RetrogeneDB ID: retro_mmus_3122

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:33691994..33692659(+)
• Located in intron of: ENSMUSG00000031584

Retrocopy information

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

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_3122
AGCAAGCATCTGGGCACCGATACACAAAAGGTGGTTGTGGCATTAGGAGACAGCATGGGTGCCTCTCATCATGCCTGTAT
TGGGGGTACCAATGTGTGTGCTGAGGTGTAGAAGCTGCAAATGGAAGCTCCCCATATCATCGTGGGCACCCCTGACCGGG
TGCTTGATGTACTTAACCGGAGATACTGTCCCCCAAATACATCAAGACGTTCGTACTGGATGAAGCAGTTGAAATGTTAA
GCCGTAGGGACAAGGATCAGATCTATGATATATTCCAAAAGCTCTACAGCAACACACAGGTAGTTTTGTTACTGTCTGCT
ACAATGGTTTCTGATGTCCTTGAGGTGACCAAGAAGTTCATGAGAGACCCTATTCGGATTCTTGCCAAGAAAGAAGAGTT
GACCCTGGAGGGTATCAGCCAGTTCTACATCAACATGGAACGAGAGGACTGGAAGCTTGGCACATCGTGTGACTTGTATG
GAACACTGCCCATCACCCAGGCAGTCATCTCTATCAACACCAGAAGGAAGGTGGACTGGCTCACTGAGAAGATGCATGCC
CGGTATCTCACGGTTTCCGCCATGCATGGAGATAGGGACCAAAAGGAACGAGATGTGATCATGAGGGAGTTCCTGTCTGG
CTCTAGCAGAGTATTACCACTGACC

Alignment

ORF - retro_mmus_3122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.96 %
• Parental protein coverage: 54.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRY-LSPKYIK
          ...L....QKVV.ALGD.MGAS.HACIGGTNV.AEV.KLQMEAPHIIVGTP.RV.D.LNRRY.LSPKYIK
Retrocopy SKHLGTDTQKVVVALGDSMGASHHACIGGTNVCAEV*KLQMEAPHIIVGTPDRVLDVLNRRY<LSPKYIK

Parental  MFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLL-SATMPSDVLEVTKKFMRDPIRILVKKEELTLEGI
          .FVLDEA.EMLSR..KDQIYDIFQKL.SNTQVVLL.SATM.SDVLEVTKKFMRDPIRIL.KKEELTLEGI
Retrocopy TFVLDEAVEMLSRRDKDQIYDIFQKLYSNTQVVLLLSATMVSDVLEVTKKFMRDPIRILAKKEELTLEGI

Parental  RQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMR
          .QFYIN.ERE.WKL.T.CDLY.TL.ITQAVI.INTRRKVDWLTEKMHAR..TVSAMHGD.DQKERDVIMR
Retrocopy SQFYINMEREDWKLGTSCDLYGTLPITQAVISINTRRKVDWLTEKMHARYLTVSAMHGDRDQKERDVIMR

Parental  EFRSGSSRVLITT
          EF.SGSSRVL..T
Retrocopy EFLSGSSRVLPLT

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	0.56 RPM	110.39 RPM
SRP007412_cerebellum	0.56 RPM	70.39 RPM
SRP007412_heart	0.50 RPM	78.01 RPM
SRP007412_kidney	0.64 RPM	113.32 RPM
SRP007412_liver	0.38 RPM	151.78 RPM
SRP007412_testis	0.09 RPM	65.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3122 was not detected

EST

No EST(s) were mapped for retro_mmus_3122 retrocopy.

TSS

No TSS is located nearby retro_mmus_3122 retrocopy 5' end.

Lab

retro_mmus_3122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3122 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,