RetrogeneDB ID: retro_oana_72

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig37152:13494..13827(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPA
• Ensembl ID: ENSOANG00000000516
• Aliases: None
• Description: centromere protein A [Source:HGNC Symbol;Acc:1851]

Sequence

>retro_oana_72
ACAAAGGCTGCTAGGAAGGCTGCTCCCCTTTCAGCCGGCATAAAAAAACCACACAGATACCGACCTGGCACCGTTGCATT
GCGTGAAATTAGGAAGTTCCAGAAGTCCACTGAATTGTTAATTAGGAAATTGCCTTTCCAGAGATTAGTTCGCGAAATTG
CACAGGATTACAAAACCGACTTGAGGTTTCAATCACAGGCAGTTTTGGCTCTCCAGGAAGCTGCCGAAGCATACTTGGTA
GGACTATTCGAGGATACCAATTTGTGTGCCATCCACGCGAAACGGGTAACCATTATGCCAAAGGACATTCAACTTGCGAG
GCGTATCCGTGGA

Alignment

ORF - retro_oana_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.06 %
• Parental protein coverage: 88.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEAQRRRAPRPTPSPRRRRYRPGKQVLKEIRRLQKSTNLLLRKTPFARLVREVCLSYTRGVDFRWQSQAL
          T.A.R..AP.........RYRPG...L.EIR..QKST.LL.RK.PF.RLVRE....Y....D.R.QSQA.
Retrocopy TKAARKAAPLSAGIKKPHRYRPGTVALREIRKFQKSTELLIRKLPFQRLVREIAQDYK--TDLRFQSQAV

Parental  LALQEAAEAFLVHLFEDSYLCSLHARRVTLFPRDIQLARRIRG
          LALQEAAEA.LV.LFED..LC..HA.RVT..P.DIQLARRIRG
Retrocopy LALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG

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	0.09 RPM
SRP007412_cerebellum	0.05 RPM	0.37 RPM
SRP007412_heart	0.27 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.30 RPM
SRP007412_liver	0.00 RPM	0.36 RPM
SRP007412_testis	0.00 RPM	3.91 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_72 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_72 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023938	1 retrocopy	retro_btau_947,
Choloepus hoffmanni	ENSCHOG00000004496	3 retrocopies	retro_chof_2096, retro_chof_2448, retro_chof_4,
Ornithorhynchus anatinus	ENSOANG00000000516	1 retrocopy	retro_oana_72 ,
Otolemur garnettii	ENSOGAG00000024154	2 retrocopies	retro_ogar_3405, retro_ogar_3505,
Ictidomys tridecemlineatus	ENSSTOG00000025168	2 retrocopies	retro_itri_835, retro_itri_994,
Tarsius syrichta	ENSTSYG00000010334	1 retrocopy	retro_tsyr_2007,
Tursiops truncatus	ENSTTRG00000010278	2 retrocopies	retro_ttru_590, retro_ttru_784,