RetrogeneDB ID: retro_oana_93

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig78145:4399..4870(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSOANG00000002646
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_oana_93
TACGCCGAACGCCAAGGCTACATCAAAGGGACCATAAAGGACATTATCCACGATCCCGGGCGAGGGGCTCCTCTGGCCAG
GGTGGCCTTCCGAAACGCGTATAGATTTTCAACAGAAACCGAAAACACAATTGCGGTGGAGGGGCTCTACACGGGGCAAT
TTGTCTACTATGGCGCTAATGCGAGTTTAACTATTGGGAATTGCCTTCCAATTGGAAAAATGCCCGAAGGAACGGTGGTG
TCGTCTTTGGAAGAAAAACGCGGAGACCGCGGCCGAGTCGCCAAAACAAGCGGCACCAGTGCGGTGATTATTGGGCATTC
CGACGACGGCAAAACTACTAGGATTAGGTTGCCATCTGGAACGCGCAAGACTTTGCCGAGTGGTTCCAGGGCTATTGTGG
GAGTGGTCGCCGGAGGCGGCCGTATCGATAAGCCGCTTTTAAAAGCTGGCACAGCCTACCACAAATACAAA

Alignment

ORF - retro_oana_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.24 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FAERHGYIKGIVKDIIHDPGRGAPLAKVAFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLP
          .AER.GYIKG..KDIIHDPGRGAPLA.VAFR..YRF...TE..IA.EG..TGQFVY.G..A.L.IGN.LP
Retrocopy YAERQGYIKGTIKDIIHDPGRGAPLARVAFRNAYRFSTETENTIAVEGLYTGQFVYYGANASLTIGNCLP

Parental  VGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGG
          .G.MPEGT.V..LEEK.GDRG..A..SG..A..I.H....K.TR..LPSG..K...S..RA.VGVVAGGG
Retrocopy IGKMPEGTVVSSLEEKRGDRGRVAKTSGTSAVIIGHSDDGKTTRIRLPSGTRKTLPSGSRAIVGVVAGGG

Parental  RIDKPILKAGRAYHKYK
          RIDKP.LKAG.AYHKYK
Retrocopy RIDKPLLKAGTAYHKYK

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	304.76 RPM
SRP007412_cerebellum	0.00 RPM	449.23 RPM
SRP007412_heart	0.00 RPM	1377.60 RPM
SRP007412_kidney	0.00 RPM	492.11 RPM
SRP007412_liver	0.00 RPM	415.86 RPM
SRP007412_testis	0.00 RPM	245.86 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_93 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_93 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Monodelphis domestica	ENSMODG00000004283	3 retrocopies	retro_mdom_1055, retro_mdom_1696, retro_mdom_253,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Ornithorhynchus anatinus	ENSOANG00000002646	1 retrocopy	retro_oana_93 ,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,