RetrogeneDB ID: retro_mmus_2800

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:4893354..4893777(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083041
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gmfg
• Ensembl ID: ENSMUSG00000060791
• Aliases: None
• Description: glia maturation factor, gamma [Source:MGI Symbol;Acc:MGI:1927135]

Sequence

>retro_mmus_2800
TCGGACTCCCTGGTGGTGTGTGAAGTGGACCCGGAGCTAAAGGAAACATTGAGGAAATTCCGTTTCCGAAAAGAGACCAA
CAATGCCGCCATCATAATGAAAGTGGACAAAGACCGGCAGATGGTGGTGCTGGAGGATGAACTCCAGAACATCTCCCCAG
AAGAACTTAAGTTGGAATTGCCAGAGAGACAGCCCAGGTTTGTGGTCTACAGCTACAAGTACGTGCATGATGACGGCAGG
GTGTCCTATCCTTTGTGCTTCATCTTCTCCAGCCCCGTGGGCTGCAAGCCTGAACAACAGATGATGTATGCAGGAAGTAA
AAACAGTCTGGTGCAGACGGCGGAGCTTACCAAGGTGTTTGAAATCCGCACCACAGACGACCTCACCGAGACCTGGCTTA
AGGAAAAGTTAGCTTTCTTTCGT

Alignment

ORF - retro_mmus_2800 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.29 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDSLVVCEVDPELKETLRKFRFRKETNNAAIIMKVDKDRQMVVLEDELQNISPEELKLELPERQPRFVVY
          SDSLVVCEVDPELKETLRKFRFRKETNNAAIIMKVDKDRQMVVLEDELQNISPEELKLELPERQPRFVVY
Retrocopy SDSLVVCEVDPELKETLRKFRFRKETNNAAIIMKVDKDRQMVVLEDELQNISPEELKLELPERQPRFVVY

Parental  SYKYVHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAELTKVFEIRTTDDLTETWLKEKLAFF
          SYKYVHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKN.LVQTAELTKVFEIRTTDDLTETWLKEKLAFF
Retrocopy SYKYVHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNSLVQTAELTKVFEIRTTDDLTETWLKEKLAFF

Parental  R
          R
Retrocopy R

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	0.40 RPM
SRP007412_cerebellum	0.00 RPM	0.39 RPM
SRP007412_heart	0.00 RPM	1.81 RPM
SRP007412_kidney	0.02 RPM	4.39 RPM
SRP007412_liver	0.05 RPM	3.39 RPM
SRP007412_testis	0.05 RPM	3.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2800 was not detected

EST

No EST(s) were mapped for retro_mmus_2800 retrocopy.

TSS

No TSS is located nearby retro_mmus_2800 retrocopy 5' end.

Lab

retro_mmus_2800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2800 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006529	2 retrocopies	retro_dnov_1062, retro_dnov_1435,
Echinops telfairi	ENSETEG00000008573	1 retrocopy	retro_etel_1630,
Gorilla gorilla	ENSGGOG00000006957	1 retrocopy	retro_ggor_1960,
Mus musculus	ENSMUSG00000060791	1 retrocopy	retro_mmus_2800 ,
Ochotona princeps	ENSOPRG00000015157	2 retrocopies	retro_opri_1160, retro_opri_160,
Sarcophilus harrisii	ENSSHAG00000008772	1 retrocopy	retro_shar_803,