RetrogeneDB ID: retro_mmus_1801

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:90310870..90311702(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3e
• Ensembl ID: ENSMUSG00000022336
• Aliases: Eif3e, 48kDa, Eif3s6, Int6, eIF3-p46, eIF3-p48
• Description: eukaryotic translation initiation factor 3, subunit E [Source:MGI Symbol;Acc:MGI:99257]

Sequence

>retro_mmus_1801
GCTTTAAGTTCGCTTTGGGGAAAACTGGCCTCTGAAATCGTAATGCAGAATTGGGATGCAGCCATGGAAGACCTTACTCG
ATTAAAAGAGACCATAGACAATAATTCTGTGAGTTCTCCACTCCAGTCTCTTCAGCAGTGAACATGGCTCATTCATTGGT
CTCTTATTTGTTTTTATCAACCATCCAAAGGGCCGTGATAACATTATTGATCTCTTCCTTTACCAACCACAGTACCTTAA
TGCAATTCAGACAATGTGTCCACATACTCTCCGCTATTTGACTACTGCCGTCATAACCAAAAAAGATGTGCGGAAACGCC
AGCAGGTGCTGAAAGTGATTCAACAGGAGTCTTACACACATAAAGACCCAATTATGGAATTTGTTGAATGCCTATATGTT
AACTTTGATTTTGACGGGGCTCAGAAAAAGCTGAGAGAATGTGAATCAGTGCTCATGAATGACTTCTTCCTGGTAGCGTG
TCTGGAGAACTTCATTGAGAATACCCGTATCTTCATATTTGAGATGTTTTGTCGTATCCACCAGTGTATCAGCATTAATA
TGTTAGCAGACAAACTGAATATGACTCCAGAAGAAGCTGAAAGATGGATTGTGAATTTGATTAGAAATGCGAGGTTGGAT
GCCAAGATTGATTCTAAACTAGGTCATGTGGTAATGGGCAACAATGCAGTCTCACCCTACCAGCAAGTGATTGAAAAGAC
TAAAAGTCTTTCTTTTAGAAGCTAAATGTTGGCCATGAATCTCGAAAAGAAACTTAATCAGAATAGTAGATCAGAGGCTC
CCAACTGGGAAACCCAAGACTCTGGCTTCTAT

Alignment

ORF - retro_mmus_1801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.55 %
• Parental protein coverage: 63.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALSSLWGKLASEILMQNWDAAMEDLTRLKETIDNNSVSSPLQSLQQRTWLIHWSL-FVFFNHPKGRDNII
          ALSSLWGKLASEI.MQNWDAAMEDLTRLKETIDNNSVSSPLQSLQQ.TWLIHWSL.FVF.NHPKGRDNII
Retrocopy ALSSLWGKLASEIVMQNWDAAMEDLTRLKETIDNNSVSSPLQSLQQ*TWLIHWSL>FVFINHPKGRDNII

Parental  DLFLYQPQYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLVKVIQQESYTYKDPITEFVECLYVNF
          DLFLYQPQYLNAIQTMCPH.LRYLTTAVIT.KDVRKR.QVL....KVIQQESYT.KDPI.EFVECLYVNF
Retrocopy DLFLYQPQYLNAIQTMCPHTLRYLTTAVITKKDVRKRQQVL----KVIQQESYTHKDPIMEFVECLYVNF

Parental  DFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCRIHQCISINMLADKLNMTPEEAERWIVN
          DFDGAQKKLRECESVL.NDFFLVACLE.FIEN.R.FIFE.FCRIHQCISINMLADKLNMTPEEAERWIVN
Retrocopy DFDGAQKKLRECESVLMNDFFLVACLENFIENTRIFIFEMFCRIHQCISINMLADKLNMTPEEAERWIVN

Parental  LIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSEAPNWATQDSG
          LIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRS.MLAMN.EKKLNQNSRSEAPNW.TQDSG
Retrocopy LIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRS*MLAMNLEKKLNQNSRSEAPNWETQDSG

Parental  FY
          FY
Retrocopy FY

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	0.35 RPM	44.69 RPM
SRP007412_cerebellum	1.35 RPM	25.40 RPM
SRP007412_heart	0.00 RPM	44.92 RPM
SRP007412_kidney	1.77 RPM	51.55 RPM
SRP007412_liver	1.83 RPM	46.10 RPM
SRP007412_testis	3.80 RPM	69.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1801 was not detected

EST

No EST(s) were mapped for retro_mmus_1801 retrocopy.

TSS

No TSS is located nearby retro_mmus_1801 retrocopy 5' end.

Lab

retro_mmus_1801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1801 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801 , retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,