RetrogeneDB ID: retro_oana_32

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig14727:5314..5794(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERGIC2
• Ensembl ID: ENSOANG00000010582
• Aliases: None
• Description: ERGIC and golgi 2 [Source:HGNC Symbol;Acc:30208]

Sequence

>retro_oana_32
GCAAGTAGGGGTACAGTTTCTCTAATTGTGTTTACCACTATGGCTTTTTAAACCATAATGGAGTTTTTGGTCTATCAGGA
TACCTGGATGAAGTATGAATATGAAGTAGACAAGTATTTTAGTAAATTAAGAATCAATATAGATATTACTGTTGTCATGA
AGTGTCAACATACTGGAACCATTGTGTTAGATTTAGCAGAAACAGTGGTTGCATCTGCAGATACCTTGGTTTATCAACCA
GTGATATTTGACCTCTCACTGCAACAAAGAGAGTGGCAGGGAATGTAGCAGATGATACAAAATAGGCTACAGGAGGAATA
TTTGCTCCAAGATGTGATATTCAAAAATGCTTTTAAAAGCACTTCAATTTCACTGCCAAGGGGAGAACTTTCATTATGAC
CTCCTGATGAATTTTGGATTCATGGACATCTGCATGATAATAAAGTGGCAAGGAATCTTCACATAACTGTGGGCAACCTA

Alignment

ORF - retro_oana_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.01 %
• Parental protein coverage: 73.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASGGTVSLIAFTTMAFLTVMEFLVYQDTWMKYEYEVDKDFASKLRINIDITVAMKCQYIGADVLDLAETM
          AS.GTVSLI.FTTMAF.T.MEFLVYQDTWMKYEYEVDK.F.SKLRINIDITV.MKCQ..G..VLDLAET.
Retrocopy ASRGTVSLIVFTTMAF*TIMEFLVYQDTWMKYEYEVDKYF-SKLRINIDITVVMKCQHTGTIVLDLAETV

Parental  VASADGLVYEPVIFDLSPQQREWQRMLQMIQNRLQEEHSLQDVIFKSAFKSASTALPPRGDLSLQPPDAC
          VASAD.LVY.PVIFDLS.QQREWQ.M.QMIQNRLQEE..LQDVIFK.AFKS.S..L.PRG.LSL.PPD..
Retrocopy VASADTLVYQPVIFDLSLQQREWQGM*QMIQNRLQEEYLLQDVIFKNAFKSTSISL-PRGELSL*PPDEF

Parental  RIHGHLYVNKVAGNFHITVGNI
          .IHGHL..NKVA.N.HITVGN.
Retrocopy WIHGHLHDNKVARNLHITVGNL

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	25.79 RPM
SRP007412_cerebellum	0.00 RPM	18.12 RPM
SRP007412_heart	0.00 RPM	12.04 RPM
SRP007412_kidney	0.00 RPM	37.90 RPM
SRP007412_liver	0.00 RPM	32.64 RPM
SRP007412_testis	0.00 RPM	40.44 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_32 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_32 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015668	1 retrocopy	retro_cpor_824,
Ornithorhynchus anatinus	ENSOANG00000010582	1 retrocopy	retro_oana_32 ,
Oryctolagus cuniculus	ENSOCUG00000017255	1 retrocopy	retro_ocun_1540,
Pongo abelii	ENSPPYG00000004390	1 retrocopy	retro_pabe_657,
Rattus norvegicus	ENSRNOG00000001852	1 retrocopy	retro_rnor_1557,
Sarcophilus harrisii	ENSSHAG00000004822	1 retrocopy	retro_shar_386,
Tupaia belangeri	ENSTBEG00000011223	1 retrocopy	retro_tbel_3783,