RetrogeneDB ID: retro_mmus_2752

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:78215877..78217110(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095908
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif4a3
• Ensembl ID: ENSMUSG00000025580
• Aliases: Eif4a3, 2400003O03Rik, Ddx48, eIF4A-III, mKIAA0111
• Description: eukaryotic translation initiation factor 4A3 [Source:MGI Symbol;Acc:MGI:1923731]

Sequence

>retro_mmus_2752
ATGGCGGCCACGGCCACGATGGCGAGGTCTGGCTCGGCGCGGAAGCGGCTGCTCAAAGAAGAGGACATGACCAAAGTGGA
GTTCGAGACGAGCGAGGAGGTGGACAGGACCCCCACGTTCGACACCATGGGCCTGCGAGAGGACCTGCTGCGCGGCATCT
ACGCCTACGGTTTTGAAAAACCTTCAGCGATCCAGCAGCGTGCTATCAAGCAGATAATGAAAGGCAGAGATGTCATTGCA
CAGTCTCAGTCTGGCACAGGCAAGACGGCCACCTTCAGTATCTCAATGCTGCAGTGCTTGGATATCCAGGTTCGAGAAAC
CCAAGCTTTGATCCTGGCTCCAACCAGAGAGTTAGCGGTACAGATTCAGAAGGGTCTGCTCACTCTGGGGGATTACATGA
ACGTGCAGTGCCATGCCTGCATCGGGGGCACCAATGTCGACGAGGACATCCGGAAGCTGGACTACGGGCAGCATGTGGTG
GCAGGCACTCCGGGACGCGTCTTTGATATGATCCGCCGGAGAAGTTTACGGACACGGGCTATCAAGATGCTGGTTTTGGA
TGAGGCTGATGAAATGTTGAACAAAGGTTTCAAGGAGCAGATCTACGATGTGTACAGGTATTTGCCACCAGCCACACAGG
TCGTTCTCATCAGTGCCACACTGCCTCATGAGATCCTGGAGATGACCAACAAGTTCATGACCGACCCCATCTGCATCCTG
GTGAAGCGTGATGAGTTGACTCTGGAAGGCATCAAACAGTTCTTTGTGGCCGTGGAAAGAGAGGAATGGAAGTTTGATAC
TCTATGTGATCTCTACGACACGCTGACCATCACCCAGGCCGTCATCTTCTGCAACACCAAGAGGAAGGTTGACTGGCTCA
CAGAGAAAATGAGAGAAGCCAATTTCACTGTGTCATCCATGCATGGAAACATGCCCCAGAAAGAACGAGAGTCTATCATG
AAGGAGTTCCGGTCAGGTGCCAGCCGGGTGCTCATCTCCACAGACATCTGGGCTCGGGGCCTGGATGTCCCTCAGGTGTC
CCTCATCATTAACTATGACCTGCCCAACAACAGAGAACTGTACATTCACAGAATTGGGAGATCGGGTCGGTATGGACGAA
AAGGTGTGGCCATCAATTTTGTGAAGAATGATGACATCCGGATTCTCAGGGACATCGAGCAGTACTACTCCACCCAGATA
GACGAGATGCCCATGAACGTGGCTGACCTCATC

Alignment

ORF - retro_mmus_2752 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIK
          MAA.ATMA.SGSARKRLLKEEDMTKVEFETSEEVD.TPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIK
Retrocopy MAATATMARSGSARKRLLKEEDMTKVEFETSEEVDRTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIK

Parental  QIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHAC
          QI.KGRDVIAQSQSGTGKTATFS.S.LQCLDIQVRETQALILAPTRELAVQIQKGLL.LGDYMNVQCHAC
Retrocopy QIMKGRDVIAQSQSGTGKTATFSISMLQCLDIQVRETQALILAPTRELAVQIQKGLLTLGDYMNVQCHAC

Parental  IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP
          IGGTNV.EDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP
Retrocopy IGGTNVDEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPP

Parental  ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA
          ATQVVLISATLPHEILEMTNKFMTDPI.ILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA
Retrocopy ATQVVLISATLPHEILEMTNKFMTDPICILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQA

Parental  VIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLII
          VIFCNTKRKVDWLTEKMREANFTVSSMHG.MPQKERESIMKEFRSGASRVLISTD.WARGLDVPQVSLII
Retrocopy VIFCNTKRKVDWLTEKMREANFTVSSMHGNMPQKERESIMKEFRSGASRVLISTDIWARGLDVPQVSLII

Parental  NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI
          NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI
Retrocopy NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

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	33.13 RPM
SRP007412_cerebellum	0.09 RPM	42.16 RPM
SRP007412_heart	0.06 RPM	41.78 RPM
SRP007412_kidney	0.10 RPM	46.58 RPM
SRP007412_liver	0.00 RPM	31.71 RPM
SRP007412_testis	0.09 RPM	59.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2752 was not detected

EST

No EST(s) were mapped for retro_mmus_2752 retrocopy.

TSS

No TSS is located nearby retro_mmus_2752 retrocopy 5' end.

Lab

retro_mmus_2752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2752 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000009136	2 retrocopies	retro_mmur_444, retro_mmur_50,
Myotis lucifugus	ENSMLUG00000009585	1 retrocopy	retro_mluc_65,
Mus musculus	ENSMUSG00000025580	2 retrocopies	retro_mmus_2752 , retro_mmus_70,
Mus musculus	ENSMUSG00000059796	7 retrocopies	retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Ornithorhynchus anatinus	ENSOANG00000000334	1 retrocopy	retro_oana_47,
Otolemur garnettii	ENSOGAG00000007495	1 retrocopy	retro_ogar_212,