RetrogeneDB ID: retro_mmus_3080

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:116824512..116825823(-)
• Located in intron of: None

Retrocopy information

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

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_3080
ATGGCGGCTGGGACCCTGTACACATACCCTGAAAATTGGAGGGCCTTCAAGGCCCTCATCGCTGCTCAGTACAGCGGGGC
TCAGGTCCGCGTGCTCTCCGCACCACCCCACTTCCACTTTGGCCAAACCAACCGCACCCCTGAATTTCTCCGAAAATTTC
CTGCCGGCAAGGTTCCAGCATTTGAGGGTGATGATGGATTCTGTGTGTTTGAGAGCAATGCCATTGCCTATTATGTAAGC
AATGAAGAGCTGCGAGGAAGTACGCCAGAGGCGGCAGCTCAGGTGGTGCAGTGGGTCAGCTTTGCTGACAGTGACATCGT
TCCTCCAGCTAGTACCTGGGTGTTCCCCACCTTGGGCATTATGCACCACAACAAACAGGCCACTGAAAATGCGAAAGAGG
AGGTGAAGCGAATCCTGGGGCTGCTGGACACTCACTTGAAGACTCGAACTTTTCTAGTGGGCGAGCGAGTGACACTGGCT
GATATTACAGTTGTCTGTACCCTGTTGTGGCTCTATAAACAGGTCTTAGAGCCTTCTTTTCGCCAGGCCTTCCCCAATAC
CAACCGGTGGTTCCTTACCTGCATTAACCAGCCCCAGTTCAGGGCTATCTTGGGGGAGGTGAAGCTGTGTGAGAAGATGG
CTCAGTTTGATGCTAAGAAGTTTGCAGAGAGCCAGTCTAAAAAAGATACCCCAAGGAAAGAAAAGGGTTCATGAGAGGAG
AAACAGAAACCCCAGGCTGAGCGGAAGGAGGAAAAAAATGCAGCTGCCCCAGCTCCTGAGGAAGAGATGGATGAGTGTGA
GCAGGCATTGGCTGCTGAGCCCAAGGCCAAGGACCCTTTCGCTCACCTGCCCAAGAGTACCTTTGTGTTGGATGAGTTTA
AGCGTAAGTACTCCAATGAGGACACCCTCTCTGTGGCACTGCCATATTTTTGGGAGCACTTTGATAAAGATGGCTGGTCC
CTGTGGTATGCCGAGTACCGCTTCCCTGAAGAGCTGACCCAGACCTTCATGAGTTGCAACCTCATCACTGGGATGTTTCA
GCGATTGGACAAACTGAGGAAGAATGCCTTTGCTAGTGTTATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGTG
TTTGGGTCTTCCGAGGCCAAGAGCTTGCCTTTCCGCTGAGTCCAGATTGGCAGGTGGACTATGAGTCGTATACATGGCGG
AAACTGGATCCTGGGAGCGAAGAAACCCAGACCCTGGTTCGAGAGTACTTTTCCTGGGAGGGGACCTTCCAGCATGTGGG
CAAAGCCGTCAATCAAGGCAAGATCTTCAAG

Alignment

ORF - retro_mmus_3080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
          MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
Retrocopy MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF

Parental  ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVKRILG
          ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVKRILG
Retrocopy ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVKRILG

Parental  LLDTHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAILGEVKLC
          LLDTHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAILGEVKLC
Retrocopy LLDTHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAILGEVKLC

Parental  EKMAQFDAKKFAESQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
          EKMAQFDAKKFAESQ.KKDTPRKEKGS.EEKQKPQAERKEEK.AAAPAPEEEMDECEQALAAEPKAKDPF
Retrocopy EKMAQFDAKKFAESQSKKDTPRKEKGS*EEKQKPQAERKEEKNAAAPAPEEEMDECEQALAAEPKAKDPF

Parental  AHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLD
          AHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLD
Retrocopy AHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLD

Parental  KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWE
          KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWE
Retrocopy KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWE

Parental  GTFQHVGKAVNQGKIFK
          GTFQHVGKAVNQGKIFK
Retrocopy GTFQHVGKAVNQGKIFK

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	0.47 RPM	74.27 RPM
SRP007412_cerebellum	0.22 RPM	52.71 RPM
SRP007412_heart	0.31 RPM	74.28 RPM
SRP007412_kidney	0.42 RPM	74.94 RPM
SRP007412_liver	0.11 RPM	53.74 RPM
SRP007412_testis	1.19 RPM	179.11 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3080 was not detected

EST

No EST(s) were mapped for retro_mmus_3080 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_128041	51 libraries	12 libraries	162 libraries	334 libraries	513 libraries

The graphical summary, for retro_mmus_3080 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3080 has 0 orthologous retrocopies within eutheria group .

---

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,