RetrogeneDB ID: retro_mmus_421

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:21511935..21513056(-)
• Located in intron of: ENSMUSG00000028033

Retrocopy information

• Ensembl ID: ENSMUSG00000082935
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif3m
• Ensembl ID: ENSMUSG00000027170
• Aliases: Eif3m, Ga17, Pcid1, Tango7
• Description: eukaryotic translation initiation factor 3, subunit M [Source:MGI Symbol;Acc:MGI:1351744]

Sequence

>retro_mmus_421
ATGAGCGTCCCGGCCTTCATCATATCAGCGAGGAAGACCAGGCCGCTGAACTTCGAGCTTATCTGAAATCAAAAGGAGCT
GAGCTCTCACAAGAAAACTCGGAAGGTGGACTTCATGTAGATTTAGCTCAGATTATTGAAGCCTGTGATGTGTGTCTGAA
AGAAGATGATAAAGATGTTGAAAGTGTGATGAACAGTGTGGTGTCCCTCCTGTTGATTCTGGAACCAGACAAGCAAGAAG
CATTGATTGAAAGTCTGTGTGAAAAGCTGGTCAAGTTTCGGGAAGGCGAACGCCCATCTCTGAGACTACAGTTGCTCAGC
ATCCTTTTCCATGGGATGGACAAGAATACTCCTGTGAGGTACACAGTGTACTGCAGCCTCATCAAAGTGGCGGCATCATG
TGGAGCCATCCAGTACATCCCAACGGAGCTGGATCAAGTGAGAAAGTGGATCTCTGACTGGAAGCTCACCACTGAAAAGA
AACACACCCTCCTAAGACTGCTCTACGAGGCGTTTGTGGATTGTAAGAAAAGTGATGCTGCATCAAAGGTCATGGTGGAA
TTGCTCGGGAGTTACACAGAGGACAATGCTTCCCAGGCTCGAGTTGATGCCCACAGGTGTATTGTGCGGGCACTAAAGGA
TCCAAATGCCTTTCTTTTTGACCATCTTCTTATTCTAAAGCCAGTCAAATTTTTGGAAGGCGAGCTTATCCATGATTTAT
TAACCATTTTTGTGAGTGCTAAATTGGCATCGTATGTCAAGTTCTATCAGAATAACAAAGACATCATAGATTCACTTGGC
TTGTTACATGAGCAAAATATGTCGAAAATGAGACTCCTCACCTTTATGGGAATGGCAGTGGAAAACAAAGAGATTTCTTT
TGACACAATGCAGCAAGAGCTACAGATTGGAGCTGATGATATTAAAGCATTTGTTATTGATGCTGTAAGAACTAAAATGG
TCTACTGCAAAATCGATCAGACCCAAAGAAAAGTAGTTGTCAGTCACAGCACACATCGGACATTTGGAAAACAGCAGTGG
CAACAACTGTATGACACTCTTAATGCCTGGAAACAGAACTTGAACAAAGTGAAAAATAGCCTTTTGAGTCTTTCAGATAC
C

Alignment

ORF - retro_mmus_421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVPAFI-DISEEDQAAELRAYLKSKGAELSEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVS
          MSVPAFI..ISEEDQAAELRAYLKSKGAELS.ENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVS
Retrocopy MSVPAFI<HISEEDQAAELRAYLKSKGAELSQENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVS

Parental  LLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQY
          LLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLS.LFHGMDKNTPVRYTVYCSLIKVAASCGAIQY
Retrocopy LLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSILFHGMDKNTPVRYTVYCSLIKVAASCGAIQY

Parental  IPTELDQVRKWISDWKLTTEKKHTLLRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIV
          IPTELDQVRKWISDWKLTTEKKHTLLRLLYEA.VDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIV
Retrocopy IPTELDQVRKWISDWKLTTEKKHTLLRLLYEAFVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIV

Parental  RALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRL
          RALKDPNAFLFDHLL.LKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKD.IDSLGLLHEQNM.KMRL
Retrocopy RALKDPNAFLFDHLLILKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDIIDSLGLLHEQNMSKMRL

Parental  LTFMGMAVENKEISFDTMQQELQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQ
          LTFMGMAVENKEISFDTMQQELQIGADD..AFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQ
Retrocopy LTFMGMAVENKEISFDTMQQELQIGADDIKAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQ

Parental  LYDTLNAWKQNLNKVKNSLLSLSDT
          LYDTLNAWKQNLNKVKNSLLSLSDT
Retrocopy LYDTLNAWKQNLNKVKNSLLSLSDT

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	0.40 RPM	37.10 RPM
SRP007412_cerebellum	0.52 RPM	31.91 RPM
SRP007412_heart	0.28 RPM	44.33 RPM
SRP007412_kidney	0.64 RPM	48.87 RPM
SRP007412_liver	0.55 RPM	34.90 RPM
SRP007412_testis	0.69 RPM	36.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_421 was not detected

EST

No EST(s) were mapped for retro_mmus_421 retrocopy.

TSS

No TSS is located nearby retro_mmus_421 retrocopy 5' end.

Lab

retro_mmus_421 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_421 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005338	2 retrocopies	retro_btau_1736, retro_btau_812,
Echinops telfairi	ENSETEG00000013437	1 retrocopy	retro_etel_120,
Myotis lucifugus	ENSMLUG00000014727	2 retrocopies	retro_mluc_1982, retro_mluc_431,
Mus musculus	ENSMUSG00000027170	1 retrocopy	retro_mmus_421 ,
Oryctolagus cuniculus	ENSOCUG00000004483	1 retrocopy	retro_ocun_282,
Otolemur garnettii	ENSOGAG00000015913	1 retrocopy	retro_ogar_1783,
Pteropus vampyrus	ENSPVAG00000015083	1 retrocopy	retro_pvam_1134,
Vicugna pacos	ENSVPAG00000007791	1 retrocopy	retro_vpac_342,