RetrogeneDB ID: retro_oana_73

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig38122:538..1249(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A2
• Ensembl ID: ENSOANG00000004908
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 2 [Source:HGNC Symbol;Acc:3192]

Sequence

>retro_oana_73
GGAAAAACGTTGGTGGAAGCACTCGATACTATGGAACCCCCAAAACGTCCGCATGACAAGCCACTGCGCCTGCCACTCCA
GGGTGTTTACAAGATTGGTGGAATTGGCACGGTGCCTGTAGGTCGCGTCGAAACCGGGCAGCTCAAAGCGGGAATGGTGC
TAACTTTTGCTCCGAATGCAATTACCACGGAGTGCAAATCCGTTGAAATGCATCACGAGGTGGTGGAGGTGGCATCTCCC
GGTGATAACGTTGGTTTTAACGTAAAGAACGTTTCCACGACGGACATTCGCGCTGGCCACGTTGCGTCGGATTCTAAAAA
TGACCCCGCCAAGGAAGCTGTGAGTTTCAGCGCGCAAGTTATCATCCTGAACCACCCGGGTACTATCAAGGCCGGCTACT
CGCCCGTTGTTGACTGCCACACCGCCCACATTTCATGCAAATTTGATGCCATAACGTGCCGCATGGATAAGCGTACGGGC
AAGTCGTTGGAGGAGAACCCAAAAACAATTAAGAACGGTGACGCTGCCATGGTGACTCTGAAGCCGAACAAACCCATGGT
CGTGGAAACATTCACAGAGTATGCACCGCTGGGTCGTTTCGCCGTTCGTGATATGAAACAAACGGTGGCCGTGGGTGTGA
TAAAATCGGTTGAGAAAAAGGACCCTGGTGCATCTGCAAAAGTGACCAAGTCCGCGATGAAGGCAGCAAAA

Alignment

ORF - retro_oana_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.89 %
• Parental protein coverage: 50.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVSLLEALDTILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGILRPGMVVTFAPVNITTEVKSVEM
          G..L.EALDT..PP.RP.DKPLRLPLQ.VYKIGGIGTVPVGRVETG.L..GMV.TFAP..ITTE.KSVEM
Retrocopy GKTLVEALDTMEPPKRPHDKPLRLPLQGVYKIGGIGTVPVGRVETGQLKAGMVLTFAPNAITTECKSVEM

Parental  HHEALSEALPGDNVGFNVKNVSVKDIRRGNVCGDSKSDPPQEAAQFTSQVIILNHPGQISAGYSPVIDCH
          HHE....A.PGDNVGFNVKNVS..DIR.G.V..DSK.DP..EA..F..QVIILNHPG.I.AGYSPV.DCH
Retrocopy HHEVVEVASPGDNVGFNVKNVSTTDIRAGHVASDSKNDPAKEAVSFSAQVIILNHPGTIKAGYSPVVDCH

Parental  TAHIACKFAELKEKIDRRSGKKLEDNPKSLKSGDAAIVEMIPGKPMCVESFSQYPPLGRFAVRDMRQTVA
          TAHI.CKF.......D.R.GK.LE.NPK..K.GDAA.V...P.KPM.VE.F..Y.PLGRFAVRDM.QTVA
Retrocopy TAHISCKFDAITCRMDKRTGKSLEENPKTIKNGDAAMVTLKPNKPMVVETFTEYAPLGRFAVRDMKQTVA

Parental  VGVIKNVEKKSGGA-GKVTKSAQKAQK
          VGVIK.VEKK..GA..KVTKSA.KA.K
Retrocopy VGVIKSVEKKDPGASAKVTKSAMKAAK

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	0.00 RPM	1050.65 RPM
SRP007412_cerebellum	0.09 RPM	1428.69 RPM
SRP007412_heart	0.09 RPM	1568.97 RPM
SRP007412_kidney	0.00 RPM	36.72 RPM
SRP007412_liver	0.00 RPM	33.45 RPM
SRP007412_testis	0.00 RPM	49.10 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_73 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_73 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus 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 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Latimeria chalumnae	ENSLACG00000002952	1 retrocopy	retro_lcha_39,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macropus eugenii	ENSMEUG00000005018	23 retrocopies	retro_meug_1067, retro_meug_110, retro_meug_1160, retro_meug_1240, retro_meug_1334, retro_meug_135, retro_meug_1421, retro_meug_1451, retro_meug_1465, retro_meug_1501, retro_meug_1662, retro_meug_1690, retro_meug_1710, retro_meug_1829, retro_meug_2023, retro_meug_2044, retro_meug_2050, retro_meug_316, retro_meug_601, retro_meug_755, retro_meug_792, retro_meug_850, retro_meug_920,
Myotis lucifugus	ENSMLUG00000016760	1 retrocopy	retro_mluc_1250,
Mustela putorius furo	ENSMPUG00000008289	3 retrocopies	retro_mputfur_1030, retro_mputfur_609, retro_mputfur_761,
Nomascus leucogenys	ENSNLEG00000010060	2 retrocopies	retro_nleu_11, retro_nleu_1489,
Ornithorhynchus anatinus	ENSOANG00000004908	1 retrocopy	retro_oana_73 ,
Otolemur garnettii	ENSOGAG00000004630	8 retrocopies	retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Ictidomys tridecemlineatus	ENSSTOG00000028862	1 retrocopy	retro_itri_1028,
Tursiops truncatus	ENSTTRG00000001835	1 retrocopy	retro_ttru_993,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,