RetrogeneDB ID: retro_mmus_527

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:10343543..10344331(+)
• Located in intron of: ENSMUSG00000050994

Retrocopy information

• Ensembl ID: ENSMUSG00000083257
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif4a1
• Ensembl ID: ENSMUSG00000059796
• Aliases: Eif4a1, BM-010, Ddx2a, Eif4
• Description: eukaryotic translation initiation factor 4A1 [Source:MGI Symbol;Acc:MGI:95303]

Sequence

>retro_mmus_527
GTGCTGAGGCTGCAAATGGAAGCTCTCCATATCATTGTGGGCAGCCCTGGCTGGGTGTTTGATATGCTTAAATGGAGATA
CCTGTCTTTCAAATACGTCAAGATGTTCATACTGGATGAAGAAGATGAAATATTAAGCTGTGGGTTCAAAGATCAGATCT
ATGACATATTCCAAAGTCTCAACAAAAACACACAGGTAGTTTTGTTATCTGCTACAATGCCTTCTGATGTCCTTGATGTG
AACAAGAAGTTCATGAGAGACCCTATTCGGAATCCTGTCAAGAAGGAAAAGTTGACCTTGTCCAGTATCTGCTAATTCTA
CGTCAATGTGGAACGAGAGGAGTGGAAGCTTGATACATTGTGCGACTTGTATAAAACATTGGCCATCAACCAGGCAGTAA
CCTTTGTCAATACCAGAAGGAAGGTGGGCTGGCTCACTGAGAAGATGCGTGCCTGGGATTTCACTGTTTCCACCATGCAT
GGAGCTATGGACCAAAAGCAATGAGGTGTGATCATGAGGGAGTTCCAGTCTGGCTCTAGCAGAGTTATTAATTACCACAG
ACTTGTTGGCCAGAGCCACTGATGTGCAGCGGGTTTCCTTAGTCATCAACAATGACCTTTCACCAACAGGGAAACTATGT
TCACAGAACTGGTTAAGGTGGTTGGTTTGGCCGGAAGGGTGTGGCTATTAACATGGTGACAGAAGAAGACAAGAGGACTC
TCTGAGACATTGAGACTTTCTACAACACCTCCATTGAAGAGATGCCCCTCAACCTTGCTGACCTCATT

Alignment

ORF - retro_mmus_527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 64.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLS
          V..LQMEA.HIIVG.PG.VFDML..RYLS.KY.KMF.LDE.DE.LS.GFKDQIYDIFQ.LN.NTQVVLLS
Retrocopy VLRLQMEALHIIVGSPGWVFDMLKWRYLSFKYVKMFILDEEDEILSCGFKDQIYDIFQSLNKNTQVVLLS

Parental  ATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRR
          ATMPSDVL.V.KKFMRDPIR..VKKE.LTL..I..FY.NVEREEWKLDTLCDLY.TL.I.QAV.F.NTRR
Retrocopy ATMPSDVLDVNKKFMRDPIRNPVKKEKLTLSSIC*FYVNVEREEWKLDTLCDLYKTLAINQAVTFVNTRR

Parental  KVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRV-LITTDLLARGIDVQQVSLVINYDLP-T
          KV.WLTEKM.A.DFTVS.MHG.MDQK...VIMREF.SGSSRV.LITTDLLAR..DVQ.VSLVIN.DL..T
Retrocopy KVGWLTEKMRAWDFTVSTMHGAMDQKQ*GVIMREFQSGSSRV>LITTDLLARATDVQRVSLVINNDLS<T

Parental  NRE-NYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          NRE.NY.HR.G.GG.FGRKGVAINMVTEEDKRTL.DIETFYNTSIEEMPLN.ADLI
Retrocopy NRE<NYVHRTG*GGWFGRKGVAINMVTEEDKRTL*DIETFYNTSIEEMPLNLADLI

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	0.02 RPM	110.39 RPM
SRP007412_cerebellum	0.09 RPM	70.39 RPM
SRP007412_heart	0.00 RPM	78.01 RPM
SRP007412_kidney	0.02 RPM	113.32 RPM
SRP007412_liver	0.16 RPM	151.78 RPM
SRP007412_testis	1.46 RPM	65.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_527 was not detected

EST

No EST(s) were mapped for retro_mmus_527 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_20	481 libraries	497 libraries	90 libraries	1 library	3 libraries

The graphical summary, for retro_mmus_527 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_527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_527 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088,
Erinaceus europaeus	ENSEEUG00000003581	1 retrocopy	retro_eeur_610,
Felis catus	ENSFCAG00000024897	1 retrocopy	retro_fcat_370,
Homo sapiens	ENSG00000161960	10 retrocopies	retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931, retro_hsap_610,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
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 ,
Nomascus leucogenys	ENSNLEG00000009547	7 retrocopies	retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Pan troglodytes	ENSPTRG00000008694	10 retrocopies	retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus	ENSSTOG00000024814	1 retrocopy	retro_itri_610,