RetrogeneDB ID: retro_mmus_2350

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:51893331..51894131(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081050
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eef1g
• Ensembl ID: ENSMUSG00000071644
• Aliases: Eef1g, 2610301D06Rik, AA407312, EF1G
• Description: eukaryotic translation elongation factor 1 gamma [Source:MGI Symbol;Acc:MGI:1914410]

Sequence

>retro_mmus_2350
TGGCTAATATCACAGTTGTCTGCACCCTGTTGTGGCTCTACAAACAGGTTTTGGAGCCTTCTTTTCCTTAACTGCCTTAA
CCAGTCCCAGTTCAGGGCCGTCTTTGGGGAGGTGAAGCTGTGTGAGAAGATGGCCCAGTTTGATGCTAAGAAGTTTTCAG
AAAGCCAACATAAAAAGAAAACCACAAGGAAAGAAAAGGGTTCATGAGAGGAGACACAGAAGCCCCAGGCTGAGCAGAAA
GAGGGGGAAAAAGACAGCTGTCCAGCTCCTGAAGAAGAGATGGATGAGTGTGAGCGGGCATTGGCTGCTGAGCCCAAGGC
CAAAGACCCTTTCGCTCGCTTGCCCAGGAGTAGCTTTGTGTTGGATGAGTTTAAGCACAAGTACTCCAATGAGGGCACCC
TCTCTGTGGCAGTGCCGTATTGTTGGGAATACTTTGAAAAGGATGGCTGGTCTCTGCGGTATGCTGAGTACTGTTTCCCT
GAAGAGCTCACCCAGACCTTCATGAATTGCAACCTCATCACCGGAATGTTCCAGCGATTGGACAAACTGAGGAAGAATGC
CTTTGCTAGTGCTGTCCTCTTTGGAACCAACAACAGCAGTTCCATCTCTGGTGTTTGGGTCTTCAGAGGCTAAGAGCTTG
CCTTTCCACTGAGTCCAGATTGGCAGGTGAACTATGAGTCGTATACATGGCAGAAACTGGATCCTGGTAGGGGGAGACCC
AGACCCTGGTTGGCGAGTACTTTTCCTGGAAGGGGGCCTTCTAGCACGTGAACAAAGCCATCAATCAAGGCAAGATCTTC

Alignment

ORF - retro_mmus_2350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.24 %
• Parental protein coverage: 61.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAILGEVKLCEKMAQFDAKKFAESQPKKDTPRKEKGSRE
          WL..Q...P............FL.C.NQ.QFRA..GEVKLCEKMAQFDAKKF.ESQ.KK.T.RKEKGS.E
Retrocopy WLISQLSAPCCGSTNRFWSLLFLNCLNQSQFRAVFGEVKLCEKMAQFDAKKFSESQHKKKTTRKEKGS*E

Parental  EKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPFAHLPKSTFVLDEFKRKYSNEDTLSVALPY
          E.QKPQAE.KE..K...PAPEEEMDECE.ALAAEPKAKDPFA.LP.S.FVLDEFK.KYSNE.TLSVA.PY
Retrocopy ETQKPQAEQKEGEKDSCPAPEEEMDECERALAAEPKAKDPFARLPRSSFVLDEFKHKYSNEGTLSVAVPY

Parental  FWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLDKLRKNAFASVILFGTNNSSSISGVWVFRG
          .WE.F.KDGWSL.YAEY.FPEELTQTFM.CNLITGMFQRLDKLRKNAFAS..LFGTNNSSSISGVWVFRG
Retrocopy CWEYFEKDGWSLRYAEYCFPEELTQTFMNCNLITGMFQRLDKLRKNAFASAVLFGTNNSSSISGVWVFRG

Parental  QELAFPLSPDWQVDYESYTWRKLDPGS-EETQTLVREYFSWEGTFQHVGKAVNQGKIF
          .ELAFPLSPDWQV.YESYTW.KLDPG...ETQTLV.EYFSW.G.F.HV.KA.NQGKIF
Retrocopy *ELAFPLSPDWQVNYESYTWQKLDPGR<GETQTLVGEYFSWKGAF*HVNKAINQGKIF

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	74.27 RPM
SRP007412_cerebellum	0.00 RPM	52.71 RPM
SRP007412_heart	0.00 RPM	74.28 RPM
SRP007412_kidney	0.00 RPM	74.94 RPM
SRP007412_liver	0.00 RPM	53.74 RPM
SRP007412_testis	0.00 RPM	179.11 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2350 was not detected

EST

No EST(s) were mapped for retro_mmus_2350 retrocopy.

TSS

No TSS is located nearby retro_mmus_2350 retrocopy 5' end.

Lab

retro_mmus_2350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Erinaceus europaeus	ENSEEUG00000001231	1 retrocopy	retro_eeur_575,
Homo sapiens	ENSG00000254772	4 retrocopies	retro_hsap_2778, retro_hsap_2982, retro_hsap_3906, retro_hsap_4744,
Gorilla gorilla	ENSGGOG00000013557	12 retrocopies	retro_ggor_1935, retro_ggor_1936, retro_ggor_1991, retro_ggor_1992, retro_ggor_2064, retro_ggor_2065, retro_ggor_2214, retro_ggor_243, retro_ggor_2542, retro_ggor_2633, retro_ggor_2946, retro_ggor_2947,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Macaca mulatta	ENSMMUG00000006598	5 retrocopies	retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mus musculus	ENSMUSG00000071644	7 retrocopies	retro_mmus_1447, retro_mmus_1839, retro_mmus_2350 , retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Ictidomys tridecemlineatus	ENSSTOG00000002851	2 retrocopies	retro_itri_852, retro_itri_886,