RetrogeneDB ID: retro_oana_91

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig67422:2890..3271(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DFFB
• Ensembl ID: ENSOANG00000013652
• Aliases: None
• Description: DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase) [Source:HGNC Symbol;Acc:2773]

Sequence

>retro_oana_91
ATGATGTATAGTTGTCAGAGCACAACTTAAATGAAAGAAGTAAACTCCTTCGGGTCTTCTGTCGGTCCCAAGGCTCAGGC
AGAAAAACTGAATATATTTGGCTGTGTGGGATAGAAGCCGAAAGTGACCACTACAATGGGGGATACTTTGACAGATGAGA
AAACAGGGCCAACTTTGTATGCCCCCAAGACTGGTTCTCTTGCCAGGGTCCATTTGACATTGATAGTTGCTCATCTAAAC
ATTCCCATCAACCAATTCAACAACAGAGAGACCACAATTCCTTTCAGTACATGTAATCTTGATCACAGGATAGAAAAGAA
ACGCACCGTCGTTCCAACCCTAGCGGAAGCTGTTAGGGAACAAAACAGAAGTGAAATAGAA

Alignment

ORF - retro_oana_91 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.65 %
• Parental protein coverage: 66.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRYSCESRIRSYMKEVNTSASAIGPKAQAEYLKIIGCMGEKLKAA-QYNGGYFDRREKRARLCTPEGWFS
          M.YSC.S.....MKEVN...S..GPKAQAE.L.I.GC.G.K.K....YNGGYFDR.E.RA....P..WFS
Retrocopy MMYSCQST--T*MKEVNSFGSSVGPKAQAEKLNIFGCVG*KPKVT<HYNGGYFDR*ENRANFVCPQDWFS

Parental  CQGPFDIDSCLSKHS-INPYSNRESRILFSTWNLDHIIEKKRTVVPTLAEAVREQDGREVD
          CQGPFDIDSC.SKHS.IN...NRE..I.FST.NLDH.IEKKRTVVPTLAEAVREQ...E..
Retrocopy CQGPFDIDSCSSKHS>INQFNNRETTIPFSTCNLDHRIEKKRTVVPTLAEAVREQNRSEIE

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	1.06 RPM
SRP007412_cerebellum	0.00 RPM	1.26 RPM
SRP007412_heart	0.00 RPM	0.62 RPM
SRP007412_kidney	0.00 RPM	0.89 RPM
SRP007412_liver	0.00 RPM	2.17 RPM
SRP007412_testis	0.00 RPM	2.37 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_91 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_91 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002834	1 retrocopy	retro_cjac_616,
Homo sapiens	ENSG00000169598	1 retrocopy	retro_hsap_4240,
Gorilla gorilla	ENSGGOG00000013452	1 retrocopy	retro_ggor_2841,
Macaca mulatta	ENSMMUG00000015174	1 retrocopy	retro_mmul_1150,
Ornithorhynchus anatinus	ENSOANG00000013652	5 retrocopies	retro_oana_116, retro_oana_117, retro_oana_125, retro_oana_27, retro_oana_91 ,