSPELPRDVVNVVFVDRSGKRIPVRGKVGDNVLYLAQRH
          GGSWGPR..HA..TSRTF.TTGE.RAGEE.AD.PELP.DVVNVVFVD.SGK.IP.RG.V.DNVLYLAQRH
Retrocopy GGSWGPRTRHATITSRTFETTGEWRAGEEEADCPELPWDVVNVVFVDCSGKQIPERGRVEDNVLYLAQRH

Parental  GVDLEGACEASLACSTCHV
          .VDLE.AC.ASLACSTCHV
Retrocopy WVDLERACKASLACSTCHV

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	17.50 RPM
SRP007412_cerebellum	0.00 RPM	7.99 RPM
SRP007412_heart	0.00 RPM	10.49 RPM
SRP007412_kidney	0.00 RPM	9.59 RPM
SRP007412_liver	0.00 RPM	8.08 RPM
SRP007412_testis	0.00 RPM	5.99 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2676 was not detected

EST

No EST(s) were mapped for retro_mmus_2676 retrocopy.

TSS

No TSS is located nearby retro_mmus_2676 retrocopy 5' end.

Lab

retro_mmus_2676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000267673	1 retrocopy	retro_hsap_331,
Gorilla gorilla	ENSGGOG00000006009	1 retrocopy	retro_ggor_355,
Macaca mulatta	ENSMMUG00000022896	1 retrocopy	retro_mmul_584,
Mus musculus	ENSMUSG00000079677	1 retrocopy	retro_mmus_2676 ,
Nomascus leucogenys	ENSNLEG00000012175	1 retrocopy	retro_nleu_1773,
Pan troglodytes	ENSPTRG00000010465	1 retrocopy	retro_ptro_267,