RetrogeneDB ID: retro_oana_89

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig5671:10880..11489(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSOANG00000015759
• Aliases: None
• Description: retinol dehydrogenase 12 (all-trans/9-cis/11-cis) [Source:HGNC Symbol;Acc:19977]

Sequence

>retro_oana_89
GAAGAGCCCCGCCTGGATGTCTTGATCAATAACGCTGGGATTTTTCAGTGTCCTTATATGAAGACGGAGGATGGTTTTGA
GATGCAGTTTGGTGTCAACCATCTGGGGCACTTCTTACTCACCAATCTCCTTCTGGATCTTCTCAAAAACTCCGCTCCAA
GCAGGATCATTGTAGTTTCTTCCAAGCTTTACAAATATGGAGACATCAACTTTGAAGATTTGAACAGTGAGATAAGCTAT
AATAAAAGTTTTGCATATAGTCGCAGCAAGCTGGCTAACATCCTGTTCACCAGGGAACTAGCTCGCCGCTTAGAAGGCAC
AGAGGTCACAGCAAACGTGCTGCATCCCGGCATTGTCCGTACCAATCTCGGCAGGTACATAGACATCCCTATATTGGTCA
AACCCCTCTTCAACCTAGTGTCCTGGGCTTTTTTTAAAACTCCACTCGAAGGAGCCCAGACATCTATTTATCTGGCCTCT
TCTCCCGAGGTAGAGGGGGTGTCGGGCAAGTATTTTGGAGATTGCAAAGAGGAAGAGCTGCTTCCAAAAGCCATGGATGA
TGCAGTTGCAAGAAAACTCTGGGATATCAGTGAAGTGATGGTCGGCATA

Alignment

ORF - retro_oana_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.71 %
• Parental protein coverage: 99.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEKQLHILINNAGVMMCPYSKTADGFEMHLGVNHLGHFLLTHLLLGRLKESAPGRVVNVSSLAHVIGKIR
          EE..L..LINNAG...CPY.KT.DGFEM..GVNHLGHFLLT.LLL..LK.SAP.R...VSS.....G.I.
Retrocopy EEPRLDVLINNAGIFQCPYMKTEDGFEMQFGVNHLGHFLLTNLLLDLLKNSAPSRIIVVSSKLYKYGDIN

Parental  FHDLQGEKYYYSNMAYCHSKLANILFTRELARRLQGTGVTTYALHPGVVQSELVRHSLLMCLVWRLFSF-
          F.DL..E..Y....AY..SKLANILFTRELARRL.GT.VT...LHPG.V...L.R......LV..LF...
Retrocopy FEDLNSEISYNKSFAYSRSKLANILFTRELARRLEGTEVTANVLHPGIVRTNLGRYIDIPILVKPLFNLV

Parental  ---FVKSSQEGAQTSLHCAVAENLEALSGEYFSDCKRAPVSARGRNGATARRLWEVSCELLGI
          ...F.K...EGAQTS...A.....E..SG.YF.DCK...........A.AR.LW..S....GI
Retrocopy SWAFFKTPLEGAQTSIYLASSPEVEGVSGKYFGDCKEEELLPKAMDDAVARKLWDISEVMVGI

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	26.67 RPM	1.32 RPM
SRP007412_cerebellum	17.70 RPM	10.53 RPM
SRP007412_heart	53.75 RPM	3.45 RPM
SRP007412_kidney	16.58 RPM	1.18 RPM
SRP007412_liver	6.24 RPM	0.72 RPM
SRP007412_testis	18.62 RPM	4.63 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_89 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_89 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068,
Equus caballus	ENSECAG00000015001	1 retrocopy	retro_ecab_1059,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89 ,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,