RetrogeneDB ID: retro_oana_38

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig167268:323..587(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOANG00000013963
• Aliases: None
• Description: None

Sequence

>retro_oana_38
ATGGATCATACAACACAATCATTGGTGCTTTCATTTTACAGTAAACAGCTTAAGTGCTTATGTGTTTCTTTTTGTTTTTT
TCTCTTCTGTCATAGACATGGGAGGCAGCACACTATCATGCCATCAGCTGTCAATTTCCAAGCCAATATTTGGGCCTTAA
AGGAGGAGGGCTGCACTCATATCATAGTGACTACTGCATGTGGCTCGTTAAGAGAGGAAATTCAACCTGGAGACATTGTC
CTGATTGACCAGTTTATTGATAGG

Alignment

ORF - retro_oana_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEGRTEKIVETPYGKPSDALILGKIKNVDCVLLARHGRQHTIMPSAVNFQANIWALKEEGCTHIIVTTAC
          ....T...V...Y.K....L.........C....RHGRQHTIMPSAVNFQANIWALKEEGCTHIIVTTAC
Retrocopy MDHTTQSLVLSFYSKQLKCLCVXXXXXLFC---HRHGRQHTIMPSAVNFQANIWALKEEGCTHIIVTTAC

Parental  GSLREEIQPGDIVLIDQFIDR
          GSLREEIQPGDIVLIDQFIDR
Retrocopy GSLREEIQPGDIVLIDQFIDR

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	6.01 RPM
SRP007412_cerebellum	0.00 RPM	3.42 RPM
SRP007412_heart	0.00 RPM	10.45 RPM
SRP007412_kidney	0.00 RPM	18.06 RPM
SRP007412_liver	0.00 RPM	13.74 RPM
SRP007412_testis	0.00 RPM	13.64 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_38 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_38 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025929	1 retrocopy	retro_btau_1049,
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38 ,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,