RetrogeneDB ID: retro_oana_125

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra56:12272426..12272841(-)
• 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_125
GGCATGGAATCTCGATTTAAGAATAAATATAGCCATATGAGGTATAGTTGTCAGAGCACAACCCAAATGAAAGAAGTAAA
CGCCTTCACTTCAGCTGTCGGTCCCAAGGCTCAGGCAGAAAAACTGAATATATTTGGCTGTGTGGGATAGAAGCCGAAAG
TGACCACTACAATGGGGGATACTTTGACAGATGAGAAAACAGGGCCAACTTTGTATGCCCCAAGACTGGTTCTCTTGCCA
GGGTCCATTTGACATTGATAGTTGCTCATCTAAACATTCCATCAACCACTTCAGCAACAGAGAGACCACAATTCCTTTCA
GTACATGTAATCTTGATCACAGGATAGAAAAGAAATGCACCGTCGTTCCAACCCTAGCGGAAGCTGTTAGGGAACAAAAC
AGAAGTGAAATAGAA

Alignment

ORF - retro_oana_125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 72.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLESRFKNKSGYMRYSCESRIRSYMKEVNTSASAIGPKAQAEYLKIIGCMGEKLKAA-QYNGGYFDRREK
          G.ESRFKNK...MRYSC.S.....MKEVN...SA.GPKAQAE.L.I.GC.G.K.K....YNGGYFDR.E.
Retrocopy GMESRFKNKYSHMRYSCQSTTQ--MKEVNAFTSAVGPKAQAEKLNIFGCVG*KPKVT<HYNGGYFDR*EN

Parental  RA-RLCTPEGWFSCQGPFDIDSCLSKHSINPYSNRESRILFSTWNLDHIIEKKRTVVPTLAEAVREQDGR
          RA..LC.P..WFSCQGPFDIDSC.SKHSIN..SNRE..I.FST.NLDH.IEKK.TVVPTLAEAVREQ...
Retrocopy RA<QLCMPQDWFSCQGPFDIDSCSSKHSINHFSNRETTIPFSTCNLDHRIEKKCTVVPTLAEAVREQNRS

Parental  EVD
          E..
Retrocopy EIE

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_125 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_125 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,