RetrogeneDB ID: retro_meug_179

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_520:8821..9690(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSMEUG00000010780
• Aliases: None
• Description: eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]

Sequence

>retro_meug_179
ATGTCTGTGAGTCAGAATTCCTGATCCAGAGACAATGGCCCTGATGGAATGGACTCTGATGGTATCATTGGAGTAACTGG
AAGGAGATTGTGGATAGCTTTGATGATATGAACCTTTCAGAATCTCTTCTTCATGGTGTACATACCTATGATTTTGAGAA
GCCATATGCTATTCAGCAACATGCAATTCTCCCTTGTATCAAGGTTTATGATGTGATTGCTCAAGCCCAGTCTGGGACTG
GGAAGACGGCTACCTTTGCCATTTCCATTTTGCAACAGATTGAACTGGACTTAAAGGGCACACAGGCCTTGGTTTTAGCA
CCCACTAAAAAGTTATTTCAACAGATCCAAAAGGTAGTGATGGCTCTGGGAGACTATATGGGTGCCTCGTACCATGCCTG
CACTGGAGAAACAAATGTTAGGGTTGAGGTTCAGAAGTTGAAAATGGAAGCTAGCCACATCATTGTTGGCACCCCAGGTC
ATGTCTTTGACATACTTATCAGGTGATACTTATCTCCTAAATACATCAAGATGTTTGTTCTGGATAAAGCAGGTAAAATG
TTGAGTCATGGTTTTAAGGATCAGATCTATGACATATGCCAGAAACTCAGTGGCAATACTCAGGTGGTACTCCTGTCAGC
AACCATGCCCTCAGATGTGCTGGAAGTGGCCAAGAAGTTTATGAGGGATCCCATCAGGATTATAGTCAAGAAGGAGGAGT
TGACATTAGAAGGCATTTGTCAATTTTACATAAATGTGGAAAGAGAGGAGTGGAAGCTAGATATCTTGTGTGATCTGTAT
GAAACACCAACTATTACCTAAGCTGTTTTCTTCATCAATATCCACCAAAAGGTGAATTGGCTCAGAGAA

Alignment

ORF - retro_meug_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 81.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMDPDGVIE-SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG
          MS.SQ.S.SRDNGPDGMD.DG.I..SNW.EIVDSFDDMNLSESLL.G...Y.FEKP.AIQQ.AILPCIK.
Retrocopy MSVSQNS*SRDNGPDGMDSDGIIG<SNWKEIVDSFDDMNLSESLLHGVHTYDFEKPYAIQQHAILPCIKV

Parental  YDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTN
          YDVIAQAQSGTGKTATFAISILQQIELDLK.TQALVLAPT..L.QQIQKVVMALGDYMGAS.HAC.G.TN
Retrocopy YDVIAQAQSGTGKTATFAISILQQIELDLKGTQALVLAPTKKLFQQIQKVVMALGDYMGASYHACTGETN

Parental  VRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLSGNTQV
          VR.EVQKL.MEA.HIIVGTPG.VFD.L.R.YLSPKYIKMFVLD.A..MLS.GFKDQIYDI.QKLSGNTQV
Retrocopy VRVEVQKLKMEASHIIVGTPGHVFDILIR*YLSPKYIKMFVLDKAGKMLSHGFKDQIYDICQKLSGNTQV

Parental  VLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFI
          VLLSATMPSDVLEV.KKFMRDPIRI.VKKEELTLEGI.QFYINVEREEWKLD.LCDLYET.TIT.AV.FI
Retrocopy VLLSATMPSDVLEVAKKFMRDPIRIIVKKEELTLEGICQFYINVEREEWKLDILCDLYETPTIT*AVFFI

Parental  NTRRKVDWLTE
          N...KV.WL.E
Retrocopy NIHQKVNWLRE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_179 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_179 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300,
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732,
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,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179 ,
Macropus eugenii	ENSMEUG00000011737	1 retrocopy	retro_meug_237,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
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	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,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020, retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,
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,